5XZD

Structure of acryloyl-CoA hydratase AcuH from Roseovarius nubinhibens ISM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular Insight into the Acryloyl-CoA Hydration by AcuH for Acrylate Detoxification in Dimethylsulfoniopropionate-Catabolizing Bacteria

Cao, H.Y.Wang, P.Xu, F.Li, P.Y.Xie, B.B.Qin, Q.L.Zhang, Y.Z.Li, C.Y.Chen, X.L.

(2017) Front Microbiol 8: 2034-2034

  • DOI: 10.3389/fmicb.2017.02034
  • Primary Citation of Related Structures:  
    5XZD

  • PubMed Abstract: 
  • Microbial cleavage of dimethylsulfoniopropionate (DMSP) producing dimethyl sulfide (DMS) and acrylate is an important step in global sulfur cycling. Acrylate is toxic for cells, and thus should be metabolized effectively for detoxification. There are two proposed pathways for acrylate metabolism in DMSP-catabolizing bacteria, the AcuN-AcuK pathway and the PrpE-AcuI pathway ...

    Microbial cleavage of dimethylsulfoniopropionate (DMSP) producing dimethyl sulfide (DMS) and acrylate is an important step in global sulfur cycling. Acrylate is toxic for cells, and thus should be metabolized effectively for detoxification. There are two proposed pathways for acrylate metabolism in DMSP-catabolizing bacteria, the AcuN-AcuK pathway and the PrpE-AcuI pathway. AcuH is an acryloyl-CoA hydratase in DMSP-catabolizing bacteria and can catalyze the hydration of toxic acryloyl-CoA to produce 3-hydroxypropionyl-CoA (3-HP-CoA) in both the AcuN-AcuK pathway and the side path of the PrpE-AcuI pathway. However, the structure and catalytic mechanism of AcuH remain unknown. Here, we cloned a putative acuH gene from Roseovarius nubinhibens ISM, a typical DMSP-catabolizing bacterium, and expressed it ( Rd AcuH) in Escherichia coli . The activity of Rd AcuH toward acryloyl-CoA was detected by liquid chromatography-mass spectrometry (LC-MS), which suggests that Rd AcuH is a functional acryloyl-CoA hydratase. Then we solved the crystal structure of Rd AcuH. Each asymmetric unit in the crystal of Rd AcuH contains a dimer of trimers and each Rd AcuH monomer contains an N-terminal domain (NTD) and a C-terminal domain (CTD). There are three active centers in each trimer and each active center is located between the NTD of a subunit and the CTD of the neighboring subunit. Site-directed mutagenesis analysis indicates that two highly conserved glutamates, Glu112 and Glu132, in the active center are essential for catalysis. Based on our results and previous research, we analyzed the catalytic mechanism of AcuH to hydrate acryloyl-CoA, in which Glu132 acts as the catalytic base. This study sheds light on the mechanism of acrylate detoxification in DMSP-catabolizing bacteria.


    Organizational Affiliation

    State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Enoyl-CoA hydrataseA, B, C, D, E, F258Roseovarius nubinhibens ISMMutation(s): 0 
Gene Names: ISM_05820
UniProt
Find proteins for A3SKA6 (Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM))
Explore A3SKA6 
Go to UniProtKB:  A3SKA6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.81α = 90
b = 119.453β = 102.77
c = 120.276γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation of ChinaChina31630012, 31290230, 31290231
National Key R&D Program of ChinaChina2016YFA0601303
Program of Shandong for Taishan ScholarsChinaTS20090803
ational Postdoctoral Program for Innovative TalentsChinaBX201600095, BX201700145

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references