7B1S

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ethyl-Coenzyme M reductase alpha subunit
A, D
595Candidatus Ethanoperedens thermophilumMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7R9R780
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ethyl-Coenzyme M reductase beta subunit
B, E
467Candidatus Ethanoperedens thermophilumMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7R9N4Z1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ethyl-Coenzyme M reductase gamma subunit
C, F
266Candidatus Ethanoperedens thermophilumMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7R9R6T0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
USN (Subject of Investigation/LOI)
Query on USN

Download Ideal Coordinates CCD File 
O [auth C],
T [auth D]
Dimethylated-F430 cofactor
C44 H55 N6 Ni O13
RAZHPFHMRANHAI-KFKQAULWSA-M
TP7 (Subject of Investigation/LOI)
Query on TP7

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H [auth A],
U [auth D]
Coenzyme B
C11 H22 N O7 P S
JBJSVEVEEGOEBZ-SCZZXKLOSA-N
UUT
Query on UUT

Download Ideal Coordinates CCD File 
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
COM (Subject of Investigation/LOI)
Query on COM

Download Ideal Coordinates CCD File 
DA [auth F],
P [auth C]
1-THIOETHANESULFONIC ACID
C2 H6 O3 S2
ZNEWHQLOPFWXOF-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
N [auth B],
Y [auth E]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth E],
G [auth A],
V [auth D],
Z [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

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I [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K

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J [auth A],
K [auth A],
R [auth C],
W [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
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
Modified Residues  7 Unique
IDChains TypeFormula2D DiagramParent
AGM
Query on AGM
A, D
L-PEPTIDE LINKINGC7 H17 N4 O2ARG
GL3
Query on GL3
A, D
L-PEPTIDE LINKINGC2 H5 N O SGLY
HIC
Query on HIC
A, D
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
I2M
Query on I2M
A, D
L-PEPTIDE LINKINGC7 H15 N O2ILE
MGN
Query on MGN
A, D
L-PEPTIDE LINKINGC6 H12 N2 O3GLN
MHS
Query on MHS
A, D
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
SMC
Query on SMC
A, D
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.736α = 90
b = 146.927β = 106.98
c = 113.128γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanyEXC-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, Refinement description