PDBsum entry: 2gqr

Ligase

PDB id: 2gqr

Contents

Protein chains

237 a.a. *

Ligands

ADP ×2

Metals

_MG ×2

Waters ×363

* Residue conservation analysis

PDB id:

2gqr

Name:

Ligase

Title:

Saicar synthetase complexed with adp-mg2+

Structure:

Phosphoribosylaminoimidazole-succinocarboxamide synthase. Chain: a, b. Synonym: saicar synthetase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: purc. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.204 R-free: 0.239

Authors:

N.D.Ginder,R.B.Honzatko

Key ref:

N.D.Ginder et al. (2006). Nucleotide complexes of Escherichia coli phosphoribosylaminoimidazole succinocarboxamide synthetase. J Biol Chem, 281, 20680-20688. PubMed id: 16687397 DOI: 10.1074/jbc.M602109200

Date:

21-Apr-06 Release date: 16-May-06

Protein chains

P0A7D7  (PUR7_ECOLI) -  Phosphoribosylaminoimidazole-succinocarboxamide synthase

Seq: 237 a.a.

Struc: 237 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.2.6 - Phosphoribosylaminoimidazolesuccinocarboxamide synthase.
• Pathway: Purine Biosynthesis (late stages)
• Reaction: ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate = ADP + phosphate + (S)-2-(5-amino-1-(5-phospho-D- ribosyl)imidazole-4-carboxamido)succinate

ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + (S)-2-(5-amino-1-(5-phospho-D- ribosyl)imidazole-4-carboxamido)succinate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (2 terms)
• Biological process: purine nucleotide biosynthetic process (1 term)
• Biochemical function: catalytic activity (6 terms)

reference

DOI no: 10.1074/jbc.M602109200

J Biol Chem 281:20680-20688 (2006)

PubMed id: 16687397

Nucleotide complexes of Escherichia coli phosphoribosylaminoimidazole succinocarboxamide synthetase.

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

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.

Selected figure(s)

Figure 3.
FIGURE 3. Variation in the folds of eSS and tSS. The superposition of subunits A and B of tSS onto eSS using the -sheet of domain 2 reveals significant variations between subunit A (white) and subunit B (gray) of tSS, as well as an even larger conformational difference between each of the tSS subunits and subunit A of eSS (black). Subunit B of eSS (not shown) is virtually identical in conformation to subunit A. Parts of this figure were drawn with MOLSCRIPT (42).

Figure 8.
FIGURE 8. Alternative pathways for the chemical transformation catalyzed by SAICAR synthetase. RibP represents the 5'-phosphoribosyl group. See text for details.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 20680-20688) copyright 2006.

Figures were selected by an automated process.