1GPM

ESCHERICHIA COLI GMP SYNTHETASE COMPLEXED WITH AMP AND PYROPHOSPHATE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 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.Mol.Biol. 3: 74-86


  • 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, histidin ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GMP SYNTHETASE
A, B, C, D
525Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: guaA
EC: 6.3.5.2
Find proteins for P04079 (Escherichia coli (strain K12))
Go to UniProtKB:  P04079
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
POP
Query on POP
Download SDF File 
Download CCD File 
A, B, C, D
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
CIT
Query on CIT
Download SDF File 
Download CCD File 
A, B, C, D
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP
Download SDF File 
Download CCD File 
A, B, C, D
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 156.000α = 90.00
b = 102.000β = 96.70
c = 78.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History 

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