3JVA

Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

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 U S A 109: 4122-4127

  • DOI: 10.1073/pnas.1112081109
  • Primary Citation of Related Structures:  
    3IJI, 3IJL, 3IJQ, 3IK4, 3JVA, 3JW7, 3JZU, 3K1G, 3KUM, 3Q45, 3Q4D, 3R0K, 3R0U, 3R10, 3R11, 3R1Z, 3RIT, 3RO6

  • 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 functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptide Epimerase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
354Enterococcus faecalis V583Mutation(s): 0 
Gene Names: EF_1511I574_01909OO5_01959
EC: 5.1.1
UniProt
Find proteins for Q834W6 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q834W6 
Go to UniProtKB:  Q834W6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ834W6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A],
Q [auth C],
R [auth C],
U [auth E],
Y [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
M [auth B],
N [auth B],
V [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth A],
O [auth B],
P [auth C],
S [auth D],
T [auth E],
J [auth A],
O [auth B],
P [auth C],
S [auth D],
T [auth E],
W [auth F],
X [auth G],
Z [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.268α = 90
b = 162.268β = 90
c = 319.561γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
BALBESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2012-05-23
    Changes: Database references