3Q4D image
Entry Detail
PDB ID:
3Q4D
Keywords:
Title:
Crystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Ala
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2010-12-23
Release Date:
2011-02-16
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.25
R-Value Work:
0.22
R-Value Observed:
0.23
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
Chain IDs:A, B, C, D, E, F, G, H, I
Chain Length:368
Number of Molecules:9
Biological Source:Cytophaga hutchinsonii
Primary Citation
Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
Proc.Natl.Acad.Sci.USA 109 4122 4127 (2012)
PMID: 22392983 DOI: 10.1073/pnas.1112081109

Abstact

The rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. The assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. Here we describe the results of a focused investigation of a group of enzymes in the enolase superfamily that are involved in epimerizing dipeptides. The first members of this group to be functionally characterized were Ala-Glu epimerases in Eschericiha coli and Bacillus subtilis, based on the operon context and enzymological studies; these enzymes are presumed to be involved in peptidoglycan recycling. We have subsequently studied more than 65 related enzymes by computational methods, including homology modeling and metabolite docking, which suggested that many would have divergent specificities;, i.e., they are likely to have different (unknown) biological roles. In addition to the Ala-Phe epimerase specificity reported previously, we describe the prediction and experimental verification of: (i) a new group of presumed Ala-Glu epimerases; (ii) several enzymes with specificity for hydrophobic dipeptides, including one from Cytophaga hutchinsonii that epimerizes D-Ala-D-Ala; and (iii) a small group of enzymes that epimerize cationic dipeptides. Crystal structures for certain of these enzymes further elucidate the structural basis of the specificities. The results highlight the potential of computational methods to guide experimental characterization of enzymes in an automated, large-scale fashion.

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