1IM5

Crystal Structure of Pyrazinamidase of Pyrococcus horikoshii in Complex with Zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structure and mechanism of catalysis of a pyrazinamidase from Pyrococcus horikoshii.

Du, X.Wang, W.Kim, R.Yakota, H.Nguyen, H.Kim, S.H.

(2001) Biochemistry 40: 14166-14172

  • DOI: 10.1021/bi0115479
  • Primary Citation of Related Structures:  
    1ILW, 1IM5

  • 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley 94720, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
180aa long hypothetical Pyrazinamidase/NicotinamidaseA180Pyrococcus horikoshiiMutation(s): 0 
Gene Names: PH 999
EC: 3.5.1.19
Find proteins for O58727 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58727 
Go to UniProtKB:  O58727
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.978α = 90
b = 43.266β = 101.34
c = 55.553γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSrefinement
SOLVEphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2001-05-09 
  • Released Date: 2001-12-12 
  • Deposition Author(s): Du, X., Kim, S.-H.

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description