PDBsum entry: 1cg4

Ligase

PDB id: 1cg4

Contents

Protein chain

431 a.a. *

Ligands

IMO

GDP

Metals

_MG

Waters ×166

* Residue conservation analysis

PDB id:

1cg4

Name:

Ligase

Title:

Structure of the mutant (r303l) of adenylosuccinate syntheta coli complexed with, gdp, 6-phosphoryl-imp, and mg2+

Structure:

Protein (adenylosuccinate synthetase). Chain: a. Synonym: ampsase. Engineered: yes. Mutation: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

2.50Å R-factor: 0.179 R-free: 0.252

Authors:

J.Y.Choe,B.W.Poland,H.Fromm,R.Honzatko

Key ref:

J.Y.Choe et al. (1999). Mechanistic implications from crystalline complexes of wild-type and mutant adenylosuccinate synthetases from Escherichia coli. Biochemistry, 38, 6953-6961. PubMed id: 10346917 DOI: 10.1021/bi990159s

Date:

26-Mar-99 Release date: 17-Jun-99

Protein chain

P0A7D4  (PURA_ECOLI) -  Adenylosuccinate synthetase

Seq: 432 a.a.

Struc: 431 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.6.3.4.4 - Adenylosuccinate synthase.
• Pathway: AMP and GMP Biosynthesis
• Reaction: GTP + IMP + L-aspartate = GDP + phosphate + N₆-(1,2-dicarboxyethyl)- AMP

GTP + IMP (Bound ligand (Het Group name = IMO) matches with 85.19% similarity) + L-aspartate = GDP (Bound ligand (Het Group name = GDP) corresponds exactly) + phosphate + N(6)-(1,2-dicarboxyethyl)- AMP

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

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (2 terms)
• Biological process: nucleobase, nucleoside and nucleotide interconversion (3 terms)
• Biochemical function: nucleotide binding (7 terms)

reference

DOI no: 10.1021/bi990159s

Biochemistry 38:6953-6961 (1999)

PubMed id: 10346917

Mechanistic implications from crystalline complexes of wild-type and mutant adenylosuccinate synthetases from Escherichia coli.

J.Y.Choe, B.W.Poland, H.J.Fromm, R.B.Honzatko.

ABSTRACT

Asp13 and His41 are essential residues of adenylosuccinate synthetase, putatively catalyzing the formation of adenylosuccinate from an intermediate of 6-phosphoryl-IMP. Wild-type adenylosuccinate synthetase and three mutant synthetases (Arg143 --> Leu, Lys16 --> Gln, and Arg303 --> Leu) from Eschericha coli have been crystallized in the presence of IMP, hadacidin (an analogue of L-aspartate), Mg2+, and GTP. The active site of each complex contains 6-phosphoryl-IMP, Mg2+, GDP, and hadacidin, except for the Arg303 --> Leu mutant, which does not bind hadacidin. In response to the formation of 6-phosphoryl-IMP, Asp13 enters the inner coordination sphere of the active site Mg2+. His41 hydrogen bonds with 6-phosphoryl-IMP, except in the Arg303 --> Leu complex, where it remains bound to the guanine nucleotide. Hence, recognition of the active site Mg2+ by Asp13 evidently occurs after the formation of 6-phosphoryl-IMP, but recognition of the intermediate by His41 may require the association of L-aspartate with the active site. Structures reported here support a mechanism in which Asp13 and His41 act as the catalytic base and acid, respectively, in the formation of 6-phosphoryl-IMP, and then act together as catalytic acids in the subsequent formation of adenylosuccinate.