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J. Biol. Chem., Vol. 280, Issue 23, 21981-21986, June 10, 2005
Crystal Structure of Dynein Light Chain TcTex-1*
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| ABSTRACT |
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-strand 2 and has a fold similar to the dynein light chain, LC8. Based on structural alignment, the TcTex-1 and LC8 sequences show no identity, although the root mean square deviation between secondary structural elements is less than 1.6 Å. Moreover, the N terminus, which is equivalent to
-strand 1 in LC8, is splayed out and binds to a crystallographic dimer as an anti-parallel
-strand at the same position as the neuronal nitric-oxide synthase peptide in the LC8 complex. Similarity to LC8 and comparison to the LC8-neuronal nitricoxide synthase complex suggest that TcTex-1 binds its targets in a similar manner as LC8 and provides insight to the lack of strict sequence identity among the targets for TcTex-1. | INTRODUCTION |
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Cytoplasmic dynein is a large, multimeric complex with a molecular mass of 1.2 MDa. There are two heavy chains, two intermediate chains, several light intermediate chains, and several light chains (3). The heavy chains (
530 kDa) dimerize and function as the motor (4). The intermediate chains (
74 kDa; dynein intermediate chain) and light intermediate chains (
2450 kDa; dynein light intermediate chain) bind the stem of the heavy chain, and the light chains (822 kDa; dynein light chains) bind to the intermediate chain.
The light chains fall into three classes, typified by TcTex-1, LC8, and LC7/Robl. The TcTex-1 class includes variants RP3 (54% identity to TcTex-1 in humans) and a more distant relative, TcTex-2 (20% identity to TcTex-1 in humans) that has a 70-residue N-terminal extension and is associated with axonemal dynein. (Two additional human TcTex-1 variants with N-terminal extensions are also found in BLAST searches but have not been described experimentally.) The LC8 class includes variants DNCL1 (93% identity to LC8 in humans) and the axonemal DNCL4 (35% identity), which also has an extended N-terminal tail (13 residues). The LC7/Robl class has at least two members (73% identical in humans).
The cargo typically associated with dynein is dynactin. Like dynein, it is a large multimeric complex (
1.2 MDa) that uses its principal component, p150glued, to bind the N terminus of the dynein intermediate chain (5). Another principal component of dynactin, Arp1, has been shown to bind spectrin and, hence, vesicles (6). However, the dynein light chains and light intermediate chains (7) have also been implicated in targeting specific proteins. Among the different light chains, TcTex-1 and LC8 have been demonstrated to bind a number of distinct cargoes (8). TcTex-1 binds the dynein intermediate chain (9, 10), the lipid-associated protein, DOC2 (11), the small GTPase, FIP1 (12), the cytoplasmic tails of the rhodopsin receptor (13), parathyroid hormone receptor (14), bone morphogenetic receptor type II (15), CD5 (16) and CD155 (17), the unique domain of Fyn (1820), Trk receptor (21), a trophinin-binding protein, tastin (22), and the voltage-dependent anion-selective channel 1 (VDAC1) (23). LC8 also binds the dynein intermediate chain as well as neuronal nitric-oxide synthase (24), BIM (25), Swallow (26), I
B
(27), lyssavirus phosphoprotein (28, 29), and other targets.
One of the best examples implicating light chains in targeting cargo to dynein is the interaction between TcTex-1 and rhodopsin (13). TcTex-1 knockouts failed to transport rhodopsin to the apical surface in vivo, and using RP3, a TcTex-1 homolog (55% identity), to rescue the knock-out also failed (30). Similarly, studies in polarized (Madin-Darby canine kidney cells showed that mutations linked to retinitis pigmentosa in the cytoplasmic tail of the rhodopsin receptor abolished TcTex-1 binding (13). Most interestingly, TcTex-1 and RP3 are temporally and spatially regulated (31). Other functions associated with TcTex-1 include non-Mendelian meiotic drive (32), the production of functional sperm in Drosophila (33), and regular oscillatory nuclear movement in the meiotic prophase in fission yeast (34).
Recently, NMR experiments measured the chemical shifts and assigned the secondary structure of elements of TcTex-1; however, sample difficulties prevented the determination of the three-dimensional structure (9, 35). Nonetheless, in their work, Mok et al. (9) identified a 19-residue stretch of the dynein intermediate chain that bound to TcTex-1 and showed that the N-terminal fraction of this peptide produced substantial chemical shifts in a set of residues in TcTex-1. Comparison of this sequence with sequences from a set of reported targets of TcTex-1 identified a region of basic residues at the N terminus, (R/K)(R/K)XX(R/K), suggesting a potential TcTex-1-targeting sequence. However, this finding remains ambiguous particularly considering that this sequence is not found in the binding regions identified for a different set of TcTex-1 ligands including rhodopsin, Fyn, and Trk receptors. In fact, another consensus sequence, (VS(K/H))T/S)X(V/T)(T/S)(N/Q)V, was reported recently (14) but again is only shared by a fraction of the reported TcTex-1 ligands. To better understand how TcTex-1 recognizes its ligands that share little sequence identity, we have solved the crystal structure of TcTex-1 as an initial step in defining the structural determinants of its target recognition.
| MATERIALS AND METHODS |
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Full-length Drosophila TcTex-1 cDNA clones were obtained by PCR using EST-clones (LP04056 and LD36706) purchased from Research Genetics and placed into pET24d between the NcoI and XhoI sites (36). PCR primers were synthesized by the biopolymer core facility (Columbia University). The sequence of this construct was confirmed by DNA sequencing, and the expression plasmid was transformed into BL21-DE3 expression cells (Novagen). Overexpression was carried out at 37 °C for 4 h.
The cells containing Drosophila TcTex-1 were sonicated and clarified by ultracentrifugation. The clarified lysate was passed over a HiLoad 26/10 Q FastFlow column (Amersham Biosciences), and protein was eluted with a NaCl gradient (100 mM to 1 M). TcTex-1 elutes at
200 mM NaCl in 50 mM Tris-HCl, pH 8.0. The protein was concentrated to a volume of 13 ml and applied to HiLoad 26/60 Superdex 75 (Amersham Biosciences) at rate of 2 ml/min. Coomassie staining indicated that the protein was more than 95% pure, and mass spectrometry (Mr = 12481.2 atomic mass units) showed that the 111-residue protein was not modified. Selenomethionyl (SeMet)-labeled TcTex-1 was prepared and purified in a similar fashion except the cells were grown in a selenomethionine minimum media (37).
Characterization of Ternary StructureSize exclusion chromatography was carried out to determine the oligomerization state of TcTex-1. Moreover, because there was a question of a pH-dependent monomerdimer equilibrium in LC8, the Superose 12 column (Amersham Biosciences) was equilibrated with two different buffers (38). The low pH buffer contained 50 mM MES, 100 mM NaCl, 1 mM EDTA, and 1 mM DTT, pH 5. The high pH buffer contained 50 mM CHES, 100 mM NaCl, 1 mM EDTA, and 1 mM DTT, pH 9. The protein applied to the column was in 10 mM Tris, 100 mM NaCl, 1 mM EDTA, and 1 mM DTT, pH 8.0. The column was calibrated using bovine serum albumin (66 kDa), ovalbumin (45 kDa), chymotrypsin (25 kDa), and lysozyme (14 kDa) for both buffers. TcTex-1 (25 µl of 2 mg/ml solution) was applied to the column. The elution volume was measured and compared with the calibration graph as well as to each other.
Crystallographic AnalysisPurified protein was concentrated to
40 mg/ml in 10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 5 mM EDTA, and 5mM DTT. Crystals were grown from 100 mM CHES over a pH range of 910 and 2.22.5 M (NH4)2SO4, 0.1 M to 0.4 M Li2SO4, or 2 M K2HPO4 and 0.5 M NaH2PO4 or 1.6 M sodium citrate as a precipitating agents, each using the hanging drop method. Crystals could be obtained by using protein concentrations of 1040 mg/ml. The largest crystals (100 x 50 x 50 µm3) were grown in 0.1 M CHES, pH 910, 2.4 M (NH4)2SO4, and 0.1 M Li2SO4 at protein concentration of 1020 mg/ml. The SeMet TcTex-1 crystals were grown under same conditions and were generally larger (150 x 50 x 50 µm3).
Diffraction data of Drosophila TcTex-1 were collected at beamline X4A, Brookhaven National Laboratory. Both native and SeMet-labeled Drosophila TcTex-1 crystals diffract to Bragg spacings beyond 1.5 Å. MAD data were collected at four wavelengths:
1 (0.99187 Å) at the low energy side remote from the absorption edge;
2 (0.97950 Å) at the inflection point;
3 (0.97897 Å) at the peak of selenium absorption curve; and
4 (0.96672 Å) at the high energy side remote from the absorption edge. One MAD data set was collected to a limit of 2.0 Å spacing, and another set was collected to 1.5 Å using a different SeMet crystal. For the 2.0 Å data set, 100 images (15 s exposure deg1 image1) were collected per wavelength for each of the direct beam and inverse beams, whereas 65 images (60 s exposure deg1 image1) were collected for the 1.5 Å data set.
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| RESULTS AND DISCUSSION |
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-helices followed by four
-strands (Fig. 1A). The N terminus of TcTex-1 is splayed away from the folded core and bound to an adjacent crystallographic "dimer" as an additional
-strand (
0) (Fig. 1B). The second
-strand (
2) is domain swapped and makes extensive main chain hydrogen bonds and side chain interactions with the other protomer. Sequence alignment shows that TcTex-1 is highly conserved across a number of species, particularly in
-strands (Fig. 2).
TcTex-1 Shares the Same Fold as PIN/LC8 Despite the lack of sequence identity, TcTex-1 has the same fold as PIN/LC8. As shown in Fig. 3A, the
-helices,
-strands, and loops are generally longer in TcTex-1 compared with PIN/LC8, but mostly to the N-terminal half of the protein (based on the orientation of the bound N-terminal tail). The r.m.s.d.1 between common elements is less than 1.6 Å. A structure-based sequence alignment of TcTex-1 and LC8 has zero sequence identity (Fig. 2). An alignment based solely on sequence, on the other hand, produced 11% identity, but this was achieved by overlapping the C terminus of LC8 with the N terminus of TcTex-1.
TcTex-1 Dimerization InterfaceThe interface between each TcTex-1 protomer is extensive and predominantly hydrophobic (supplemental Fig. 1). In our calculations, each protomer buries 1532 Å2 of surface area, whereas each protomer in PIN/LC8 buries 760 Å2. It is interesting to note that there is a solvent channel running through the center of the TcTex-1 dimer (Fig. 3B), whereas the PIN/LC8 structure does not have such a feature. The function, if any, of this solvent channel is unclear. It does, however, produce a dimer interface with two hydrophobic patches. These patches include residues Met-66, Met-68, Leu-103, Leu-75', and the methyl of Thr-77' for the N-terminal half of the molecule and residues Leu-49, Thr-53, Ile-62, Cys-81', Tyr-82, Trp-83, Phe-107', and Leu-109 for the C-terminal half (nonprimed and prime residues denote individual protomers).
Several polar interactions also participate in and possibly stabilize the dimeric state. One that stands out is between the highly conserved His-76' (Asn in Caenorhabditis elegans), part of the domain swapped
-strand, and completely conserved Tyr-34 in the
1
2 loop and the highly conserved Asn-38 in the
-helix 2 (Ser in Chlamydomonas sp.). Because the molecule is symmetric, each interaction listed occurs twice.
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Peptides derived from putative LC8 cargo bind as an extended anti-parallel strand to swapped
-strand 2 of LC8, making eight backbone hydrogen bonds. This strand is surrounded by
-helix 2 on one side and
-strands 3 and 4 on the other.
Superposition of the common
-helices and
-strands of the core region of TcTex-1 and LC8 shows that the N-terminal tail and the nNOS peptide have similar backbone hydrogen bonding patterns (supplemental Fig. 2, A and B). Moreover, residues Ser-8 to Val-12 of the TcTex-1 tail based on this superposition align well with Gly-8 to Asp-12 of the nNOS peptide (r.m.s.d. = 0.95 Å). Residues in TcTex-1 equivalent to the residues that line the LC8 groove include His-34', Asn-38', and Glu-46' of
-helix 2; Ser-90, Thr-92, and Arg-94 of
-strand 3; and Tyr-101, Ile-103, and Ser-105 of
-strand 4.
All LC8 targets encode an invariant glutamine that caps the
-helix 2. The residues that precede and succeed this glutamine bind to hydrophobic sites derived from residues in the
-strands 3 and 4. Similarly, in TcTex-1, the residues directly before (Gln-9) and after (Ile-11) Phe-10, which corresponds to Gln-10 of LC8, are both buried in hydrophobic cavities.
A major difference between the binding groove of LC8 and the putative TcTex-1 groove is at the site on LC8 that interacts with the invariant glutamine in LC8 targets (Fig. 3, B and C). In TcTex-1,
-helix 2 is extended by an additional N-terminal turn that presents conserved residues His-34 and Asn-38 to the site.
The mechanism used by LC8 and TcTex-1, as we presume, to bind their respective targets provides a possible explanation of the low sequence identity observed among the LC8 target peptides and among the TcTex-1 target peptides. Arguments like those that explain sequence promiscuity in subtilisin substrate (46) and major histocompatibility complex-antigen complexes (47) also apply here; backbone hydrogen bonds and hydrophobic interactions do not place absolute restrictions on the sequence identity.
Our prediction for the importance of hydrophobic peptide residues on the binding targets to TcTex-1 differs from the basic motif, (R/K)(R/K)XX(R/K), proposed by Mok et al. (9). Glutathione S-transferase pull-down studies showed that a peptide derived from the dynein intermediate chain, LGRRLNKLGVSKVTQVDF, could bind TcTex-1. Titration of a truncated peptide (underlined) produced chemical shifts that map to the N-terminal half of the TcTex-1 structure (supplemental Fig. 2C) (9); however, this truncated positively charged peptide could not pull-down TcTex-1 (9). The chemical shift differences coincide with the negative charged surface of TcTex-1 (Fig. 3B) and likely reflect adventitious electrostatic binding.
A Potential Second Binding SiteIt was shown recently that exchanging a single residue that differs between the two LC8 isoforms (98% identity) altered partitioning of the isoform from myosin V to the dynein intermediate chain (48). This position maps to
-helix 2, away from the nNOS- and Bim-binding site (48). Most interestingly, a point mutation in TcTex-1 that is associated with T-specific overexpression of TcTex-1, a phenotype associated with transmission ratio distortion or meiotic drive, maps to nearly an identical region on the surface (supplemental Fig. 2, A and B) (49). Additional differences between TcTex-1 and RP3 also map to solvent-exposed areas away from the hydrophobic pocket (data not shown). As in the case of DLC2, the differences found in the solvent-exposed helix suggest the possibility of an additional binding site or regulatory role. Consequently, it is possible that the flanking helices form a secondary binding site for additional targets.
Post-translational Modification of TcTex-1 Should Not Affect Ligand BindingCampbell et al. (18) and Mou et al. (20) found that TcTex-1 is tyrosine-phosphorylated. There are four tyrosines in human TcTex-1 and three are conserved throughout the family (Fig. 2). Moreover, the conserved three are either buried or involved in extensive side chain interaction. However, there is an incompletely conserved tyrosine, Tyr-4, in the human, bovine, and the torpedo sequences, whereas it is a phenylalanine in mouse and rat and valine in Chlamydomonas. This position corresponds to the flexible region that is splayed away from the dimer core and, thus, potentially available for post-translational modification. However, Campbell et al. (18) showed that phosphorylation of TcTex-1 did not affect the binding of Fyn.
ConclusionsWe have shown that TcTex-1 is similar to LC8 in tertiary and quaternary structure despite no sequence identity. Based on this similarity and common modes of peptide binding, we suggest that TcTex-1 binds its targets in a similar manner.
| FOOTNOTES |
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The on-line version of this article (available at http://www.jbc.org) contains Figs. 1 and 2.
The atomic coordinates and structure factors (code 1YGT) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/). ![]()
Both authors equally contributed to this work. ![]()
¶ Present address: Kimmel Cancer Center, Thomas Jefferson University, 233 South 10th St., BLSB 826, Philadelphia, PA 19107. ![]()

To whom correspondence should be addressed: Dept. of Biochemistry and Molecular Biophysics, New York, NY 10032. Tel.: 212-305-1846; Fax: 212-305-7379; E-mail: wayne{at}convex.hhmi.columbia.edu.
1 The abbreviations used are: r.m.s.d., root mean square deviation; nNOS, neuronal nitric-oxide synthase; DTT, dithiothreitol; CHES, (2-(cyclohexylamino)ethanesulfonic acid); MES, 4-morpholineethanesulfonic acid; SeMet, selenomethionyl. ![]()
| ACKNOWLEDGMENTS |
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| REFERENCES |
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