7B2H

Crystal structure of the methyl-coenzyme M reductase from Methanothermobacter Marburgensis derivatized with xenon

PDB DOI: https://doi.org/10.2210/pdb7B2H/pdb

Classification: TRANSFERASE
Organism(s): Methanothermobacter marburgensis str. Marburg
Mutation(s): No

Deposited: 2020-11-27 Released: 2021-07-14
Deposition Author(s): Wagner, T., Lemaire, O.N., Engilberge, S.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.204
R-Value Work: 0.177
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a key enzyme for anaerobic ethane activation.

Hahn, C.J., Lemaire, O.N., Kahnt, J., Engilberge, S., Wegener, G., Wagner, T.

(2021) Science 373: 118-121

PubMed: 34210888 Search on PubMed
DOI: https://doi.org/10.1126/science.abg1765
Primary Citation of Related Structures:
7B1S, 7B2C, 7B2H

PubMed Abstract:
Ethane, the second most abundant hydrocarbon gas in the seafloor, is efficiently oxidized by anaerobic archaea in syntrophy with sulfate-reducing bacteria. Here, we report the 0.99-angstrom-resolution structure of the proposed ethane-activating enzyme and describe the specific traits that distinguish it from methane-generating and -consuming methyl-coenzyme M reductases. The widened catalytic chamber, harboring a dimethylated nickel-containing F ₄₃₀ cofactor, would adapt the chemistry of methyl-coenzyme M reductases for a two-carbon substrate. A sulfur from methionine replaces the oxygen from a canonical glutamine as the nickel lower-axial ligand, a feature conserved in thermophilic ethanotrophs. Specific loop extensions, a four-helix bundle dilatation, and posttranslational methylations result in the formation of a 33-angstrom-long hydrophobic tunnel, which guides the ethane to the buried active site as confirmed with xenon pressurization experiments.

Organizational Affiliation

Max Planck Institute for Marine Microbiology, Bremen 28359, Germany.

Macromolecule Content

Total Structure Weight: 279.59 kDa
Atom Count: 20,066
Modelled Residue Count: 2,465
Deposited Residue Count: 2,484
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase I subunit alpha	A, D	550	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for P11558 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11558 Go to UniProtKB: P11558
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11558
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase I subunit beta	B, E	443	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for P11560 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11560 Go to UniProtKB: P11560
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11560
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase I subunit gamma	C, F	249	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for P11562 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11562 Go to UniProtKB: P11562
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11562
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F43 Query on F43 Download Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain N [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain N [auth A]	IA [auth D], N [auth A]	FACTOR 430 C₄₂ H₅₁ N₆ Ni O₁₃ XLFIRMYGVLUNOY-SXMZNAGASA-M		Interactions Focus chain IA [auth D] Focus chain N [auth A] Interactions & Density Focus chain IA [auth D] Focus chain N [auth A]
TP7 Query on TP7 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain KA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain KA [auth D]	H [auth A], KA [auth D]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain H [auth A] Focus chain KA [auth D] Interactions & Density Focus chain H [auth A] Focus chain KA [auth D]
COM Query on COM Download Ideal Coordinates CCD File SDF format, chain JA [auth D] SDF format, chain G [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain G [auth A]	G [auth A], JA [auth D]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain JA [auth D] Interactions & Density Focus chain G [auth A] Focus chain JA [auth D]
XE (Subject of Investigation/LOI) Query on XE Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EB [auth F] SDF format, chain FA [auth B] SDF format, chain QA [auth D] SDF format, chain S [auth A] SDF format, chain XA [auth E] SDF format, chain ZA [auth E] SDF format, chain EA [auth B] SDF format, chain YA [auth E] MOL2 format, chain AB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EB [auth F] MOL2 format, chain FA [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain XA [auth E] MOL2 format, chain ZA [auth E] MOL2 format, chain EA [auth B] MOL2 format, chain YA [auth E]	AB [auth E] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AB [auth E], BA [auth B], CA [auth B], DA [auth B], EA [auth B], EB [auth F], FA [auth B], QA [auth D], S [auth A], XA [auth E], YA [auth E], ZA [auth E]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain EB [auth F] Focus chain FA [auth B] Focus chain QA [auth D] Focus chain S [auth A] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain EB [auth F] Focus chain FA [auth B] Focus chain QA [auth D] Focus chain S [auth A] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain DB [auth F] SDF format, chain TA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain DB [auth F] MOL2 format, chain TA [auth E]	DB [auth F] J [auth A] K [auth A] MA [auth D] NA [auth D] DB [auth F], J [auth A], K [auth A], MA [auth D], NA [auth D], OA [auth D], TA [auth E], W [auth B], X [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DB [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain TA [auth E] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain DB [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain TA [auth E] Focus chain W [auth B] Focus chain X [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A]	T [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain RA [auth D] SDF format, chain U [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain U [auth A]	HA [auth B], I [auth A], RA [auth D], U [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain I [auth A] Focus chain RA [auth D] Focus chain U [auth A] Interactions & Density Focus chain HA [auth B] Focus chain I [auth A] Focus chain RA [auth D] Focus chain U [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BB [auth E] SDF format, chain GA [auth B] MOL2 format, chain BB [auth E] MOL2 format, chain GA [auth B]	BB [auth E], GA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BB [auth E] Focus chain GA [auth B] Interactions & Density Focus chain BB [auth E] Focus chain GA [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CB [auth F] SDF format, chain LA [auth D] SDF format, chain O [auth A] SDF format, chain PA [auth D] SDF format, chain SA [auth E] SDF format, chain UA [auth E] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain WA [auth E] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain CB [auth F] MOL2 format, chain LA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain SA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A]	AA [auth B] CB [auth F] LA [auth D] O [auth A] P [auth A] AA [auth B], CB [auth F], LA [auth D], O [auth A], P [auth A], PA [auth D], Q [auth A], R [auth A], SA [auth E], UA [auth E], V [auth B], VA [auth E], WA [auth E], Y [auth B], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain CB [auth F] Focus chain LA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain SA [auth E] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain CB [auth F] Focus chain LA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain SA [auth E] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain Y [auth B] Focus chain Z [auth B]

Modified Residues 6 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGM Query on AGM	A, D	L-PEPTIDE LINKING	C₇ H₁₇ N₄ O₂		ARG
DYA Query on DYA	A, D	L-PEPTIDE LINKING	C₄ H₅ N O₄		ASP
GL3 Query on GL3	A, D	L-PEPTIDE LINKING	C₂ H₅ N O S		GLY
MGN Query on MGN	A, D	L-PEPTIDE LINKING	C₆ H₁₂ N₂ O₃		GLN
MHS Query on MHS	A, D	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS
SMC Query on SMC	A, D	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.204
R-Value Work: 0.177
R-Value Observed: 0.179
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.719	α = 90
b = 116.386	β = 92.36
c = 123.07	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-07-14

Deposition Author(s):

Wagner, T.

Lemaire, O.N.

Engilberge, S.

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
German Research Foundation (DFG)	Germany	EXC-2077 390741603

Revision History (Full details and data files)

Version 1.0: 2021-07-14
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Derived calculations, Refinement description