Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 55.81 kDa 
• Atom Count: 4207 
• Residue Count: 474 
• Unique protein chains: 1

2GQR

SAICAR Synthetase Complexed with ADP-Mg2+

• DOI: 10.2210/pdb2GQR/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-04-21 Released: 2006-05-16 
• Deposition Author(s): Ginder, N.D., Honzatko, R.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.239 
• R-Value Work: 0.204 
• R-Value Observed: 0.208 

Literature

Nucleotide Complexes of Escherichia coli Phosphoribosylaminoimidazole Succinocarboxamide Synthetase.

Ginder, N.D., Binkowski, D.J., Fromm, H.J., Honzatko, R.B.

(2006) J Biol Chem 281: 20680-20688

• PubMed: 16687397 
• DOI: 10.1074/jbc.M602109200
• Primary Citation of Related Structures:  
  2GQS, 2GQR


• PubMed Abstract: 
  

Phosphoribosylaminoimidazole-succinocarboxamide synthetase (SAICAR synthetase) converts 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) to 4-(N-succinylcarboxamide)-5-aminoimidazole ribonucleotide (SAICAR). The enzyme is a target of natural products that impair cell growth. Reported here are the crystal structures of the ADP and the ADP.CAIR complexes of SAICAR synthetase from Escherichia coli, the latter being the first instance of a CAIR-ligated SAICAR synthetase. ADP and CAIR bind to the active site in association with three Mg(2+), two of which coordinate the same oxygen atom of the 4-carboxyl group of CAIR; whereas, the third coordinates the alpha- and beta-phosphoryl groups of ADP. The ADP.CAIR complex is the basis for a transition state model of a phosphoryl transfer reaction involving CAIR and ATP, but also supports an alternative chemical pathway in which the nucleophilic attack of l-aspartate precedes the phosphoryl transfer reaction. The polypeptide fold for residues 204-221 of the E. coli structure differs significantly from those of the ligand-free SAICAR synthetase from Thermatoga maritima and the adenine nucleotide complexes of the synthetase from Saccharomyces cerevisiae. Conformational differences between the E. coli, T. maritima, and yeast synthetases suggest the possibility of selective inhibition of de novo purine nucleotide biosynthesis in microbial organisms.

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Organizational Affiliation: 

Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, 50011, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole-succinocarboxamide synthase	A, B	237	Escherichia coli	Mutation(s): 9  Gene Names: purC EC: 6.3.2.6
Find proteins for P0A7D7 (Escherichia coli (strain K12)) Explore P0A7D7  Go to UniProtKB:  P0A7D7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A, B	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.239 
• R-Value Work: 0.204 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.29	α = 90
b = 67.16	β = 90
c = 148.78	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-04-21 
• Released Date: 2006-05-16 
Deposition Author(s): Ginder, N.D., Honzatko, R.B.

Revision History 

• Version 1.0: 2006-05-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance