3IJI

Structure of dipeptide epimerase from Bacteroides thetaiotaomicron complexed with L-Ala-D-Glu; nonproductive substrate binding.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.

Lukk, T., Sakai, A., Kalyanaraman, C., Brown, S.D., Imker, H.J., Song, L., Fedorov, A.A., Fedorov, E.V., Toro, R., Hillerich, B., Seidel, R., Patskovsky, Y., Vetting, M.W., Nair, S.K., Babbitt, P.C., Almo, S.C., Gerlt, J.A., Jacobson, M.P.

(2012) Proc.Natl.Acad.Sci.USA 109: 4122-4127

  • DOI: 10.1073/pnas.1112081109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • 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 functi ...

    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.

    Organizational Affiliation: 

    Department of Biochemistry, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Muconate cycloisomerase
A, B
338Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)Mutation(s): 0 
EC: 5.1.1.20
Find proteins for Q8A861 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q8A861
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGL
Query on DGL
Download SDF File 
Download CCD File 
A, B
D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ALA
Query on ALA
Download SDF File 
Download CCD File 
A, B
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 141.432α = 90.00
b = 100.079β = 90.25
c = 60.000γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
BALBESphasing
SCALEPACKdata scaling
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Database references
  • Version 1.3: 2012-04-04
    Type: Database references