8HGN | pdb_00008hgn

Crystal structure of MeaC (Mesaconyl-CoA hydratase)

• PDB DOI: https://doi.org/10.2210/pdb8HGN/pdb

• Classification: LYASE
• Organism(s): Methylorubrum extorquens CM4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-11-15 Released: 2023-09-27 
• Deposition Author(s): Ahn, J.W., Hong, J., Kim, K.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

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

• PubMed: 36788474 
• DOI: https://doi.org/10.4014/jmb.2212.12003
• Primary Citation 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.

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Organizational Affiliation: 
• Postech Biotech Center, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
Center for Biomolecular Capture Technology, Bio Open Innovation Center, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.99 kDa 
• Atom Count: 2,817 
• Modeled Residue Count: 353 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-methylmalyl-CoA dehydratase	A	356	Methylorubrum extorquens CM4	Mutation(s): 0  Gene Names: Mchl_4075
UniProt
Find proteins for B7KZU4 (Methylorubrum extorquens (strain CM4 / NCIMB 13688)) Explore B7KZU4  Go to UniProtKB:  B7KZU4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLT	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 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.224	α = 90
b = 79.224	β = 90
c = 91.008	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Ahn, J.W., Hong, J., Kim, K.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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