1IM5

Crystal Structure of Pyrazinamidase of Pyrococcus horikoshii in Complex with Zinc

Summary for 1IM5

• Entry DOI: 10.2210/pdb1im5/pdb
• Related: 1ILW
• Descriptor: 180aa long hypothetical Pyrazinamidase/Nicotinamidase, ZINC ION (3 entities in total)
• Functional Keywords: pyrazinamidase, pyrazinamide, nicotinamidase, tuberculosis, pza resistance, drug resistance, metal ion catalysis, cysteine hydrolase, hydrolase, amidase, covalent catalysis
• Biological source: Pyrococcus horikoshii
• Total number of polymer chains: 1
• Total formula weight: 20287.65

Authors

Du, X.,Kim, S.-H. (deposition date: 2001-05-09, release date: 2001-12-12, Last modification date: 2024-04-03)

Primary citation

Du, X.,Wang, W.,Kim, R.,Yakota, H.,Nguyen, H.,Kim, S.H.
Crystal structure and mechanism of catalysis of a pyrazinamidase from Pyrococcus horikoshii.
Biochemistry, 40:14166-14172, 2001

PubMed 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.

PubMed: 11714269
DOI: 10.1021/bi0115479

Experimental method

X-RAY DIFFRACTION (1.65 Å)