PDBsum entry 3e9b

Hydrolase

PDB id: 3e9b

Contents

Protein chains

308 a.a. *

Ligands

S2C ×3

Metals

_MN ×6

Waters ×339

* Residue conservation analysis

PDB id:

3e9b

Name:

Hydrolase

Title:

X-ray structure of rat arginase i-t135a mutant: the complex with bec

Structure:

Arginase-1. Chain: a, b, c. Synonym: type i arginase, liver-type arginase. Engineered: yes. Mutation: yes

Source:

Rattus norvegicus. Brown rat, rat, rats. Organism_taxid: 10116. Gene: arg1. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.15Å R-factor: 0.216 R-free: 0.274

Authors:

E.Y.Shishova,L.Di Costanzo,D.W.Christianson

Key ref:

E.Y.Shishova et al. (2009). Probing the specificity determinants of amino acid recognition by arginase. Biochemistry, 48, 121-131. PubMed id: 19093830

Date:

21-Aug-08 Release date: 02-Dec-08

Protein chains

P07824  (ARGI1_RAT) -  Arginase-1 from Rattus norvegicus

Seq: 323 a.a.

Struc: 308 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.5.3.1 - arginase.
• Pathway: Urea Cycle and Arginine Biosynthesis
• Reaction: L-arginine + H2O = urea + L-ornithine
• Cofactor: Mn(2+)

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

reference

Biochemistry 48:121-131 (2009)

PubMed id: 19093830

Probing the specificity determinants of amino acid recognition by arginase.

E.Y.Shishova, L.Di Costanzo, F.A.Emig, D.E.Ash, D.W.Christianson.

ABSTRACT

Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site-directed mutagenesis, enzyme kinetics, and X-ray crystallography to probe the molecular recognition of the amino acid moiety (i.e., the alpha-amino and alpha-carboxylate groups) of substrate l-arginine and inhibitors in the active site of arginase I. Specifically, we focus on (1) a water-mediated hydrogen bond between the substrate alpha-carboxylate and T135, (2) a direct hydrogen bond between the substrate alpha-carboxylate and N130, and (3) a direct charged hydrogen bond between the substrate alpha-amino group and D183. Amino acid substitutions for T135, N130, and D183 generally compromise substrate affinity as reflected by increased K(M) values but have less pronounced effects on catalytic function as reflected by minimal variations of k(cat). As with substrate K(M) values, inhibitor K(d) values increase for binding to enzyme mutants and suggest that the relative contribution of intermolecular interactions to amino acid affinity in the arginase active site is water-mediated hydrogen bond < direct hydrogen bond < direct charged hydrogen bond. Structural comparisons of arginase with the related binuclear manganese metalloenzymes agmatinase and proclavaminic acid amidinohydrolase suggest that the evolution of substrate recognition in the arginase fold occurs by mutation of residues contained in specificity loops flanking the mouth of the active site (especially loops 4 and 5), thereby allowing diverse guanidinium substrates to be accommodated for catalysis.