5IE9

Crystal structure of the Bacillus-conserved MazG protein, a nucleotide pyrophosphohydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the Bacillus-conserved MazG protein, a nucleotide pyrophosphohydrolase.

Kim, M.I.Hong, M.

(2016) Biochem.Biophys.Res.Commun. 472: 237-242

  • DOI: 10.1016/j.bbrc.2016.02.097

  • PubMed Abstract: 
  • BA1544 from Bacillus anthracis was previously annotated as a transcription factor for the gene cluster ba1554 - ba1558, but has not been experimentally characterized. B. anthracis is an obligate pathogen causing fatal inhalational anthrax, and BA1544 ...

    BA1544 from Bacillus anthracis was previously annotated as a transcription factor for the gene cluster ba1554 - ba1558, but has not been experimentally characterized. B. anthracis is an obligate pathogen causing fatal inhalational anthrax, and BA1544 is absolutely conserved in Bacillus species, including Bacillus cereus, Bacillus thuringiensis and Bacillus mycoides, with 100% sequence identity. To address the function of BA1544, we performed structural and biochemical studies, which revealed that BA1544 is a MazG protein. Thus, herein, the protein is defined as Bacillus-conserved MazG (BcMazG). Like other MazG structures, BcMazG assembles into a tetrameric architecture. Each monomer adopts a four-α-helix bundle that accommodates a metal ion using four acidic residues, and presents one putative substrate-binding site. Enzymatic characterization demonstrated that BcMazG is a nucleoside triphosphate (NTP) pyrophosphohydrolase and prefers adenosine triphosphate as a substrate among canonical NTPs. Moreover, structural comparison of BcMazG with its homologues revealed a potential regulation mechanism whereby the enzymatic activity of BcMazG is regulated by its C-terminal region.


    Organizational Affiliation

    Division of Biological Science and Technology, Yonsei University, Wonju 220-710, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleotide pyrophosphohydrolase
A, B, C, D
103Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)Mutation(s): 0 
Find proteins for Q813T0 (Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711))
Go to UniProtKB:  Q813T0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 90.578α = 90.00
b = 90.578β = 90.00
c = 97.056γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-02-25 
  • Released Date: 2016-03-30 
  • Deposition Author(s): Kim, M., Hong, M.

Funding OrganizationLocationGrant Number
The ministry of Science, ICT & Future planningKorea, Republic Of2013R1A1A1008707

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Data collection, Database references, Derived calculations