8W33

Structure of McrD (methyl-coenzyme M reductase operon protein D) from Methanomassiliicoccus luminyensis

• PDB DOI: https://doi.org/10.2210/pdb8W33/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Methanomassiliicoccus luminyensis B10
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-02-21 Released: 2024-07-03 
• Deposition Author(s): Sutherland-Smith, A.J., Carbone, V., Schofield, L.R., Ronimus, R.S.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.192 
• R-Value Work: 0.178 

Literature

The crystal structure of methanogen McrD, a methyl-coenzyme M reductase-associated protein.

Sutherland-Smith, A.J., Carbone, V., Schofield, L.R., Cronin, B., Duin, E.C., Ronimus, R.S.

(2024) FEBS Open Bio 14: 1222-1229

• PubMed: 38877345 
• DOI: https://doi.org/10.1002/2211-5463.13848
• Primary Citation of Related Structures:  
  8W33


• PubMed Abstract: 
  

  Methyl-coenzyme M reductase (MCR) is a multi-subunit (α ₂ β ₂ γ ₂ ) enzyme responsible for methane formation via its unique F ₄₃₀ cofactor. The genes responsible for producing MCR (mcrA, mcrB and mcrG) are typically colocated with two other highly conserved genes mcrC and mcrD. We present here the high-resolution crystal structure for McrD from a human gut methanogen Methanomassiliicoccus luminyensis strain B10. The structure reveals that McrD comprises a ferredoxin-like domain assembled into an α + β barrel-like dimer with conformational flexibility exhibited by a functional loop. The description of the M. luminyensis McrD crystal structure contributes to our understanding of this key conserved methanogen protein typically responsible for promoting MCR activity and the production of methane, a greenhouse gas.

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Organizational Affiliation: 

School of Natural Sciences, Massey University, Palmerston North, New Zealand.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 39.04 kDa 
• Atom Count: 2,474 
• Modelled Residue Count: 288 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
McrD (methyl-coenzyme M reductase operon protein D)	A, B	172	Methanomassiliicoccus luminyensis B10	Mutation(s): 0  Gene Names: mcrD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.192 
• R-Value Work: 0.178 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.062	α = 90
b = 90.224	β = 90
c = 121.415	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data reduction
Aimless	data scaling
BUCCANEER	model building
CRANK2	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Sutherland-Smith, A.J., Carbone, V., Schofield, L.R., Ronimus, R.S.

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Funding Organization	Location	Grant Number
Other government	New Zealand	--

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release
  
• Version 1.1: 2024-08-21
  Changes: Database references
• Version 1.2: 2024-08-28
  Changes: Database references