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J. Biol. Chem., Vol. 282, Issue 48, 35328-35336, November 30, 2007

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A Family 2 Pectate Lyase Displays a Rare Fold and Transition Metal-assisted β-Elimination^*

From the Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada

The family 2 pectate lyase from Yersinia enterocolitica (YePL2A), solved to 1.5Å_, reveals it to be the first prokaryotic protein reported to display the rare (/)₇ barrel fold. In addition to its apo form, we have also determined the structure of a metal-bound form of YePL2A (to 2.0Å₎ and a trigalacturonic acid-bound substrate complex (to 2.1Å_). Although its fold is rare, the catalytic center of YePL2A can be superimposed with structurally unrelated families, underlining the conserved catalytic amino acid architecture of the β-elimination mechanism. In addition to its overall structure, YePL2A also has two other unique features: 1) it utilizes a metal atom other than calcium for catalysis, and 2) its Brønstead base is in an alternate conformation and directly interacts with the uronate group of the substrate.

Received for publication, July 5, 2007 , and in revised form, September 10, 2007.

The atomic coordinates and structure factors (code 2V8I, 2V8J, and 2V8K) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported by a grant from the Canadian Institutes of Health Research. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Fig. S1.

¹ Canada Research Chair in Molecular Interactions. To whom correspondence should be addressed: Biochemistry & Microbiology, University of Victoria, P.O. Box 3055 STN CSC, Victoria, BC V8W 3P6, Canada. Tel.: 250-472-4168; Fax: 250-721-8855; E-mail: boraston{at}uvic.ca.

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