PDBsum entry 1ynh

Hydrolase

PDB id: 1ynh

Contents

Protein chains

439 a.a. *

Ligands

SUO ×4

Metals

__K ×4

Waters ×982

* Residue conservation analysis

PDB id:

1ynh

Name:

Hydrolase

Title:

Crystal structure of n-succinylarginine dihydrolase, astb, bound to substrate and product, an enzyme from the arginine catabolic pathway of escherichia coli

Structure:

Succinylarginine dihydrolase. Chain: a, b, c, d. Synonym: n-succinylarginine dihydrolase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

1.95Å R-factor: 0.219 R-free: 0.246

Authors:

A.Tocilj,J.D.Schrag,Y.Li,B.L.Schneider,L.Reitzer,A.Matte,M.Cygler

Key ref:

A.Tocilj et al. (2005). Crystal structure of N-succinylarginine dihydrolase AstB, bound to substrate and product, an enzyme from the arginine catabolic pathway of Escherichia coli. J Biol Chem, 280, 15800-15808. PubMed id: 15703173 DOI: 10.1074/jbc.M413833200

Date:

24-Jan-05 Release date: 22-Mar-05

Protein chains

P76216  (ASTB_ECOLI) -  N-succinylarginine dihydrolase from Escherichia coli (strain K12)

Seq: 447 a.a.

Struc: 439 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.3.23 - N-succinylarginine dihydrolase.
• Reaction: N₂-succinyl-L-arginine + 2 H2O + 2 H⁺ = N₂-succinyl-L-ornithine + 2 NH4⁺ + CO2

N(2)-succinyl-L-arginine + 2 × H2O + 2 × H(+) = N(2)-succinyl-L-ornithine + 2 × NH4(+) (Bound ligand (Het Group name = SUO) corresponds exactly) + CO2

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

reference

DOI no: 10.1074/jbc.M413833200

J Biol Chem 280:15800-15808 (2005)

PubMed id: 15703173

Crystal structure of N-succinylarginine dihydrolase AstB, bound to substrate and product, an enzyme from the arginine catabolic pathway of Escherichia coli.

A.Tocilj, J.D.Schrag, Y.Li, B.L.Schneider, L.Reitzer, A.Matte, M.Cygler.

ABSTRACT

The ammonia-producing arginine succinyltransferase pathway is the major pathway in Escherichia coli and related bacteria for arginine catabolism as a sole nitrogen source. This pathway consists of five steps, each catalyzed by a distinct enzyme. Here we report the crystal structure of N-succinylarginine dihydrolase AstB, the second enzyme of the arginine succinyltransferase pathway, providing the first structural insight into enzymes from this pathway. The enzyme exhibits a pseudo 5-fold symmetric alpha/beta propeller fold of circularly arranged betabetaalphabeta modules enclosing the active site. The crystal structure indicates clearly that this enzyme belongs to the amidinotransferase (AT) superfamily and that the active site contains a Cys-His-Glu triad characteristic of the AT superfamily. Structures of the complexes of AstB with the reaction product and a C365S mutant with bound the N-succinylarginine substrate suggest a catalytic mechanism that consists of two cycles of hydrolysis and ammonia release, with each cycle utilizing a mechanism similar to that proposed for arginine deiminases. Like other members of the AT superfamily of enzymes, AstB possesses a flexible loop that is disordered in the absence of substrate and assumes an ordered conformation upon substrate binding, shielding the ligand from the bulk solvent, thereby controlling substrate access and product release.

Selected figure(s)

Figure 1.
FIG. 1. The AST pathway (after EcoCyc (3)).

Figure 4.
FIG. 4. Structural comparison of E. coli AstB with a representative amidinotransferase. a, the active site residues of the AstB C365S mutant with the N-succinylarginine substrate. In this figure Ser365 was replaced by the native Cys365 taken from the native structure. The oxygen atoms are red, nitrogen atoms are blue, sulfur atoms are yellow, and carbon atoms are gray. The hydrogen bonds between the ligand and protein atoms are marked by green dashed lines. b, the active site of arginine deaminase (Protein Data Bank codes 1LXY [PDB] or 1S9R) with the reaction product in a similar orientation to that shown in a.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 15800-15808) copyright 2005.

Figures were selected by an automated process.