6A8L

Crystal structure of nicotinamidase/ pyrazinamidase PncA from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the nicotinamidase/pyrazinamidase PncA from Bacillus subtilis.

Shang, F.Chen, J.Wang, L.Jin, L.Zou, L.Bu, T.Dong, Y.Ha, N.C.Nam, K.H.Quan, C.Xu, Y.

(2018) Biochem Biophys Res Commun 503: 2906-2911

  • DOI: 10.1016/j.bbrc.2018.08.067
  • Primary Citation of Related Structures:  
    5ZN8, 6A8L

  • PubMed Abstract: 
  • The nicotinamidase/pyrazinamidase PncA is a member of a large family of hydrolase enzymes that catalyze the deamination of nicotinamide to nicotinic acid. PncA also functions as a pyrazinamidase in a wide variety of eubacteria and is an essential coenzyme in many cellular redox reactions in living systems ...

    The nicotinamidase/pyrazinamidase PncA is a member of a large family of hydrolase enzymes that catalyze the deamination of nicotinamide to nicotinic acid. PncA also functions as a pyrazinamidase in a wide variety of eubacteria and is an essential coenzyme in many cellular redox reactions in living systems. We report the crystal structure of substrate-free PncA from Bacillus subtilis (BsPncA) at 2.0 Å resolution to improve our understanding of the PncA family. The structure of BsPncA consists of an α/β domain and a subdomain. The subdomain of BsPncA has a different conformation than that of PncA enzymes from other organisms. The B-factor analysis revealed a rigid structure of the α/β domain, while the subdomain is highly flexible. Both dimers and tetramers were observed in BsPncA protein crystals, but only dimers were observed in solution. Our results provide useful information that will further enhance our understanding of the molecular functions of PncA family members.


    Organizational Affiliation

    Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China. Electronic address: yongbinxu@dlnu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IsochorismataseA, B183Bacillus subtilisMutation(s): 2 
Gene Names: BMJ37_14840
EC: 3
UniProt
Find proteins for A0A223CGG0 (Bacillus velezensis)
Explore A0A223CGG0 
Go to UniProtKB:  A0A223CGG0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.177 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.037α = 90
b = 90.037β = 90
c = 86.181γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXmodel building
Blu-Icedata collection

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31200556
National Natural Science Foundation of ChinaChina21272031

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-26
    Changes: Data collection, Database references