|
Volume 272, Number 36,
Issue of September 5, 1997
pp. 22417-22424
©1997 by The American Society for Biochemistry and Molecular Biology, Inc.
Cysteine Sulfinate Desulfinase, a NIFS-like Protein of
Escherichia coli with Selenocysteine Lyase and Cysteine
Desulfurase Activities
GENE CLONING, PURIFICATION, AND CHARACTERIZATION OF A NOVEL
PYRIDOXAL ENZYME*
(Received for publication, April 3, 1997, and in revised form, June 20, 1997)
Hisaaki
Mihara
§,
Tatsuo
Kurihara
§,
Tohru
Yoshimura
,
Kenji
Soda
¶ and
Nobuyoshi
Esaki

From the Laboratory of Microbial Biochemistry,
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611, Japan and the ¶ Department of Biotechnology, Faculty of
Engineering, Kansai University, 3-3-35 Yamate-Cho, Suita,
Osaka 564, Japan
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
FOOTNOTES
ACKNOWLEDGEMENT
REFERENCES
ABSTRACT
Selenocysteine lyase (EC 4.4.1.16) exclusively
decomposes selenocysteine to alanine and elemental selenium, whereas
cysteine desulfurase (NIFS protein) of Azotobacter
vinelandii acts indiscriminately on both cysteine and
selenocysteine to produce elemental sulfur and selenium respectively,
and alanine. These proteins exhibit some sequence homology. The
Escherichia coli genome contains three genes with sequence
homology to nifS. We have cloned the gene mapped at 63.4 min in the chromosome and have expressed, purified to homogeneity, and
characterized the gene product. The enzyme comprises two identical
subunits with 401 amino acid residues (Mr
43,238) and contains pyridoxal 5 -phosphate as a coenzyme. The enzyme
catalyzes the removal of elemental sulfur and selenium atoms from
L-cysteine, L-cystine,
L-selenocysteine, and L-selenocystine to
produce L-alanine. Because L-cysteine sulfinic
acid was desulfinated to form L-alanine as the
preferred substrate, we have named this new enzyme cysteine sulfinate
desulfinase. Mutant enzymes having alanine substituted for each of
the four cysteinyl residues (Cys-100, Cys-176, Cys-323, and Cys-358)
were all active. Cys-358 corresponds to Cys-325 of A. vinelandii NIFS, which is conserved among all NIFS-like proteins
and catalytically essential (Zheng, L., White, R. H., Cash,
V. L., and Dean, D. R. (1994) Biochemistry 33, 4714-4720), is not required for cysteine sulfinate desulfinase. Thus,
the enzyme is distinct from A. vinelandii NIFS in this
respect.
INTRODUCTION
Selenium, a homolog of sulfur, is an essential trace element for
mammals and other organisms. It occurs in some selenoproteins as a
selenocysteine residue (1-3), which is incorporated co-translationally into the proteins as directed by the unique codon, UGA (4, 5). Other
selenoproteins contain selenium in a dissociable form, coordinated with
molybdenum (6, 7). Selenium is metabolized by enzymes including
selenophosphate synthetase (8), selenocysteine synthase (9),
selenocysteine lyase (10, 11), and selenocysteine methyltransferase
(12). Some enzymes participating in sulfur metabolism also act on the
selenium analogs of the substrates.
We found selenocysteine lyase in mammals (10) and bacteria (13), and
purified the enzyme from pig liver (10) and Citrobacter freundii (11). The enzyme specifically decomposes
L-selenocysteine into L-alanine and elemental
selenium; L-cysteine is inert as a substrate. Zheng
et al. (14) recently demonstrated the function of NIFS
protein, which is required for the efficient construction of the Fe-S
clusters of nitrogenase in a diazotrophic bacterium Azotobacter
vinelandii. NIFS catalyzes the same type of reaction as
selenocysteine lyase, but acts on both L-cysteine and
L-selenocysteine indiscriminately. The enzyme was named
cysteine desulfurase, based on its inherent physiological role. Genes
with a sequence similarity to that of nifS have been found
not only in diazotrophs but also in non-diazotrophic microorganisms. It
has been reported that the nifS-like genes of Bacillus
subtilis and Saccharomyces cerevisiae are involved in
NAD+ biosynthesis (15) and tRNA processing (16),
respectively.
The nucleotide sequence of the whole Escherichia coli genome
has been determined (17), and the bacterium appears to contain three
nifS-like genes (18, 19). One of the genes located at 57.3 min (18) in the chromosome presumably encodes the NIFS-like protein
purified by Flint (20). Not only the amino acid sequence but also the
catalytic properties of the enzyme resemble those of A. vinelandii NIFS. We have found that the N-terminal amino acid
sequence of pig liver selenocysteine lyase is similar to that of
A. vinelandii NIFS
(21).1 If we assume that
E. coli contains selenocysteine lyase and that the enzyme
resembles NIFS, one or both of the other two nifS-like genes
may encode selenocysteine lyase(s). Alternatively, the genes may encode
new enzymes participating in an unknown metabolism of sulfur or
selenium amino acids. We have cloned the nifS-like gene
mapped at 63.4 min (18), and found that the gene product is a novel
PLP2-dependent
enzyme decomposing L-selenocysteine,
L-selenocystine, L-cysteine, and
L-cystine. L-Cysteine sulfinic acid is also
decomposed to L-alanine as the best substrate of the
enzyme. We have tentatively named it cysteine sulfinate desulfinase. We
describe here the characteristics of the enzyme and compare it with
other related enzymes such as selenocysteine lyase and NIFS.
EXPERIMENTAL PROCEDURES
Materials
Molecular weight markers for SDS-PAGE and gel
filtration were purchased from Pharmacia Biotech Inc. and Oriental
Yeast, respectively; restriction enzymes and other DNA modifying
enzymes from Takara Shuzo; synthetic oligonucleotides from Japan Bio
Service and Biologica. L-Selenocystine was synthesized from
L- -chloroalanine, which was kindly provided by Showa
Denko, and from disodium diselenide, as described previously (22).
L-Selenocysteine was prepared from
L-selenocystine according to the previous method (10). All
other chemicals were of analytical grade.
Cloning of Cysteine Sulfinate Desulfinase Gene
The DNA
fragment containing the ORF for cysteine sulfinate desulfinase was
amplified with a Perkin-Elmer Thermal Cycler 480. The reaction mixture
(50 µl) contained: 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM MgCl2, 10%
Me2SO, 400 µM each dNTP, 0.2 µM
each primer
(5 -GGAATTCATCAAGCCGAGGAGTAC-CATGAACG-3 and
5 -AACTGCAGCGGCGAATTGCGGGTTTGTCATTAA-3 ; underlines
indicate EcoRI and PstI sites, and boldface
letters indicate a putative ribosome binding sequence), 2.5 units of Ex Taq DNA polymerase (Takara Shuzo), and 100 ng of template
DNA from E. coli JM109 isolated by the method reported (23).
The conditions were as follows: first cycle, 2 min (94 °C), 5 min (55 °C), and 10 min (72 °C); subsequent 24 cycles, 1 min
(94 °C), 1 min (58 °C), then 3 min (72 °C); last cycle, 1 min
(94 °C), 1 min (58 °C), 15 min (72 °C). The
EcoRI-PstI fragment was ligated into pUC118 to
give a plasmid pCSD1.
Assays and Definition of Units
Cysteine sulfinate
desulfinase was assayed by determination of H2Se formed
from L-selenocysteine with lead acetate as described previously (10). A standard reaction mixture containing 5 mM L-selenocysteine, 50 mM
dithiothreitol, 0.02 mM PLP, 120 mM
Tricine-NaOH buffer (pH 7.5), and enzyme (0.006-0.032 units) in a
final volume of 0.1 ml was incubated at 37 °C. A molar turbidity
coefficient of PbSe at 400 nm, 1.18 × 104
M 1·cm 1, was used. One unit of
enzyme was defined as the amount of enzyme that catalyzes the formation
of 1 µmol of the product (alanine or elemental selenium)/min.
Specific activity was expressed as units/mg of protein.
Cysteine desulfurase activity was measured by the determination of
H2S formed from L-cysteine with lead acetate in
the manner described above. An apparent molar turbidity coefficient of
colloidal PbS at 360 nm, 1.31 × 104
M 1·cm 1, was used (24).
Pyruvate was determined with lactate dehydrogenase (Sigma) at 37 °C
in a reaction mixture (1 ml) containing 5 mM L- -chloroalanine, lactate dehydrogenase (22 units), 0.02 mM PLP, 0.15 mM NADH, 120 mM
Tricine-NaOH buffer (pH 8.5), and enzyme. Sulfite produced from
L-cysteine sulfinic acid was determined with fuchsin (25).
Protein was determined with a Bio-Rad protein assay kit with bovine
serum albumin as a standard.
Purification of Cysteine Sulfinate Desulfinase
The buffer
used throughout the purification was 10 mM potassium
phosphate (pH 7.4) and was supplemented with salts when required for
chromatographies. All operations (Table I) were done at 4 °C. Elution patterns of protein were estimated by absorption at 280 nm.
E. coli XL1-Blue (Stratagene) carrying pCSD1 was cultured aerobically in Luria-Bertani broth (3 liters) supplemented with ampicillin (200 µg/ml) at 37 °C for 11 h, and then
isopropyl-1-thio- -D-galactopyranoside was added to the
culture at a final concentration of 1 mM. The cells were
cultured for another 2 h, and harvested by centrifugation. The
final preparation of the enzyme was stored frozen at 30 °C in the
buffer supplemented with 0.02 mM PLP until use.
Table I.
Purification of cysteine sulfinate desulfinase
|
| Step |
Total protein |
Total
activitya |
Specific activity |
Yield
|
|
|
mg |
units |
units/mg |
% |
| Crude
extractb |
1900 |
1100 |
0.58 |
100 |
| Ammonium
sulfatec |
720 |
920 |
1.3 |
84 |
| 1st
DEAE-Toyopearld |
420 |
790 |
1.9 |
72 |
| 2nd
DEAE-Toyopearle |
90 |
360 |
4.0 |
33 |
| 1st
Phenyl-Toyopearlf |
29 |
190 |
6.6 |
17 |
| 2nd
Phenyl-Toyopearlg |
28 |
230 |
8.2 |
21 |
|
|
a
Determined with L-selenocysteine as a
substrate.
|
|
b
Cells (13.8 g) suspended in 50 ml of buffer were sonicated.
|
|
c
The fraction between 25 and 50% saturation was collected,
then dialyzed.
|
|
d
Column size, 3.0 × 18 cm; elution, with 0.15 M NaCl. The active fractions were concentrated with 55%
saturation of ammonium sulfate, then dialyzed.
|
|
e
Column size, 3.0 × 18 cm; elution, by 1000-ml linear
gradient of 0-0.2 M NaCl. The active fractions were
concentrated with an UP-20 membrane (Advantec), then dialyzed against
0.4 M ammonium sulfate.
|
|
f
Column size, 0.7 × 6 cm; equilibration, with 0.4 M ammonium sulfate; elution, with 0.4 M
ammonium sulfate. The active fractions were concentrated with an UP-20
membrane, then dialyzed against 0.65 M ammonium sulfate.
|
|
g
Column size, 0.7 × 6 cm; equilibration, with 0.65 M ammonium sulfate; elution, by 100-ml linear gradient of
0.65-0.3 M ammonium sulfate. The active fractions were
concentrated with an UP-20 membrane, then dialyzed against the buffer
containing 0.02 mM PLP.
|
|
Mass Spectrometry
The molecular mass of the enzyme was
determined with a Vision 2000 reflector-type time-of-flight mass
spectrometer (Thermoquest, Tokyo, Japan) equipped with a nitrogen laser
(337 nm, pulse length 10 ns). The enzyme solution (1.0 × 10 5 ~ 2.5 × 10 6 M) was
mixed with the same volume of 1% (w/v) 2,5-dihydroxybenzoic acid
solution in 10% acetonitrile containing 0.1% (v/v) trifluoroacetic acid. Spectral measurements were repeated 100 times, and the average of
their sum was recorded. Bovine serum albumin was used as a standard
protein.
Site-directed Mutagenesis
The alanine mutants for cysteine
residues were prepared by the Kunkel method (26). Single-stranded DNA
was obtained with another plasmid named pCSD2, which was constructed in
the same manner as pCSD1, except that the following primer was used for the upstream region:
5 -GGGAATTCCATATGAACGTTTTTAATCCCGCGCAGTTTCG-3 (the
EcoRI site is underlined). The single-stranded DNA was
prepared from E. coli BW313 carrying pCSD2, by infection
with helper phage VCSM13 (Stratagene). The following mutagenic primers
were used: 5 -ACGCGCATAGGCTTGTGCC-AC-3 (Cys-100),
5 -CAGATCCGGGGCACCGCCAGT-3 (Cys-176),
5 -GGAATCCTGGGCGCGGAATGA-3 (Cys-323),
5 -GGCTGAGCGGCATGCTGCCC-3 (Cys-358) (mutagenized
nucleotides are underlined). The nucleotide sequences were confirmed
with a Dye Terminator sequencing kit and an Applied Biosystems 370A DNA
sequencer. Mutant enzymes were prepared with E. coli JM109
as a host.
RESULTS
Cloning and Expression of Cysteine Sulfinate Desulfinase
Gene
We determined the N-terminal amino acid sequence of
selenocysteine lyase purified from pig liver, and found that 8 out of 14 residues at the N-terminal sequence coincide with the residues at
the corresponding positions in the A. vinelandii NIFS
sequence (21). Thus, selenocysteine lyase, if it occurs in E. coli, probably has a primary structure similar to that of A. vinelandii NIFS. The amino acid sequence deduced from ORF o401
located at 63.4 min (18) in the E. coli K-12 genome was
found to have about 20% homology with that of A. vinelandii
NIFS. We cloned the gene by polymerase chain reaction, with the
E. coli JM109 chromosomal DNA as a template and the
synthetic primers shown above. The DNA sequence of the gene thus cloned
agreed completely with that registered in GenBankTM (accession number
U295810).
The molecular weight of the homogeneous preparation of the gene product
estimated by SDS-PAGE (27) (about 43,000) agreed with the value
calculated from the deduced amino acid sequence (43,238). The
N-terminal amino acid sequence of the purified protein agreed with that
deduced from the nucleotide sequence (Fig.
1). Although we did not determine the
C-terminal amino acid sequence of the protein, the molecular mass of
the protein determined by mass spectrometry was essentially identical
with the predicted value: m/z 43279.6 corresponding to (M + H)1+. The molecular weight of the purified protein in the
native form was estimated to be about 97,000 by gel filtration with a
Superose 12 (1 × 30 cm) column.
Fig. 1.
Nucleotide and the deduced amino acid
sequences of the gene encoding cysteine sulfinate desulfinase. The
possible Shine-Dalgarno sequence is double underlined; the
N-terminal amino acid sequence determined with a Shimadzu protein
sequencer PPSQ-10 is underlined. The nucleotide sequence is
available from the GenBank/EMBL data bases with the accession number
U295810 (ORF o401). The nucleotide sequence in the region from base
number 13 to 1256 was also confirmed in our experiment.
[View Larger Version of this Image (62K GIF file)]
Catalytic Activity of Cysteine Sulfinate Desulfinase
An
extract of the cloned cells showed both selenocysteine lyase and
cysteine desulfurase activity. Because the selenocysteine lyase
activity was higher than that of cysteine desulfurase, we routinely
used L-selenocysteine as a substrate of the enzyme
throughout the purification (Table
I).
The specific activity of the homogeneous preparation of the enzyme
toward L-selenocysteine (8.1 units/mg) was comparable to that of selenocysteine lyase from C. freundii (6.47 units/mg) (11). However, these values were about 5 times lower than
that of selenocysteine lyase from pig liver (37 units/mg) (10).
The cysteine desulfurase activity of our new enzyme (3.4 units/mg) was
also much higher than that of A. vinelandii NIFS (14) and
the E. coli NIFS-like enzyme (20). However, the
concentration of L-cysteine we used (80 mM) was
much higher than that used for the other enzymes (A. vinelandii NIFS, 0.5 mM; E. coli NIFS-like protein, 2.5 mM). The specific activity of our enzyme
decreased at lower L-cysteine concentrations (0.050 unit/mg
at 0.5 mM; 0.23 unit/mg at 2.5 mM). These
values were comparable to those reported for A. vinelandii
NIFS (0.089 unit/mg at 0.5 mM) (28) and the E. coli NIFS-like protein (0.078 unit/mg at 2.5 mM)
(20).
The optimal pH values for the removal of selenium and sulfur atoms from
L-selenocysteine and L-cysteine were around pH
7.0 and 7.5, respectively, in Tricine-NaOH. The enzyme kept essentially the same activity at 4 °C for at least 2 weeks, as well as at 30 °C for more than 6 months.
Cofactor
The enzyme showed at pH 7.4 an absorption maximum at
420 nm (Fig. 2, curve a) that
is characteristic of bound PLP. Reduction with sodium borohydride
resulted in the disappearance of the absorption band at 420 nm with a
concomitant increase in the absorbance at 335 nm (Fig. 2, curve
b). The reduced enzyme was catalytically inactive, and the
addition of PLP did not reverse the inactivation. These results show
that the enzyme requires PLP as a cofactor.
Fig. 2.
Absorption spectra of cysteine sulfinate
desulfinase. Absorption spectra were taken in 10 mM
potassium phosphate buffer (pH 7.4) at an enzyme concentration of 0.4 mg/ml. Curve a, native enzyme; curve b, 1 min
after addition of sodium borohydride (1 mM) to the enzyme
solution.
[View Larger Version of this Image (17K GIF file)]
Substrate Specificity
The enzyme resembles selenocysteine
lyase and NIFS in that it removes elemental sulfur or selenium from
L-cysteine or L-selenocysteine in the reaction.
L-Cysteine sulfinic acid acted as the best substrate of the
enzyme, and essentially the same amounts of L-alanine and sulfite were produced in the reaction (data not shown). Maximum activity for the desulfination was found at around pH 8.2 in
Tricine-NaOH. We named our new enzyme cysteine sulfinate desulfinase,
because the enzyme showed the lowest Km value and
the highest kcat and
kcat/Km values for
L-cysteine sulfinic acid (Table
II).
Table II.
Substrate specificity of cysteine sulfinate desulfinase and kinetic
constants of the enzyme reactions
The following amino acids and derivatives were inert as the substrates,
when production of alanine or consumption of the substrates were
examined with a Beckman high performance amino acid analyzer 7300:
D-cysteine, D-cystine, DL-cysteic
acid, DL-serine,
S-methyl-L-cysteine, S-benzyl-L-cysteine,
DL-homocysteine, DL-homocystine,
DL-methionine, DL-homoserine,
L-homocysteic acid, cysteamine, cystamine, selenocystamine, L-asparagine, L-aspartic acid,
L-kynurenine, DL-lanthionine,
L-cystathionine, L-allocystathionine, and
DL-djenkolic acid.
|
|
Km |
Vmax |
kcat |
kcat/Km
|
|
|
mM |
µmol·min 1·mg 1 |
s 1 |
mM 1·s 1
|
| L-Cysteine sulfinic
acida |
0.24 |
20 |
15 |
63
|
| L-Selenocysteineb |
1.0 |
7.4 |
5.3 |
5.3
|
| L-Cysteineb |
35 |
3.4 |
2.4 |
0.070
|
| L-Cystinea |
3.3 |
0.017 |
0.012 |
0.0036 |
|
|
a
Alanine formed, in the reaction system with
Tricine-NaOH (pH 8.5), was determined with alanine dehydrogenase with a
mixture (1.0 ml) containing 5 mM substrate, 0.02 mM PLP, 2.5 mM NAD+, 0.3 unit of
L-alanine dehydrogenase (Unitika), 120 mM
Tricine-NaOH buffer (pH 8.5), and enzyme at 37 °C.
|
|
b
The reactions were carried out in Tricine-NaOH (pH 7.5), and
H2Se and H2S formed were determined with lead
acetate.
|
|
The enzyme resembles aspartate -decarboxylase (EC 4.1.1.12) and
kynureninase (EC 3.7.1.3) because alanine is produced from the
substrate. However, both L-aspartate and
L-kynurenine were inert as the substrates (Table II).
L-Aspartate was not converted to alanine even at pH 5.0 in
an acetate buffer, which are the optimum conditions for the aspartate
-decarboxylase reaction (29).
Cysteine sulfinate desulfinase is distinct from selenocysteine lyase
and NIFS in that it acts also on L-cystine and
L-selenocystine. L-Alanine was produced from
either substrate as well as elemental sulfur or selenium. The amount of
L-alanine produced was only 1.5 times larger than that of
L-cystine consumed in the reaction. We expected that double
amounts of alanine would be produced from cystine in the reaction,
because S-sulfocysteine is presumably produced from cystine
and then converted with the release of elemental sulfur to reproduce
cysteine, which would give another molecule of alanine in the second
reaction. Therefore, some part of the S-sulfocysteine is
probably converted to another unknown compound, which is inert as a
substrate.
Action on -Chloroalanine
-Chloroalanine is a
mechanism-based inactivator for several PLP-dependent
enzymes (30). Cysteine sulfinate desulfinase was incubated with various
concentrations of L- -chloroalanine (0.5-8.0
mM) for various periods up to 4.5 h, and the remaining activity was determined with L-selenocysteine as a
substrate. No inactivation of the enzyme was observed. The enzyme
catalyzed only , -elimination of -chloroalanine to form
pyruvate without formation of alanine.
Role of Cysteinyl Residues of Cysteine Sulfinate
Desulfinase
Both A. vinelandii NIFS and the E. coli NIFS-like protein contain cysteinyl residues that are
catalytically essential (14, 20). Selenocysteine lyase from C. freundii was completely inactivated by thiol reagents (11).
Cysteinyl residues corresponding to Cys-325 of A. vinelandii
NIFS, which was shown to be catalytically essential (14), are fully
conserved among all NIFS family proteins (Fig. 3). We examined the
roles of all cysteinyl residues of cysteine sulfinate desulfinase
including Cys-358, which corresponds to the conserved Cys-325 of
A. vinelandii NIFS, by site-directed mutagenesis. All the
alanine mutants for Cys-100, Cys-176, Cys-323, and Cys-358 were fully
active. Thus, cysteine sulfinate desulfinase has no essential cysteine
residues and differs markedly from A. vinelandii NIFS and
the NIFS-like protein of E. coli.
Fig. 3.
Sequence alignment of cysteine sulfinate
desulfinase, NIFSs and NIFS-like proteins. NIFS-like proteins with
sequence similarity to that of A. vinelandii NIFS were
searched with BLAST (60) and FASTA (61) programs, and aligned with
CLUSTAL V program of a DNASTAR software (DNASTAR, Inc.). Gaps (shown
with dashes) are introduced in the sequences where necessary
to give better alignment. The black boxes show the residues
that are identical or similar (classified into the groups PAGST, QNED,
ILVM, HKR, YFW, and C) to one another in the sequences. The residues
conserved among more than 23 of total 26 sequences are indicated by
filled circles. Conserved Cys is indicated by an
arrow. Numbers refer to amino acid residues. The
regions a-d show the parts in which the sequences of two
groups differ markedly from each other. The groups are shown by
braces, and I and II indicate Group I
and II, respectively. Lys, indicated by an arrow, is
conserved among all sequences and suggested to be the PLP-binding
residue (28). Abbreviations of protein names are given in Table III.
Cysteine sulfinate desulfinase (CSD) is
asterisked.
[View Larger Versions of these Images (78 + 135K GIF file)]
DISCUSSION
NIFS of A. vinelandii participates in construction of
the Fe-S clusters of not only nitrogenase (31), but also other
iron-sulfur proteins such as SoxR (32) and FNR (33). The NIFS-like
enzyme of E. coli found by Flint (20) also provides
apo-dihydroxy-acid dehydratase with a [4Fe-4S] cluster to
reconstitute the enzyme in vitro. The N-terminal amino acid
sequence of the enzyme was identical with that deduced from another
nifS-like gene of E. coli (Eco1 in Table
III). This gene, together with a
nifU-like gene, forms a unique gene cluster, which is
similar to that found for nifS of Anabaena sp.
(34-36). Three nifS-like genes have been demonstrated also
in the genome of Haemophilus influenzae, and a similar gene
cluster occurs around the Hin1 gene (Table III) of the genome.
Therefore, Eco1 and Hin1 probably participate in construction of the
Fe-S clusters of iron-sulfur proteins, in the same manner as NIFS of
A. vinelandii. Synechocystis sp. PCC6803 also
contains three nifS-like genes. However, we found no such gene organization around it. Similarly, none of the cysteine sulfinate desulfinase genes and the third nifS-like gene (Eco2 in
Table III) of E. coli form such gene clusters. The same is
true for the other nifS-like genes of H. influenzae (Hin2 and Hin3). Therefore, these NIFS-like proteins
probably have biochemical functions different from those of Eco1, Hin1,
and A. vinelandii NIFS.
Table III.
NIFSs and NIFS-like proteins
Accession indicates the accession numbers. Length is the length of the
protein. The corresponding sequence data are indicated in Footnotes
d-j.
|
| Source |
Abbreviation |
Accession |
Length |
Ref. |
|
| A.
vinelandii |
Avi |
P05341a |
402 |
(21)
|
| Azotobacter
chroococcum |
Ach |
P23120a |
396 |
(48)
|
| Azospirillum
brasilense |
Abr |
U26427b |
398 |
(49)
|
| Enterobacter
agglomerans |
Eag |
X99694b |
401 |
| Klebsiella
pneumoniae |
Kpn |
P053344a |
397 |
(21)
|
| Rhodobacter
sphaeroides |
Rsh |
Q01179a |
387 |
(50)
|
| Rhodobacter
capsulatus |
Rca |
Q07177a |
384 |
(51)
|
| Anabaena sp.
PCC7120 |
Asp |
P12623a |
400 |
(35) |
| Anabaena
variabilis |
Ava2 |
U49859b |
398 |
(52)
|
| Anabaena
azollae |
Aaz |
L34879b |
400 |
(36)
|
| Synechocystis sp.
PCC6803 |
Ssp1 |
D64004b,d |
420 |
(53)
|
| Synechocystis sp.
PCC6803 |
Ssp2 |
D63999b,e |
386 |
(53)
|
| Synechocystis sp.
PCC6803 |
Ssp3 |
D90899b,f |
391 |
(54) |
| H.
influenzae Rd |
Hin1 |
HI0378c |
406 |
(55)
|
| H. influenzae
Rd |
Hin2 |
HI1295c |
437 |
(55) |
| H.
influenzae Rd |
Hin3 |
HI1343c |
238 |
(55)
|
| E. coli K-12 |
Eco1 |
D90883b,g |
404 |
(18)
|
| E. coli K-12 |
Eco2 |
D90811b,h |
406 |
(19)
|
| E. coli K-12 |
CSD |
U295810b,i |
401 |
(18)
|
| S. cerevisiae |
Sce |
P25374a |
497 |
(15)
|
| Lactobacillus
delbrueckii |
Lde |
P31672a |
355 |
(56) |
| B.
subtilis |
Bsu |
P38033a |
395 |
(14)
|
| Caenorhabditis
elegans |
Cel |
U23139b,j |
328 |
(57)
|
| Mycobacterium leprae |
Mle |
U00013b |
418
|
| Mycoplasma
pneumoniae |
Mpn |
AE000034b |
408 |
(58)
|
| Mycoplasma
genitalium |
Mge |
U39716b |
408 |
(59) |
|
|
a
SWISS-PROT.
|
|
b
GenBankTM/EMBL.
|
|
c
TIGR microbial data base.
|
|
d
slr0077.
|
|
e
slr0387.
|
|
f
sll0704.
|
|
g
yzz0.
|
|
h
o320#17.
|
|
i
o401.
|
|
j
F13H8.9.
|
|
NIFS has been classified into the same group as aminotransferases of
class V (37) and subgroup IV (38), which include serine-pyruvate
aminotransferase (EC 2.6.1.51) and phosphoserine aminotransferase (EC
2.6.1.52), on the basis of sequence homology analysis.
Isopenicillin-N-epimerase belongs to the same group as
various PLP-dependent enzymes, other than aminotransferases (37, 38). It has therefore been suggested that NIFS and
isopenicillin-N-epimerase evolved from the common ancestral
protein for the aminotransferases of these classes (37, 38).
We have found that NIFS family proteins are classified into two groups,
I and II, according to their sequence similarities. The two groups are
clearly distinct from each other in the regions named a,
b, c, and d (Fig.
3).
Average sequence similarities of cysteine sulfinate desulfinase to Group I and II members were 23 and
37%, respectively. The similarity relationship among NIFS family
proteins is shown in a phylogenetic tree (Fig.
4), which also indicates that the
proteins are classified into two major groups. The proteins Cel, Lde,
Bsu, and Ssp3 are far from the others, but are close to the members of
Group I than to the Group II proteins.
Fig. 4.
Phylogenetic relations of NIFS family
proteins. The protein sequences were aligned as shown in Fig. 3,
and their similarity relationships were calculated with the MegAlign
program of the DNASTAR package. Abbreviations of protein names are
shown in Table III. Cysteine sulfinate desulfinase (CSD) is
asterisked. The proteins are classified into two groups as
shown by braces, and I and II indicate
Group I and II, respectively.
[View Larger Version of this Image (23K GIF file)]
We have shown that selenocysteine lyase from C. freundii is
quite different from the pig liver enzyme in various physicochemical properties (11). The amino acid compositions of pig liver
selenocysteine lyase (PIG), cysteine sulfinate desulfinase
(CSD), A. vinelandii NIFS (Avi), and
E. coli NIFS-like protein (Eco1) resemble each other, but are distinct from that of selenocysteine lyase from C. freundii (CFR) (Fig. 5).
Therefore, the latter enzyme probably belongs to a different family of
proteins.
Fig. 5.
Comparison of the amino acid compositions of
selenocysteine lyase and NIFS family proteins. The amino acid
compositions of selenocysteine lyases were obtained from the previous
report (11). Those of NIFS family proteins were calculated from the amino acid sequences deduced from the nucleotide sequences of the
genes. Histograms show the amino acid compositions: Avi,
A. vinelandii NIFS; Eco1, E. coli
NIFS-like protein; CSD, cysteine sulfinate desulfinase;
PIG, pig liver selenocysteine lyase; CFR, C. freundii selenocysteine lyase.
[View Larger Version of this Image (49K GIF file)]
The NIFS-like protein from E. coli and NIFS from A. vinelandii have common characteristics; both contain essential
cysteinyl residues at the active sites. The thiol group presumably
attacks as a nucleophile the sulfur atom of the substrate, cysteine, to form the intermediate, enzyme-bound cysteinyl persulfide (14, 20). By
contrast, no cysteinyl residue of cysteine sulfinate desulfinase is
essential for catalysis. The cysteine sulfinate desulfinase reaction is
assumed to proceed through direct release of elemental selenium or
sulfur atom from the substrate, selenocysteine or cysteine. It has been
assumed that formation of the enzyme-bound cysteinyl persulfide is
crucial to deliver sulfur atoms efficiently to iron-sulfur proteins. If
this is the case, cysteine sulfinate desulfinase will not be related
metabolically to the formation of Fe-S clusters, although sulfur atoms
produced from cysteine by the enzyme are probably incorporated into
iron-sulfur proteins with low efficiency in the same manner as observed
for O-acetylserine sulfhydrylase A (EC 4.2.99.8),
O-acetylserine sulfhydrylase B (EC 4.2.99.8), and
-cystathionase (EC 4.4.1.8) (39). The fact that the
Km value of cysteine sulfinate desulfinase for
cysteine is high also suggests that cysteine is not the physiological substrate of the enzyme.
The irreversible inactivation of PLP enzymes by -chloroalanine has
been shown to proceed through modification of the enzyme-bound PLP with
nascent -aminoacrylate formed from -chloroalanine (40-42). Cysteine sulfinate desulfinase catalyzes the same type of reaction as
do selenocysteine lyase, aspartate -decarboxylase, and kynureninase. All these enzymes except cysteine sulfinate desulfinase are inactivated by -chloroalanine (10, 43, 44). Nascent -aminoacrylate is
probably released from the active site of cysteine sulfinate desulfinase much more quickly than from those of the other enzymes. Alternatively, -aminoacrylate may be hydrolyzed quickly to pyruvate and ammonia, and so the enzyme can escape from modification with -aminoacrylate.
In mammals, cysteine is oxidized by cysteine dioxygenase (EC
1.13.11.20) to form cysteine sulfinic acid, which is decarboxylated to
form hypotaurine by cysteine sulfinate decarboxylase (EC 4.1.1.29). cDNAs for cysteine dioxygenase (45) and cysteine sulfinate
decarboxylase (46) were cloned and sequenced. We found no sequences
similar to those of the cDNAs in the whole genomic sequence of
E. coli K-12. If E. coli has a cysteine
dioxygenase, it will have little sequence similarity to the mammalian
enzyme. Alternatively, if no cysteine dioxygenase occurs in E. coli, the cysteine desulfination may be a side function of the
enzyme with no metabolic relevance. Aspartate -decarboxylase and
aspartate aminotransferase also use cysteine sulfinate as a good
substrate and desulfinate it (29, 43, 47). Whatever the physiological
function of cysteine sulfinate desulfinase is, this is the first enzyme
in Group II whose catalytic function has been clarified (Fig. 4). Other
proteins of this group probably have a similar catalytic function to
cysteine sulfinate desulfinase. Cloning and expression of the Eco2
gene, the last nifS-like gene of E. coli mapped
at 38.3 min (19) in the chromosome, and characterization of the gene
product, are now being studied.
FOOTNOTES
*
This work was supported in part by the Research for the
Future Program from the Japan Society for the Promotion of Science.The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
§
These authors contributed equally to this work and should be
considered equivalent first authors.
To whom correspondence should be addressed. Tel.:
81-774-38-3240; Fax: 81-774-38-3248; E-mail:
esaki{at}pclsp2.kuicr.kyoto-u.ac.jp.
1
H. Mihara, T. Kurihara, T. Yoshimura, K. Soda,
and N. Esaki, manuscript in preparation.
2
The abbreviations used are: PLP, pyridoxal
5 -phosphate; ORF, open reading frame; PAGE, polyacrylamide gel
electrophoresis; Tricine,
N-tris(hydroxymethyl)methylglycine.
ACKNOWLEDGEMENT
We gratefully appreciate the advice of Dr. Jun
Hiratake on performing matrix-assisted laser desorption mass
spectrometry.
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F. W. Outten, M. J. Wood, F. M. Munoz, and G. Storz
The SufE Protein and the SufBCD Complex Enhance SufS Cysteine Desulfurase Activity as Part of a Sulfur Transfer Pathway for Fe-S Cluster Assembly in Escherichia coli
J. Biol. Chem.,
November 14, 2003;
278(46):
45713 - 45719.
[Abstract]
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L. Loiseau, S. Ollagnier-de-Choudens, L. Nachin, M. Fontecave, and F. Barras
Biogenesis of Fe-S Cluster by the Bacterial Suf System: SufS AND SufE FORM A NEW TYPE OF CYSTEINE DESULFURASE
J. Biol. Chem.,
October 3, 2003;
278(40):
38352 - 38359.
[Abstract]
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J. T. Kaiser, S. Bruno, T. Clausen, R. Huber, F. Schiaretti, A. Mozzarelli, and D. Kessler
Snapshots of the Cystine Lyase C-DES during Catalysis. STUDIES IN SOLUTION AND IN THE CRYSTALLINE STATE
J. Biol. Chem.,
January 3, 2003;
278(1):
357 - 365.
[Abstract]
[Full Text]
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C. T. Lauhon
Requirement for IscS in Biosynthesis of All Thionucleosides in Escherichia coli
J. Bacteriol.,
December 15, 2002;
184(24):
6820 - 6829.
[Abstract]
[Full Text]
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E. A.H. Pilon-Smits, G. F. Garifullina, S. Abdel-Ghany, S.-I. Kato, H. Mihara, K. L. Hale, J. L. Burkhead, N. Esaki, T. Kurihara, and M. Pilon
Characterization of a NifS-Like Chloroplast Protein from Arabidopsis. Implications for Its Role in Sulfur and Selenium Metabolism
Plant Physiology,
November 1, 2002;
130(3):
1309 - 1318.
[Abstract]
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H. Mihara, S.-i. Kato, G. M. Lacourciere, T. C. Stadtman, R. A. J. D. Kennedy, T. Kurihara, U. Tokumoto, Y. Takahashi, and N. Esaki
The iscS gene is essential for the biosynthesis of 2-selenouridine in tRNA and the selenocysteine-containing formate dehydrogenase H
PNAS,
May 14, 2002;
99(10):
6679 - 6683.
[Abstract]
[Full Text]
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S.-i. Kato, H. Mihara, T. Kurihara, Y. Takahashi, U. Tokumoto, T. Yoshimura, and N. Esaki
Cys-328 of IscS and Cys-63 of IscU are the sites of disulfide bridge formation in a covalently bound IscS/IscU complex: Implications for the mechanism of iron-sulfur cluster assembly
PNAS,
April 30, 2002;
99(9):
5948 - 5952.
[Abstract]
[Full Text]
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G. M. Lacourciere
Selenium Is Mobilized In Vivo from Free Selenocysteine and Is Incorporated Specifically into Formate Dehydrogenase H and tRNA Nucleosides
J. Bacteriol.,
April 1, 2002;
184(7):
1940 - 1946.
[Abstract]
[Full Text]
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J. Tachezy, L. B. Sanchez, and M. Muller
Mitochondrial Type Iron-Sulfur Cluster Assembly in the Amitochondriate Eukaryotes Trichomonas vaginalis and Giardia intestinalis, as Indicated by the Phylogeny of IscS
Mol. Biol. Evol.,
October 1, 2001;
18(10):
1919 - 1928.
[Abstract]
[Full Text]
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C. J. Schwartz, O. Djaman, J. A. Imlay, and P. J. Kiley
The cysteine desulfurase, IscS, has a major role in in vivo Fe-S cluster formation in Escherichia coli
PNAS,
July 19, 2000;
(2000)
160261497.
[Abstract]
[Full Text]
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T. Kiyasu, A. Asakura, Y. Nagahashi, and T. Hoshino
Contribution of Cysteine Desulfurase (NifS Protein) to the Biotin Synthase Reaction of Escherichia coli
J. Bacteriol.,
May 15, 2000;
182(10):
2879 - 2885.
[Abstract]
[Full Text]
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T. Clausen, J. T. Kaiser, C. Steegborn, R. Huber, and D. Kessler
Crystal structure of the cystine C-S lyase from Synechocystis: Stabilization of cysteine persulfide for FeS cluster biosynthesis
PNAS,
April 11, 2000;
97(8):
3856 - 3861.
[Abstract]
[Full Text]
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H. Mihara, T. Kurihara, T. Watanabe, T. Yoshimura, and N. Esaki
cDNA Cloning, Purification, and Characterization of Mouse Liver Selenocysteine Lyase. CANDIDATE FOR SELENIUM DELIVERY PROTEIN IN SELENOPROTEIN SYNTHESIS
J. Biol. Chem.,
February 25, 2000;
275(9):
6195 - 6200.
[Abstract]
[Full Text]
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H. Mihara, M. Maeda, T. Fujii, T. Kurihara, Y. Hata, and N. Esaki
A nifS-like Gene, csdB, Encodes an Escherichia coli Counterpart of Mammalian Selenocysteine Lyase. GENE CLONING, PURIFICATION, CHARACTERIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC STUDIES
J. Biol. Chem.,
May 21, 1999;
274(21):
14768 - 14772.
[Abstract]
[Full Text]
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S. I. Patzer and K. Hantke
SufS Is a NifS-Like Protein, and SufD Is Necessary for Stability of the [2Fe-2S] FhuF Protein in Escherichia coli
J. Bacteriol.,
May 15, 1999;
181(10):
3307 - 3309.
[Abstract]
[Full Text]
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T. Lang and D. Kessler
Evidence for Cysteine Persulfide as Reaction Product of L-Cyst(e)ine C-S-Lyase (C-DES) from Synechocystis. ANALYSES USING CYSTINE ANALOGUES AND RECOMBINANT C-DES
J. Biol. Chem.,
January 1, 1999;
274(1):
189 - 195.
[Abstract]
[Full Text]
[PDF]
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G. M. Lacourciere and T. C. Stadtman
The NIFS Protein Can Function as a Selenide Delivery Protein in the Biosynthesis of Selenophosphate
J. Biol. Chem.,
November 20, 1998;
273(47):
30921 - 30926.
[Abstract]
[Full Text]
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M. K. B. Berlyn
Linkage Map of Escherichia coli K-12, Edition 10: The Traditional Map
Microbiol. Mol. Biol. Rev.,
September 1, 1998;
62(3):
814 - 984.
[Abstract]
[Full Text]
[PDF]
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L. Zheng, V. L. Cash, D. H. Flint, and D. R. Dean
Assembly of Iron-Sulfur Clusters. IDENTIFICATION OF AN iscSUA-hscBA-fdx GENE CLUSTER FROM AZOTOBACTER VINELANDII
J. Biol. Chem.,
May 22, 1998;
273(21):
13264 - 13272.
[Abstract]
[Full Text]
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G. M. Lacourciere, H. Mihara, T. Kurihara, N. Esaki, and T. C. Stadtman
Escherichia coli NifS-like Proteins Provide Selenium in the Pathway for the Biosynthesis of Selenophosphate
J. Biol. Chem.,
July 28, 2000;
275(31):
23769 - 23773.
[Abstract]
[Full Text]
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C. T. Lauhon and R. Kambampati
The iscS Gene in Escherichia coli Is Required for the Biosynthesis of 4-Thiouridine, Thiamin, and NAD
J. Biol. Chem.,
June 23, 2000;
275(26):
20096 - 20103.
[Abstract]
[Full Text]
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S. Leimkuhler and K. V. Rajagopalan
A Sulfurtransferase Is Required in the Transfer of Cysteine Sulfur in the in Vitro Synthesis of Molybdopterin from Precursor Z in Escherichia coli
J. Biol. Chem.,
June 15, 2001;
276(25):
22024 - 22031.
[Abstract]
[Full Text]
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S. Leimkuhler, M. M. Wuebbens, and K. V. Rajagopalan
Characterization of Escherichia coli MoeB and Its Involvement in the Activation of Molybdopterin Synthase for the Biosynthesis of the Molybdenum Cofactor
J. Biol. Chem.,
September 7, 2001;
276(37):
34695 - 34701.
[Abstract]
[Full Text]
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S.-i. Kato, H. Mihara, T. Kurihara, Y. Takahashi, U. Tokumoto, T. Yoshimura, and N. Esaki
Cys-328 of IscS and Cys-63 of IscU are the sites of disulfide bridge formation in a covalently bound IscS/IscU complex: Implications for the mechanism of iron-sulfur cluster assembly
PNAS,
April 30, 2002;
99(9):
5948 - 5952.
[Abstract]
[Full Text]
[PDF]
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C. J. Schwartz, O. Djaman, J. A. Imlay, and P. J. Kiley
The cysteine desulfurase, IscS, has a major role in in vivo Fe-S cluster formation in Escherichia coli
PNAS,
August 1, 2000;
97(16):
9009 - 9014.
[Abstract]
[Full Text]
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Copyright © 1997 by the American Society for Biochemistry and Molecular Biology.
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