PDBsum entry 1kh3

Ligase

PDB id: 1kh3

Contents

Protein chains

380 a.a. *

Ligands

SO4 ×4

ANP ×4

ARG ×4

ASP ×4

Metals

_MG ×4

Waters ×567

* Residue conservation analysis

PDB id:

1kh3

Name:

Ligase

Title:

Crystal structure of thermus thermophilus hb8 argininosuccinate synthetase in complex with inhibitor

Structure:

Argininosuccinate synthetase. Chain: a, b, c, d. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Gene: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.15Å R-factor: 0.226 R-free: 0.256

Authors:

M.Goto,K.Hirotsu,I.Miyahara,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

M.Goto et al. (2003). Structures of argininosuccinate synthetase in enzyme-ATP substrates and enzyme-AMP product forms: stereochemistry of the catalytic reaction. J Biol Chem, 278, 22964-22971. PubMed id: 12684518 DOI: 10.1074/jbc.M213198200

Date:

29-Nov-01 Release date: 22-Apr-03

Protein chains

P59846  (ASSY_THET8) -  Argininosuccinate synthase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 400 a.a.

Struc: 380 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.4.5 - argininosuccinate synthase.
• Pathway: Urea Cycle and Arginine Biosynthesis
• Reaction: L-citrulline + L-aspartate + ATP = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H⁺

L-citrulline + L-aspartate (Bound ligand (Het Group name = ASP) corresponds exactly) + ATP (Bound ligand (Het Group name = ARG) matches with 84.62% similarity) = 2-(N(omega)-L-arginino)succinate + AMP (Bound ligand (Het Group name = ANP) matches with 74.19% similarity) + diphosphate + H(+)

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

reference

DOI no: 10.1074/jbc.M213198200

J Biol Chem 278:22964-22971 (2003)

PubMed id: 12684518

Structures of argininosuccinate synthetase in enzyme-ATP substrates and enzyme-AMP product forms: stereochemistry of the catalytic reaction.

M.Goto, R.Omi, I.Miyahara, M.Sugahara, K.Hirotsu.

ABSTRACT

Argininosuccinate synthetase reversibly catalyzes the ATP-dependent condensation of a citrulline with an aspartate to give argininosuccinate. The structures of the enzyme from Thermus thermophilus HB8 complexed with intact ATP and substrates (citrulline and aspartate) and with AMP and product (argininosuccinate) have been determined at 2.1- and 2.0-A resolution, respectively. The enzyme does not show the ATP-induced domain rotation observed in the enzyme from Escherichia coli. In the enzyme-substrate complex, the reaction sites of ATP and the bound substrates are adjacent and are sufficiently close for the reaction to proceed without the large conformational change at the domain level. The mobility of the triphosphate group in ATP and the side chain of citrulline play an important role in the catalytic action. The protonated amino group of the bound aspartate interacts with the alpha-phosphate of ATP and the ureido group of citrulline, thus stimulating the adenylation of citrulline. The enzyme-product complex explains how the citrullyl-AMP intermediate is bound to the active site. The stereochemistry of the catalysis of the enzyme is clarified on the basis of the structures of tAsS (argininosuccinate synthetase from T. thermophilus HB8) complexes.

Selected figure(s)

Figure 5.
FIG. 5. The superposition of the substrate analogue (arginine) in tAsS·AMP-PNP·arginine·succinate onto the substrate (citrulline) in tAsS·ATP·citrulline·aspartate. The arrangement of arginine (heavily shaded), ATP, and substrates (citrulline and aspartate) is displayed. Arginine might imitate the approach of citrulline to the -phosphate of ATP. Important short contacts are shown by dotted lines.

Figure 6.
FIG. 6. Proposed stereochemistry along the catalytic process based on x-ray structures of tAsS complexes. Putative hydrogen bonds are shown by dotted lines. A, tAsS complex with U-shaped ATP and citrulline. B, tAsS complex with U-shaped ATP, citrulline, and aspartate. Aspartate is adjacent to the -phosphate of ATP and the ureido group of citrulline. C and D, tAsS complex with S-shaped ATP, citrulline, and aspartate. ATP changes its triphosphate conformation. D, citrulline changes its side-chain conformation to approach the -phosphate of ATP (D). E, tAsS complex with citrullyl-AMP intermediate. F, tAsS complex with AMP and the product argininosuccinate.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 22964-22971) copyright 2003.

Figures were selected by an automated process.