7B2C

Crystal structure of the ethyl-coenzyme M reductase from Candidatus Ethanoperedens thermophilum gassed with xenon

PDB DOI: https://doi.org/10.2210/pdb7B2C/pdb

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

Deposited: 2020-11-26 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: 1.80 Å
R-Value Free: 0.201
R-Value Work: 0.174
R-Value Observed: 0.176

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 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: 300.58 kDa
Atom Count: 23,280
Modelled Residue Count: 2,646
Deposited Residue Count: 2,656
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R9R780
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R9N4Z1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R9R6T0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 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 G [auth A] SDF format, chain GB [auth F] MOL2 format, chain G [auth A] MOL2 format, chain GB [auth F]	G [auth A], GB [auth F]	Dimethylated-F430 cofactor C₄₄ H₅₅ N₆ Ni O₁₃ RAZHPFHMRANHAI-KFKQAULWSA-M		Interactions Focus chain G [auth A] Focus chain GB [auth F] Interactions & Density Focus chain G [auth A] Focus chain GB [auth F]
TP7 (Subject of Investigation/LOI) Query on TP7 Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain J [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain J [auth A]	HA [auth D], J [auth A]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain HA [auth D] Focus chain J [auth A] Interactions & Density Focus chain HA [auth D] Focus chain J [auth A]
UWT Query on UWT Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain IB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain IB [auth F]	CA [auth C], IB [auth F]	(2R)-2-[(2S)-2-[(2S)-2-oxidanylpropoxy]propoxy]propan-1-ol C₉ H₂₀ O₄ LCZVSXRMYJUNFX-YIZRAAEISA-N		Interactions Focus chain CA [auth C] Focus chain IB [auth F] Interactions & Density Focus chain CA [auth C] Focus chain IB [auth F]
COM (Subject of Investigation/LOI) Query on COM Download Ideal Coordinates CCD File SDF format, chain HB [auth F] SDF format, chain K [auth A] MOL2 format, chain HB [auth F] MOL2 format, chain K [auth A]	HB [auth F], K [auth A]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain HB [auth F] Focus chain K [auth A] Interactions & Density Focus chain HB [auth F] Focus chain K [auth A]
XE (Subject of Investigation/LOI) Query on XE Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain DB [auth E] SDF format, chain EB [auth E] SDF format, chain FA [auth C] SDF format, chain FB [auth E] SDF format, chain GA [auth C] SDF format, chain KB [auth F] SDF format, chain LB [auth F] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth E] MOL2 format, chain GA [auth C] MOL2 format, chain KB [auth F] MOL2 format, chain LB [auth F] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] DB [auth E] EB [auth E] FA [auth C] AA [auth B], BA [auth B], DB [auth E], EB [auth E], FA [auth C], FB [auth E], GA [auth C], KB [auth F], LB [auth F], N [auth A], O [auth A], OA [auth D], P [auth A], PA [auth D], QA [auth D], Z [auth B]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain DB [auth E] Focus chain EB [auth E] Focus chain FA [auth C] Focus chain FB [auth E] Focus chain GA [auth C] Focus chain KB [auth F] Focus chain LB [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain DB [auth E] Focus chain EB [auth E] Focus chain FA [auth C] Focus chain FB [auth E] Focus chain GA [auth C] Focus chain KB [auth F] Focus chain LB [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain Z [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain SA [auth E] MOL2 format, chain SA [auth E]	SA [auth E]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain SA [auth E] Interactions & Density Focus chain SA [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain MB [auth F] SDF format, chain Q [auth A] SDF format, chain R [auth B] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain MB [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth B]	H [auth A] IA [auth D] JA [auth D] MB [auth F] Q [auth A] H [auth A], IA [auth D], JA [auth D], MB [auth F], Q [auth A], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain MB [auth F] Focus chain Q [auth A] Focus chain R [auth B] Interactions & Density Focus chain H [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain MB [auth F] Focus chain Q [auth A] Focus chain R [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain CB [auth E] SDF format, chain EA [auth C] SDF format, chain JB [auth F] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain NA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain Y [auth B] SDF format, chain YA [auth E] SDF format, chain ZA [auth E] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain EA [auth C] MOL2 format, chain JB [auth F] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth E]	AB [auth E] BB [auth E] CB [auth E] EA [auth C] JB [auth F] AB [auth E], BB [auth E], CB [auth E], EA [auth C], JB [auth F], L [auth A], M [auth A], NA [auth D], S [auth B], T [auth B], TA [auth E], W [auth B], X [auth B], XA [auth E], Y [auth B], YA [auth E], ZA [auth E]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain EA [auth C] Focus chain JB [auth F] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth E] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain EA [auth C] Focus chain JB [auth F] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth E] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain ZA [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain WA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E]	U [auth B], UA [auth E], V [auth B], VA [auth E], WA [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Interactions & Density Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain WA [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain RA [auth D] MOL2 format, chain RA [auth D]	RA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain RA [auth D] Interactions & Density Focus chain RA [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain I [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D]	DA [auth C], I [auth A], KA [auth D], LA [auth D], MA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain I [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Interactions & Density Focus chain DA [auth C] Focus chain I [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D]

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