3Q4D

Crystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Ala


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.5 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
Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
A, B, C, D, E, F, G, H, I
368Cytophaga hutchinsonii (strain ATCC 33406 / NCIMB 9469)Mutation(s): 0 
Gene Names: tfdD
EC: 5.1.1.-
Find proteins for Q11T61 (Cytophaga hutchinsonii (strain ATCC 33406 / NCIMB 9469))
Go to UniProtKB:  Q11T61
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DAL
Query on DAL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
D-ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-UWTATZPHSA-N
 Ligand Interaction
ALA
Query on ALA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 94.560α = 90.00
b = 158.090β = 100.04
c = 182.180γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
HKL-2000data collection
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-02-22
    Type: Database references
  • Version 1.3: 2012-03-14
    Type: Database references
  • Version 1.4: 2012-03-21
    Type: Database references
  • Version 1.5: 2012-03-28
    Type: Database references