1GPM | pdb_00001gpm

ESCHERICHIA COLI GMP SYNTHETASE COMPLEXED WITH AMP AND PYROPHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb1GPM/pdb

• Classification: TRANSFERASE (GLUTAMINE AMIDOTRANSFERASE)
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

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

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

• PubMed: 8548458 
• DOI: https://doi.org/10.1038/nsb0196-74
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 238.31 kDa 
• Atom Count: 16,797 
• Modeled Residue Count: 2,000 
• Deposited Residue Count: 2,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMP SYNTHETASE	A, B, C, D	525	Escherichia coli K-12	Mutation(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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	G [auth A], L [auth B], Q [auth C], V [auth D]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
CIT	H [auth A], M [auth B], R [auth C], W [auth D]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
POP	F [auth A], K [auth B], P [auth C], U [auth D]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
PO4	E [auth A], I [auth B], N [auth C], S [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	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 (Depositor) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156	α = 90
b = 102	β = 96.7
c = 78.8	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  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