7QBS | pdb_00007qbs

B12-dependent radical SAM methyltransferase, Mmp10 with [4Fe-4S] cluster, cobalamin, S-adenosyl-L-methionine, and peptide bound.

PDB DOI: https://doi.org/10.2210/pdb7QBS/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Methanosarcina acetivorans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-11-19 Released: 2022-02-02
Deposition Author(s): Bernardo-Garcia, N., Fyfe, C.D., Chavas, L.M.G., Legrand, P., Benjdia, A., Berteau, O.
Funding Organization(s): European Research Council (ERC), Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.235 (Depositor), 0.225 (DCC)
R-Value Work:
0.182 (Depositor), 0.176 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystallographic snapshots of a B 12 -dependent radical SAM methyltransferase.

Fyfe, C.D., Bernardo-Garcia, N., Fradale, L., Grimaldi, S., Guillot, A., Brewee, C., Chavas, L.M.G., Legrand, P., Benjdia, A., Berteau, O.

(2022) Nature 602: 336-342

PubMed: 35110733 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-021-04355-9
Primary Citation Related Structures:
7QBS, 7QBT, 7QBU, 7QBV

PubMed Abstract:
By catalysing the microbial formation of methane, methyl-coenzyme M reductase has a central role in the global levels of this greenhouse gas ^1,2. The activity of methyl-coenzyme M reductase is profoundly affected by several unique post-translational modifications ^3-6, such as a unique C-methylation reaction catalysed by methanogenesis marker protein 10 (Mmp10), a radical S-adenosyl-L-methionine (SAM) enzyme ^7,8. Here we report the spectroscopic investigation and atomic resolution structure of Mmp10 from Methanosarcina acetivorans, a unique B ₁₂ (cobalamin)-dependent radical SAM enzyme ⁹. The structure of Mmp10 reveals a unique enzyme architecture with four metallic centres and critical structural features involved in the control of catalysis. In addition, the structure of the enzyme-substrate complex offers a glimpse into a B ₁₂-dependent radical SAM enzyme in a precatalytic state. By combining electron paramagnetic resonance spectroscopy, structural biology and biochemistry, our study illuminates the mechanism by which the emerging superfamily of B ₁₂-dependent radical SAM enzymes catalyse chemically challenging alkylation reactions and identifies distinctive active site rearrangements to provide a structural rationale for the dual use of the SAM cofactor for radical and nucleophilic chemistry.

Organizational Affiliation

Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.

Macromolecule Content

Total Structure Weight: 51.64 kDa
Atom Count: 3,577
Modeled Residue Count: 419
Deposited Residue Count: 449
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl coenzyme M reductase-arginine methyltransferase Mmp10	A	436	Methanosarcina acetivorans	Mutation(s): 0 Gene Names: mmp10, HA338_00275 EC: 2.1.1 (PDB Primary Data), 2.1.1.379 (UniProt)
UniProt
Find proteins for Q8THG6 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)) Explore Q8THG6 Go to UniProtKB: Q8THG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8THG6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Methyl-coenzyme M reductase subunit alpha from Methanosarcina acetivorans	B	13	Methanosarcina acetivorans	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for Q8THH1 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)) Explore Q8THH1 Go to UniProtKB: Q8THH1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8THH1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COB (Subject of Investigation/LOI) Query on COB Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CO-METHYLCOBALAMIN C₆₃ H₉₁ Co N₁₃ O₁₄ P BMOGZGJBQIUQJG-BYLSPCLQSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SAM (Subject of Investigation/LOI) Query on SAM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]