1GPM

ESCHERICHIA COLI GMP SYNTHETASE COMPLEXED WITH AMP AND PYROPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families.

Tesmer, J.J.Klem, T.J.Deras, M.L.Davisson, V.J.Smith, J.L.

(1996) Nat Struct Biol 3: 74-86

  • DOI: 10.1038/nsb0196-74
  • Primary Citation of Related Structures:  
    1GPM

  • PubMed Abstract: 
  • The crystal structure of GMP synthetase serves as a prototype for two families of metabolic enzymes. The Class I glutamine amidotransferase domain of GMP synthetase is found in related enzymes of the purine, pyrimidine, tryptophan, arginine, histidine and folic acid biosynthetic pathways ...

    The crystal structure of GMP synthetase serves as a prototype for two families of metabolic enzymes. The Class I glutamine amidotransferase domain of GMP synthetase is found in related enzymes of the purine, pyrimidine, tryptophan, arginine, histidine and folic acid biosynthetic pathways. This domain includes a conserved Cys-His-Glu triad and is representative of a new family of enzymes that use a catalytic triad for enzymatic hydrolysis. The structure and conserved sequence fingerprint of the nucleotide-binding site in a second domain of GMP synthetase are common to a family of ATP pyrophosphatases, including NAD synthetase, asparagine synthetase and argininosuccinate synthetase.


    Related Citations: 
    • Preliminary X-Ray Analysis of Escherichia Coli Gmp Synthetase: Determination of Anomalous Scattering Factors for a Cysteinyl Mercury Derivative
      Tesmer, J.J.G., Stemmler, T.L., Penner-Hahn, J.E., Davisson, V.J., Smith, J.L.
      (1994) Proteins 18: 394

    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GMP SYNTHETASEA, B, C, D525Escherichia coli K-12Mutation(s): 0 
Gene Names: guaAb2507JW2491
EC: 6.3.5.2
Find proteins for P04079 (Escherichia coli (strain K12))
Explore P04079 
Go to UniProtKB:  P04079
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
G [auth A], L [auth B], Q [auth C], V [auth D]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
H [auth A], M [auth B], R [auth C], W [auth D]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
POP
Query on POP

Download Ideal Coordinates CCD File 
F [auth A], K [auth B], P [auth C], U [auth D]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A], I [auth B], N [auth C], S [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth B], O [auth C], T [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156α = 90
b = 102β = 96.7
c = 78.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1995-04-04 
  • Released Date: 1996-01-29 
  • Deposition Author(s): Tesmer, J.J.G.

Revision History  (Full details and data files)

  • Version 1.0: 1996-01-29
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance