7B1S | pdb_00007b1s

Crystal structure of the ethyl-coenzyme M reductase from Candidatus Ethanoperedens thermophilum at 0.994-A resolution

PDB DOI: https://doi.org/10.2210/pdb7B1S/pdb

Classification: TRANSFERASE
Organism(s): Candidatus Ethanoperedens thermophilum
Mutation(s): No

Deposited: 2020-11-25 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: 0.99 Å
R-Value Free:
0.128 (Depositor), 0.141 (DCC)
R-Value Work:
0.112 (Depositor), 0.128 (DCC)
R-Value Observed:
0.113 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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 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: 297.86 kDa
Atom Count: 25,172
Modeled Residue Count: 2,646
Deposited Residue Count: 2,656
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ethyl-Coenzyme M reductase alpha subunit	A, D	595	Candidatus Ethanoperedens thermophilum	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for A0A7R9R780 (Candidatus Methanoperedenaceae archaeon GB50) Explore A0A7R9R780 Go to UniProtKB: A0A7R9R780
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7R9R780
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ethyl-Coenzyme M reductase beta subunit	B, E	467	Candidatus Ethanoperedens thermophilum	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for A0A7R9N4Z1 (Candidatus Methanoperedenaceae archaeon GB50) Explore A0A7R9N4Z1 Go to UniProtKB: A0A7R9N4Z1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7R9N4Z1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ethyl-Coenzyme M reductase gamma subunit	C, F	266	Candidatus Ethanoperedens thermophilum	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for A0A7R9R6T0 (Candidatus Methanoperedenaceae archaeon GB50) Explore A0A7R9R6T0 Go to UniProtKB: A0A7R9R6T0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7R9R6T0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
USN (Subject of Investigation/LOI) Query on USN Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain O [auth C] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C]	O [auth C], T [auth D]	Dimethylated-F430 cofactor C₄₄ H₅₅ N₆ Ni O₁₃ RAZHPFHMRANHAI-KFKQAULWSA-M		Interactions Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain O [auth C] Focus chain T [auth D]
TP7 (Subject of Investigation/LOI) Query on TP7 Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain H [auth A] MOL2 format, chain U [auth D] MOL2 format, chain H [auth A] mmCIF format, chain U [auth D] mmCIF format, chain H [auth A]	H [auth A], U [auth D]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain H [auth A] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain U [auth D]
UUT Query on UUT Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain S [auth C] MOL2 format, chain X [auth D] MOL2 format, chain S [auth C] mmCIF format, chain X [auth D] mmCIF format, chain S [auth C]	S [auth C], X [auth D]	(2S)-2-{[(2S)-2-{[(2S)-2-hydroxypropyl]oxy}propyl]oxy}propan-1-ol C₉ H₂₀ O₄ LCZVSXRMYJUNFX-CIUDSAMLSA-N		Interactions Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain S [auth C] Focus chain X [auth D]
COM (Subject of Investigation/LOI) Query on COM Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain DA [auth F] MOL2 format, chain P [auth C] MOL2 format, chain DA [auth F] mmCIF format, chain P [auth C] mmCIF format, chain DA [auth F]	DA [auth F], P [auth C]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain P [auth C] Interactions & Density Focus chain DA [auth F] Focus chain P [auth C]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain N [auth B] MOL2 format, chain Y [auth E] MOL2 format, chain N [auth B] mmCIF format, chain Y [auth E] mmCIF format, chain N [auth B]	N [auth B], Y [auth E]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain N [auth B] Focus chain Y [auth E] Interactions & Density Focus chain N [auth B] Focus chain Y [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain V [auth D] SDF format, chain G [auth A] SDF format, chain CA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth D] MOL2 format, chain G [auth A] MOL2 format, chain CA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth D] mmCIF format, chain G [auth A] mmCIF format, chain CA [auth E]	CA [auth E], G [auth A], V [auth D], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain G [auth A] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth E] Focus chain G [auth A] Focus chain V [auth D] Focus chain Z [auth E]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain R [auth C] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain W [auth D] MOL2 format, chain R [auth C] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain W [auth D] mmCIF format, chain R [auth C] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], R [auth C], W [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth C] Focus chain W [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain EA [auth F] SDF format, chain BA [auth E] SDF format, chain AA [auth E] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain EA [auth F] MOL2 format, chain BA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain EA [auth F] mmCIF format, chain BA [auth E] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth E] EA [auth F] L [auth B] M [auth B] AA [auth E], BA [auth E], EA [auth F], L [auth B], M [auth B], Q [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C]

Modified Residues 7 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGM Query on AGM	A, D	L-PEPTIDE LINKING	C₇ H₁₇ N₄ O₂		ARG
GL3 Query on GL3	A, D	L-PEPTIDE LINKING	C₂ H₅ N O S		GLY
HIC Query on HIC	A, D	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS
I2M Query on I2M	A, D	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		ILE
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