PDBsum entry: 1kkf

Ligase

PDB id: 1kkf

Contents

Protein chain

431 a.a. *

Ligands

DPO

HDA

IMP

Metals

_MG

Waters ×344

* Residue conservation analysis

PDB id:

1kkf

Name:

Ligase

Title:

Complex of e. Coli adenylosuccinate synthetase with imp, had pyrophosphate, and mg

Structure:

Adenylosuccinate synthetase. Chain: a. Engineered: yes

Source:

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

Biol. unit:

Dimer (from PDB file)

Resolution:

2.60Å R-factor: 0.190 R-free: 0.270

Authors:

Z.Hou,W.Wang,H.J.Fromm,R.B.Honzatko

Key ref:

Z.Hou et al. (2002). IMP Alone Organizes the Active Site of Adenylosuccinate Synthetase from Escherichia coli. J Biol Chem, 277, 5970-5976. PubMed id: 11741996 DOI: 10.1074/jbc.M109561200

Date:

07-Dec-01 Release date: 20-Mar-02

Protein chain

P0A7D4  (PURA_ECOLI) -  Adenylosuccinate synthetase

Seq: 432 a.a.

Struc: 431 a.a.

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 = IMP) corresponds exactly) + L-aspartate (Bound ligand (Het Group name = HDA) matches with 41.67% similarity) = GDP + phosphate (Bound ligand (Het Group name = DPO) matches with 55.56% similarity) + 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: 10.1074/jbc.M109561200

J Biol Chem 277:5970-5976 (2002)

PubMed id: 11741996

IMP Alone Organizes the Active Site of Adenylosuccinate Synthetase from Escherichia coli.

Z.Hou, W.Wang, H.J.Fromm, R.B.Honzatko.

ABSTRACT

A complete set of substrate/substrate analogs of adenylosuccinate synthetase from Escherichia coli induces dimer formation and a transition from a disordered to an ordered active site. The most striking of the ligand-induced effects is the movement of loop 40-53 by up to 9 A. Crystal structures of the partially ligated synthetase, which either combine IMP and hadacidin or IMP, hadacidin, and Mg(2+)-pyrophosphate, have ordered active sites, comparable with the fully ligated enzyme. More significantly, a crystal structure of the synthetase with IMP alone exhibits a largely ordered active site, which includes the 9 A movement of loop 40-53 but does not include conformational adjustments to backbone carbonyl 40 (Mg(2+) interaction element) and loop 298-304 (L-aspartate binding element). Interactions involving the 5'-phosphoryl group of IMP evidently trigger the formation of salt links some 30 A away. The above provides a structural basis for ligand binding synergism, effects on k(cat) due to mutations far from the site of catalysis, and the complete loss of substrate efficacy due to minor alterations of the 5'-phosphoryl group of IMP.

Selected figure(s)

Figure 2.
Fig. 2. Stereoview of ligand interactions in the pyrophosphate complex. Dashed lines are donor-acceptor interactions between pyrophosphate-Mg2+ and the active site.

Figure 5.
Fig. 5. Stereoview of the IMP-ligated active site. Dashed lines represent donor-acceptor interactions.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 5970-5976) copyright 2002.

Figures were selected by an automated process.