5YMR

The Crystal Structure of IseG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria.

Xing, M.Wei, Y.Zhou, Y.Zhang, J.Lin, L.Hu, Y.Hua, G.N Nanjaraj Urs, A.Liu, D.Wang, F.Guo, C.Tong, Y.Li, M.Liu, Y.Ang, E.L.Zhao, H.Yuchi, Z.Zhang, Y.

(2019) Nat Commun 10: 1609-1609

  • DOI: https://doi.org/10.1038/s41467-019-09618-8
  • Primary Citation of Related Structures:  
    5YMR

  • PubMed Abstract: 

    Bacterial degradation of organosulfonates plays an important role in sulfur recycling, and has been extensively studied. However, this process in anaerobic bacteria especially gut bacteria is little known despite of its potential significant impact on human health with the production of toxic H 2 S. Here, we describe the structural and biochemical characterization of an oxygen-sensitive enzyme that catalyzes the radical-mediated C-S bond cleavage of isethionate to form sulfite and acetaldehyde. We demonstrate its involvement in pathways that enables C2 sulfonates to be used as terminal electron acceptors for anaerobic respiration in sulfate- and sulfite-reducing bacteria. Furthermore, it plays a key role in converting bile salt-derived taurine into H 2 S in the disease-associated gut bacterium Bilophila wadsworthia. The enzymes and transporters in these anaerobic pathways expand our understanding of microbial sulfur metabolism, and help deciphering the complex web of microbial pathways involved in the transformation of sulfur compounds in the gut.


  • Organizational Affiliation

    Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, 300072, Tianjin, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formate acetyltransferaseA [auth B],
B [auth D],
C,
D [auth A]
808Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 3 
Gene Names: DVU_2824
UniProt
Find proteins for Q727N1 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q727N1 
Go to UniProtKB:  Q727N1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ727N1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8X3
Query on 8X3

Download Ideal Coordinates CCD File 
E [auth B],
H [auth D],
J [auth C],
L [auth A]
2-hydroxyethylsulfonic acid
C2 H6 O4 S
SUMDYPCJJOFFON-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth B]
G [auth B]
I [auth D]
K [auth C]
M [auth A]
F [auth B],
G [auth B],
I [auth D],
K [auth C],
M [auth A],
N [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.111α = 90
b = 159.444β = 91.66
c = 115.378γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation of ChinaChina31570060
National Key Research and Development Program of ChinaChina2017YFD0201403

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references