6LON

Crystal structure of HPSG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate.

Liu, J.Wei, Y.Lin, L.Teng, L.Yin, J.Lu, Q.Chen, J.Zheng, Y.Li, Y.Xu, R.Zhai, W.Liu, Y.Liu, Y.Cao, P.Ang, E.L.Zhao, H.Yuchi, Z.Zhang, Y.

(2020) Proc Natl Acad Sci U S A 

  • DOI: 10.1073/pnas.2003434117
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 2( S )-dihydroxypropanesulfonate (DHPS) is a microbial degradation product of 6-deoxy-6-sulfo-d-glucopyranose (sulfoquinovose), a component of plant sulfolipid with an estimated annual production of 10 10 tons. DHPS is also at mill ...

    2( S )-dihydroxypropanesulfonate (DHPS) is a microbial degradation product of 6-deoxy-6-sulfo-d-glucopyranose (sulfoquinovose), a component of plant sulfolipid with an estimated annual production of 10 10 tons. DHPS is also at millimolar levels in highly abundant marine phytoplankton. Its degradation and sulfur recycling by microbes, thus, play important roles in the biogeochemical sulfur cycle. However, DHPS degradative pathways in the anaerobic biosphere are not well understood. Here, we report the discovery and characterization of two O 2 -sensitive glycyl radical enzymes that use distinct mechanisms for DHPS degradation. DHPS-sulfolyase (HpsG) in sulfate- and sulfite-reducing bacteria catalyzes C-S cleavage to release sulfite for use as a terminal electron acceptor in respiration, producing H 2 S. DHPS-dehydratase (HpfG), in fermenting bacteria, catalyzes C-O cleavage to generate 3-sulfopropionaldehyde, subsequently reduced by the NADH-dependent sulfopropionaldehyde reductase (HpfD). Both enzymes are present in bacteria from diverse environments including human gut, suggesting the contribution of enzymatic radical chemistry to sulfur flux in various anaerobic niches.


    Organizational Affiliation

    Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, 300072 Tianjin, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PFL2/glycerol dehydratase family glycyl radical enzyme
A, B, C, D
824Bilophila wadsworthia 3_1_6Mutation(s): 4 
Gene Names: HMPREF0179_02149
Find proteins for E5Y7I4 (Bilophila wadsworthia 3_1_6)
Go to UniProtKB:  E5Y7I4
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LLQ
Query on LLQ

Download CCD File 
A, B, C, D
(2~{S})-2,3-bis(oxidanyl)propane-1-sulfonic acid
C3 H8 O5 S
YPFUJZAAZJXMIP-VKHMYHEASA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B, C, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.917α = 90
b = 219.401β = 98.04
c = 213.141γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31870049

Revision History 

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references