8HGN

Crystal structure of MeaC (Mesaconyl-CoA hydratase)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


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Literature

Crystal Structure of Mesaconyl-CoA Hydratase from Methylorubrum extorquens CM4.

Ahn, J.W.Hong, J.Kim, K.J.

(2023) J Microbiol Biotechnol 33: 485-492

  • DOI: https://doi.org/10.4014/jmb.2212.12003
  • Primary Citation of Related Structures:  
    8HGN

  • PubMed Abstract: 

    Methylorubrum extorquens , a facultative methylotroph, assimilates C 1 compounds and accumulates poly-β-hydroxylbutyrate (PHB) as carbon and energy sources. The ethylmalonyl pathway is central to the carbon metabolism of M. extorquens , and is linked with a serine cycle and a PHB biosynthesis pathway. Understanding the ethylmalonyl pathway is vital in utilizing methylotrophs to produce value-added chemicals. In this study, we determined the crystal structure of the mesaconyl-CoA hydratase from M. extorquens ( Me MeaC) that catalyzes the reversible conversion of mesaconyl-CoA to β-methylmalyl-CoA. The crystal structure of Me MeaC revealed that the enzyme belongs to the MaoC-like dehydratase domain superfamily and functions as a trimer. In our current Me MeaC structure, malic acid occupied the substrate binding site, which reveals how Me MeaC recognizes the β-methylmalyl-moiety of its substrate. The active site of the enzyme was further speculated by comparing its structure with those of other MaoC-like hydratases.


  • Organizational Affiliation

    Postech Biotech Center, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-methylmalyl-CoA dehydratase356Methylorubrum extorquens CM4Mutation(s): 0 
Gene Names: Mchl_4075
UniProt
Find proteins for B7KZU4 (Methylorubrum extorquens (strain CM4 / NCIMB 13688))
Explore B7KZU4 
Go to UniProtKB:  B7KZU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7KZU4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLT
Query on MLT

Download Ideal Coordinates CCD File 
B [auth A]D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.224α = 90
b = 79.224β = 90
c = 91.008γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release