3TVZ

Structure of Bacillus subtilis HmoB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Bacillus subtilis HmoB is a heme oxygenase with a novel structure.

Park, S.Choi, S.Choe, J.

(2012) BMB Rep 45: 239-241


  • PubMed Abstract: 
  • Iron availability is limited in the environment and most bacteria have developed a system to acquire iron from host hemoproteins. Heme oxygenase plays an important role by degrading heme group and releasing the essential nutrient iron. The structure ...

    Iron availability is limited in the environment and most bacteria have developed a system to acquire iron from host hemoproteins. Heme oxygenase plays an important role by degrading heme group and releasing the essential nutrient iron. The structure of Bacillus subtilis HmoB was determined to 2.0 A resolution. B. subtilis HmoB contains a typical antibiotic biosynthesis monooxygenase (ABM) domain that spans from 71 to 146 residues and belongs to the IsdG family heme oxygenases. Comparison of HmoB and IsdG family proteins showed that the C-terminal region of HmoB has similar sequence and structure to IsdG family proteins and contains conserved critical residues for heme degradation. However, HmoB is distinct from other IsdG family proteins in that HmoB is about 60 amino acids longer in the N-terminus and does not form a dimer whereas previously studied IsdG family heme oxygenases form functional homodimers. Interestingly, the structure of monomeric HmoB resembles the dimeric structure of IsdG family proteins. Hence, B. subtilis HmoB is a heme oxygenase with a novel structural feature.


    Organizational Affiliation

    Department of Life Science, University of Seoul, Seoul, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein yhgC
A, B, C
172Bacillus subtilis subsp. spizizenii (strain ATCC 23059 / NRRL B-14472 / W23)Mutation(s): 0 
Gene Names: yhgC
Find proteins for E0TXX3 (Bacillus subtilis subsp. spizizenii (strain ATCC 23059 / NRRL B-14472 / W23))
Go to UniProtKB:  E0TXX3
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.196 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 64.799α = 90.00
b = 64.799β = 90.00
c = 392.591γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SOLVEphasing
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-07-18
    Type: Structure summary
  • Version 1.2: 2017-11-08
    Type: Refinement description