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 1.3 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: https://doi.org/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. 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.

    • Organizational Affiliation: 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GMP SYNTHETASE
A, B, C, D
525Escherichia coli K-12Mutation(s): 0 
Gene Names: GUAA
EC: 6.3.5.2
UniProt
Find proteins for P04079 (Escherichia coli (strain K12))
Explore P04079 
Go to UniProtKB:  P04079
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04079
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / 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
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
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
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
MG
Query on MG
Download Ideal Coordinates CCD File 
J [auth B],
O [auth C],
T [auth D]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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

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Entry History 

Deposition Data

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
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other