5T5M

TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANOTHERMOBACTER WOLFEII, TRIGONAL FORM AT 2.5 A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters.

Wagner, T.Ermler, U.Shima, S.

(2016) Science 354: 114-117

  • DOI: https://doi.org/10.1126/science.aaf9284
  • Primary Citation of Related Structures:  
    5T5I, 5T5M, 5T61

  • PubMed Abstract: 

    Biological methane formation starts with a challenging adenosine triphosphate (ATP)-independent carbon dioxide (CO 2 ) fixation process. We explored this enzymatic process by solving the x-ray crystal structure of formyl-methanofuran dehydrogenase, determined here as Fwd(ABCDFG) 2 and Fwd(ABCDFG) 4 complexes, from Methanothermobacter wolfeii The latter 800-kilodalton apparatus consists of four peripheral catalytic sections and an electron-supplying core with 46 electronically coupled [4Fe-4S] clusters. Catalysis is separately performed by subunits FwdBD (FwdB and FwdD), which are related to tungsten-containing formate dehydrogenase, and subunit FwdA, a binuclear metal center carrying amidohydrolase. CO 2 is first reduced to formate in FwdBD, which then diffuses through a 43-angstrom-long tunnel to FwdA, where it condenses with methanofuran to formyl-methanofuran. The arrangement of [4Fe-4S] clusters functions as an electron relay but potentially also couples the four tungstopterin active sites over 206 angstroms.


  • Organizational Affiliation

    Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdA569Methanothermobacter wolfeiiMutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for O74030 (Methanothermobacter wolfeii)
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Go to UniProtKB:  O74030
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74030
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdB432Methanothermobacter wolfeiiMutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for O74032 (Methanothermobacter wolfeii)
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Go to UniProtKB:  O74032
Entity Groups  
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UniProt GroupO74032
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C270Methanothermobacter wolfeiiMutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for O74031 (Methanothermobacter wolfeii)
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UniProt GroupO74031
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdD130Methanothermobacter wolfeiiMutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for O74029 (Methanothermobacter wolfeii)
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UniProt GroupO74029
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdFE [auth F]349Methanothermobacter wolfeiiMutation(s): 0 
UniProt
Find proteins for O74028 (Methanothermobacter wolfeii)
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UniProt GroupO74028
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdGF [auth G]82Methanothermobacter wolfeiiMutation(s): 0 
UniProt
Find proteins for Q1MVD4 (Methanothermobacter wolfeii)
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UniProt GroupQ1MVD4
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD
Query on MGD

Download Ideal Coordinates CCD File 
P [auth B],
Q [auth B]
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
SF4
Query on SF4

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AA [auth F]
BA [auth F]
CA [auth G]
DA [auth G]
N [auth B]
AA [auth F],
BA [auth F],
CA [auth G],
DA [auth G],
N [auth B],
U [auth F],
V [auth F],
W [auth F],
X [auth F],
Y [auth F],
Z [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
W
Query on W

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O [auth B]TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
GOL
Query on GOL

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K [auth A],
L [auth A],
T [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

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H [auth A],
I [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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M [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
H2S
Query on H2S

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R [auth B]HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
MG
Query on MG

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G [auth A],
J [auth A],
S [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.543α = 90
b = 105.543β = 90
c = 340.549γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
PRESTOJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description