PDBsum entry 2jer

Hydrolase

PDB id: 2jer

Contents

Protein chains

(+ 2 more) 366 a.a. *

Waters ×2174

* Residue conservation analysis

PDB id:

2jer

Name:

Hydrolase

Title:

Agmatine deiminase of enterococcus faecalis catalyzing its reaction.

Structure:

Agmatine deiminase. Chain: a, b, c, d, e, f, g, h. Synonym: agmatine iminohydrolase. Engineered: yes. Other_details: carbon atom of the guanidinium group of agmatine covalently linked with the thiol group of cys357

Source:

Enterococcus faecalis. Organism_taxid: 1351. Strain: sd10. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.65Å R-factor: 0.168 R-free: 0.192

Authors:

S.Tavarez,J.L.Llacer,V.Rubio

Key ref:

J.L.Llácer et al. (2007). The gene cluster for agmatine catabolism of Enterococcus faecalis: study of recombinant putrescine transcarbamylase and agmatine deiminase and a snapshot of agmatine deiminase catalyzing its reaction. J Bacteriol, 189, 1254-1265. PubMed id: 17028272

Date:

19-Jan-07 Release date: 30-Jan-07

Supersedes:

2j2t

Protein chains

Q837U5  (AGUA_ENTFA) -  Putative agmatine deiminase from Enterococcus faecalis (strain ATCC 700802 / V583)

Seq: 365 a.a.

Struc: 366 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.5.3.12 - agmatine deiminase.
• Reaction: agmatine + H2O = N-carbamoylputrescine + NH4⁺

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

Added reference

J Bacteriol 189:1254-1265 (2007)

PubMed id: 17028272

The gene cluster for agmatine catabolism of Enterococcus faecalis: study of recombinant putrescine transcarbamylase and agmatine deiminase and a snapshot of agmatine deiminase catalyzing its reaction.

J.L.Llácer, L.M.Polo, S.Tavárez, B.Alarcón, R.Hilario, V.Rubio.

ABSTRACT

Enterococcus faecalis makes ATP from agmatine in three steps catalyzed by agmatine deiminase (AgDI), putrescine transcarbamylase (PTC), and carbamate kinase (CK). An antiporter exchanges putrescine for agmatine. We have cloned the E. faecalis ef0732 and ef0734 genes of the reported gene cluster for agmatine catabolism, overexpressed them in Escherichia coli, purified the products, characterized them functionally as PTC and AgDI, and crystallized and X-ray diffracted them. The 1.65-Angstroms-resolution structure of AgDI forming a covalent adduct with an agmatine-derived amidine reactional intermediate is described. We provide definitive identification of the gene cluster for agmatine catabolism and confirm that ornithine is a genuine but poor PTC substrate, suggesting that PTC (found here to be trimeric) evolved from ornithine transcarbamylase. N-(Phosphonoacetyl)-putrescine was prepared and shown to strongly (K(i) = 10 nM) and selectively inhibit PTC and to improve PTC crystallization. We find that E. faecalis AgDI, which is committed to ATP generation, closely resembles the AgDIs involved in making polyamines, suggesting the recruitment of a polyamine-synthesizing AgDI into the AgDI pathway. The arginine deiminase (ADI) pathway of arginine catabolism probably supplied the genes for PTC and CK but not those for the agmatine/putrescine antiporter, and thus the AgDI and ADI pathways are not related by a single "en bloc" duplication event. The AgDI crystal structure reveals a tetramer with a five-blade propeller subunit fold, proves that AgDI closely resembles ADI despite a lack of sequence identity, and explains substrate affinity, selectivity, and Cys357-mediated-covalent catalysis. A three-tongued agmatine-triggered gating opens or blocks access to the active center.