7B2C

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


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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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

  • 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
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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 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
USN (Subject of Investigation/LOI)
Query on USN

Download Ideal Coordinates CCD File 
G [auth A],
GB [auth F]
Dimethylated-F430 cofactor
C44 H55 N6 Ni O13
RAZHPFHMRANHAI-KFKQAULWSA-M
TP7 (Subject of Investigation/LOI)
Query on TP7

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HA [auth D],
J [auth A]
Coenzyme B
C11 H22 N O7 P S
JBJSVEVEEGOEBZ-SCZZXKLOSA-N
UWT
Query on UWT

Download Ideal Coordinates CCD File 
CA [auth C],
IB [auth F]
(2R)-2-[(2S)-2-[(2S)-2-oxidanylpropoxy]propoxy]propan-1-ol
C9 H20 O4
LCZVSXRMYJUNFX-YIZRAAEISA-N
COM (Subject of Investigation/LOI)
Query on COM

Download Ideal Coordinates CCD File 
HB [auth F],
K [auth A]
1-THIOETHANESULFONIC ACID
C2 H6 O3 S2
ZNEWHQLOPFWXOF-UHFFFAOYSA-N
XE (Subject of Investigation/LOI)
Query on XE

Download Ideal Coordinates CCD File 
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
TRS
Query on TRS

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SA [auth E]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL
Query on GOL

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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
K
Query on K

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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
CL
Query on CL

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U [auth B],
UA [auth E],
V [auth B],
VA [auth E],
WA [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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RA [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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DA [auth C],
I [auth A],
KA [auth D],
LA [auth D],
MA [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
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: 1.80 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.791α = 90
b = 147.186β = 107.2
c = 113.376γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
PHENIXphasing

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