3RIT

Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg and dipeptide L-Arg-D-Lys


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptide epimerase
A, B, C, D, E
356Methylococcus capsulatusMutation(s): 0 
Gene Names: MCA1834
EC: 5.1.1
UniProt
Find proteins for Q607C7 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore Q607C7 
Go to UniProtKB:  Q607C7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ607C7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
DA [auth C],
NA [auth D],
O [auth A],
WA [auth E]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
ARG
Query on ARG

Download Ideal Coordinates CCD File 
AA [auth C],
KA [auth D],
L [auth A],
T [auth B],
TA [auth E]
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
DLY
Query on DLY

Download Ideal Coordinates CCD File 
BA [auth C],
LA [auth D],
M [auth A],
U [auth B],
UA [auth E]
D-LYSINE
C6 H14 N2 O2
KDXKERNSBIXSRK-RXMQYKEDSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
EA [auth D]
F [auth A]
FA [auth D]
G [auth A]
GA [auth D]
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
OA [auth E],
P [auth B],
PA [auth E],
Q [auth B],
QA [auth E],
R [auth B],
RA [auth E],
S [auth B],
SA [auth E],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth C],
MA [auth D],
N [auth A],
V [auth B],
VA [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 275.32α = 90
b = 275.32β = 90
c = 275.32γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-22
    Changes: Database references
  • Version 1.3: 2012-03-14
    Changes: Database references
  • Version 1.4: 2012-03-21
    Changes: Database references
  • Version 1.5: 2012-03-28
    Changes: Database references
  • Version 1.6: 2024-02-28
    Changes: Data collection, Database references, Derived calculations