5T5M

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1126/science.aaf9284
  • Primary Citation of Related Structures:  5T5I, 5T61

  • PubMed Abstract: 
  • Biological methane formation starts with a challenging adenosine triphosphate (ATP)-independent carbon dioxide (CO2) fixation process. We explored this enzymatic process by solving the x-ray crystal structure of formyl-methanofuran dehydrogenase, det ...

    Biological methane formation starts with a challenging adenosine triphosphate (ATP)-independent carbon dioxide (CO2) 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. CO2 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-Stra├če 10, 35043 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tungsten formylmethanofuran dehydrogenase subunit fwdA
A
569Methanothermobacter wolfeiiGene Names: fwdA
Find proteins for O74030 (Methanothermobacter wolfeii)
Go to UniProtKB:  O74030
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tungsten formylmethanofuran dehydrogenase subunit fwdB
B
432Methanothermobacter wolfeiiGene Names: fwdB
Find proteins for O74032 (Methanothermobacter wolfeii)
Go to UniProtKB:  O74032
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
C
270Methanothermobacter wolfeiiGene Names: fwdC
EC: 1.2.7.12
Find proteins for O74031 (Methanothermobacter wolfeii)
Go to UniProtKB:  O74031
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Tungsten formylmethanofuran dehydrogenase subunit fwdD
D
130Methanothermobacter wolfeiiGene Names: fwdD
Find proteins for O74029 (Methanothermobacter wolfeii)
Go to UniProtKB:  O74029
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Tungsten formylmethanofuran dehydrogenase subunit fwdF
F
349Methanothermobacter wolfeiiGene Names: fwdF
Find proteins for O74028 (Methanothermobacter wolfeii)
Go to UniProtKB:  O74028
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Tungsten formylmethanofuran dehydrogenase subunit fwdG
G
82Methanothermobacter wolfeiiGene Names: fwdG
Find proteins for Q1MVD4 (Methanothermobacter wolfeii)
Go to UniProtKB:  Q1MVD4
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

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B, F, G
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
H2S
Query on H2S

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B
HYDROSULFURIC ACID
HYDROGEN SULFIDE
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
W
Query on W

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B
TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
 Ligand Interaction
MGD
Query on MGD

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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
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.158 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.543α = 90.00
b = 105.543β = 90.00
c = 340.549γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Max Planck SocietyGermany--
PRESTOJapan--

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references