5T5I

TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANOTHERMOBACTER WOLFEII, ORTHORHOMBIC FORM AT 1.9 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.172 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

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Ligand Structure Quality Assessment 

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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 fwdAA,
G [auth I]
569Methanothermobacter wolfeiiMutation(s): 0 
UniProt
Find proteins for O74030 (Methanothermobacter wolfeii)
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74030
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit BB,
H [auth J]
432Methanothermobacter sp. CaT2Mutation(s): 0 
UniProt
Find proteins for T2GJQ6 (Methanothermobacter sp. CaT2)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2GJQ6
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten-containing formylmethanofuran dehydrogenase 2 subunit CC,
I [auth K]
270Methanothermobacter wolfeiiMutation(s): 0 
EC: 1.2.99.5 (PDB Primary Data), 1.2.7.12 (UniProt)
UniProt
Find proteins for O74031 (Methanothermobacter wolfeii)
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UniProt GroupO74031
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdDD,
J [auth L]
130Methanothermobacter wolfeiiMutation(s): 0 
UniProt
Find proteins for O74029 (Methanothermobacter wolfeii)
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UniProt GroupO74029
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdFE [auth F],
K [auth N]
349Methanothermobacter wolfeiiMutation(s): 0 
UniProt
Find proteins for O74028 (Methanothermobacter wolfeii)
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UniProt GroupO74028
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdGF [auth G],
L [auth P]
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 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD
Query on MGD

Download Ideal Coordinates CCD File 
HB [auth J],
IB [auth J],
Y [auth B],
Z [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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BC [auth P]
CC [auth P]
EA [auth F]
FA [auth F]
FB [auth J]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
W
Query on W

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GB [auth J],
X [auth B]
TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
GOL
Query on GOL

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AC [auth N]
BB [auth I]
CA [auth B]
CB [auth I]
DB [auth I]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

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M [auth A],
N [auth A],
VA [auth I],
WA [auth I]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

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DA [auth B],
MB [auth J]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

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BA [auth B]
DC [auth P]
KB [auth J]
MA [auth F]
NA [auth F]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
H2S
Query on H2S

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AA [auth B],
JB [auth J]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
MG
Query on MG

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O [auth A],
XA [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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AB [auth I],
EB [auth I],
NB [auth L],
R [auth A],
V [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A,
G [auth I]
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.172 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.644α = 90
b = 174.576β = 90
c = 205.425γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MGDClick on this verticalbar to view details

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