3R0U

Crystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Tartrate and Mg complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
Enzyme of enolase superfamilyA, B379Francisella philomiragia subsp. philomiragia ATCC 25017Mutation(s): 0 
Gene Names: Fphi_1647
EC: 5.1.1
UniProt
Find proteins for B0TZW0 (Francisella philomiragia subsp. philomiragia (strain ATCC 25017 / FSC 153 / O#319-036))
Explore B0TZW0 
Go to UniProtKB:  B0TZW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0TZW0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAR
Query on TAR

Download Ideal Coordinates CCD File 
G [auth A]D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
J [auth B],
K [auth B],
D [auth A],
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B],
O [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
I [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.07α = 90
b = 121.07β = 90
c = 149.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-06
    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: 2012-03-21
    Changes: Database references
  • Version 1.4: 2012-03-28
    Changes: Database references