PDBsum entry 1im5

Hydrolase

PDB id: 1im5

Contents

Protein chain

179 a.a. *

Metals

_ZN

Waters ×128

* Residue conservation analysis

References listed in PDB file

Key reference

• Title: Crystal structure and mechanism of catalysis of a pyrazinamidase from pyrococcus horikoshii.
• Authors: X.Du, W.Wang, R.Kim, H.Yakota, H.Nguyen, S.H.Kim.
• Ref.: Biochemistry, 2001, 40, 14166-14172. [DOI no: 10.1021/bi0115479]
• PubMed id: 11714269

Abstract

Bacterial pyrazinamidase (PZAase)/nicotinamidase converts pyrazinamide (PZA) to ammonia and pyrazinoic acid, which is active against Mycobacterium tuberculosis. Loss of PZAase activity is the major mechanism of pyrazinamide-resistance by M. tuberculosis. We have determined the crystal structure of the gene product of Pyrococcus horikoshii 999 (PH999), a PZAase, and its complex with zinc ion by X-ray crystallography. The overall fold of PH999 is similar to that of N-carbamoylsarcosine amidohydrolase (CSHase) of Arthrobacter sp. and YcaC of Escherichia coli, a protein with unknown physiological function. The active site of PH999 was identified by structural features that are also present in the active sites of CSHase and YcaC: a triad (D10, K94, and C133) and a cis-peptide (between V128 and A129). Surprisingly, a metal ion-binding site was revealed in the active site and subsequently confirmed by crystal structure of PH999 in complex with Zn(2+). The roles of the triad, cis-peptide, and metal ion in the catalysis are proposed. Because of extensive homology between PH999 and PZAase of M. tuberculosis (37% sequence identity), the structure of PH999 provides a structural basis for understanding PZA-resistance by M. tuberculosis harboring PZAase mutations.