5YHH

Crystal structure of YiiM from Geobacillus stearothermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of the hydroxylaminopurine resistance protein, YiiM, and its putative molybdenum cofactor-binding catalytic site.

Namgung, B.Kim, J.H.Song, W.S.Yoon, S.I.

(2018) Sci Rep 8: 3304-3304

  • DOI: 10.1038/s41598-018-21660-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The molybdenum cofactor (Moco) is a molybdenum-conjugated prosthetic group that is ubiquitously found in plants, animals, and bacteria. Moco is required for the nitrogen-reducing reaction of the Moco sulfurase C-terminal domain (MOSC) family. Despite ...

    The molybdenum cofactor (Moco) is a molybdenum-conjugated prosthetic group that is ubiquitously found in plants, animals, and bacteria. Moco is required for the nitrogen-reducing reaction of the Moco sulfurase C-terminal domain (MOSC) family. Despite the biological significance of MOSC proteins in the conversion of prodrugs and resistance against mutagens, their structural features and Moco-mediated catalysis mechanism have not been described in detail. YiiM is a MOSC protein that is involved in reducing mutagenic 6-N-hydroxylaminopurine to nontoxic adenine in bacteria. Here, we report two crystal structures of YiiM: one from Gram-positive Geobacillus stearothermophilus (gsYiiM) and the other from Gram-negative Escherichia coli (ecYiiM). Although gsYiiM and ecYiiM differ in oligomerization state and protein stability, both consist of three structural modules (a β-barrel and two α-helix bundles) and feature a cavity surrounded by the three modules. The cavity is characterized by positive electrostatic potentials and high sequence conservation. Moreover, the ecYiiM cavity houses a phosphate group, which emulates a part of Moco, and contains a highly reactive invariant cysteine residue. We thus propose that the cavity is the catalytic site where Moco binds and the substrate is reduced. Moreover, our comparative structural analysis highlights the common but distinct structural features of MOSC proteins.


    Organizational Affiliation

    Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.,Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea. sungil@kangwon.ac.kr.,Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, 24341, Republic of Korea. sungil@kangwon.ac.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized conserved protein YiiM
A
221Geobacillus stearothermophilusMutation(s): 0 
Find proteins for A0A150NEL9 (Geobacillus stearothermophilus)
Go to UniProtKB:  A0A150NEL9
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.420α = 90.00
b = 51.526β = 90.00
c = 94.210γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PHASERphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release