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 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

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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 ...

    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: 

    Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 332-0012 Saitama, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdAA,
G [auth I]		569Methanothermobacter wolfeiiMutation(s): 0 
Gene Names: fwdA
UniProt
Find proteins for O74030 (Methanothermobacter wolfeii)
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Entity Groups  
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UniProt GroupO74030
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit BB,
H [auth J]		432Methanothermobacter sp. CaT2Mutation(s): 0 
Gene Names: MTCT_1424
UniProt
Find proteins for T2GJQ6 (Methanothermobacter sp. CaT2)
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2GJQ6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tungsten-containing formylmethanofuran dehydrogenase 2 subunit CC,
I [auth K]		270Methanothermobacter wolfeiiMutation(s): 0 
Gene Names: fwdC
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
MoleculeChainsSequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdDD,
J [auth L]		130Methanothermobacter wolfeiiMutation(s): 0 
Gene Names: fwdD
UniProt
Find proteins for O74029 (Methanothermobacter wolfeii)
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UniProt GroupO74029
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdFE [auth F],
K [auth N]		349Methanothermobacter wolfeiiMutation(s): 0 
Gene Names: fwdF
UniProt
Find proteins for O74028 (Methanothermobacter wolfeii)
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UniProt GroupO74028
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdGF [auth G],
L [auth P]		82Methanothermobacter wolfeiiMutation(s): 0 
Gene Names: fwdG
UniProt
Find proteins for Q1MVD4 (Methanothermobacter wolfeii)
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UniProt GroupQ1MVD4
Protein Feature View
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Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGD
Query on MGD
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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		 Ligand Interaction
SF4
Query on SF4
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BC [auth P],
CC [auth P],
EA [auth F],
FA [auth F],
FB [auth J],
BC [auth P],
CC [auth P],
EA [auth F],
FA [auth F],
FB [auth J],
GA [auth F],
HA [auth F],
IA [auth F],
JA [auth F],
KA [auth F],
LA [auth F],
OB [auth N],
PB [auth N],
QB [auth N],
RA [auth G],
RB [auth N],
SA [auth G],
SB [auth N],
TB [auth N],
UB [auth N],
VB [auth N],
W [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
W
Query on W
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GB [auth J],
X [auth B]		TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
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AC [auth N],
BB [auth I],
CA [auth B],
CB [auth I],
DB [auth I],
AC [auth N],
BB [auth I],
CA [auth B],
CB [auth I],
DB [auth I],
LB [auth J],
S [auth A],
T [auth A],
U [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
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		 Ligand Interaction
CA
Query on CA
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DA [auth B],
MB [auth J]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
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BA [auth B],
DC [auth P],
KB [auth J],
MA [auth F],
NA [auth F],
BA [auth B],
DC [auth P],
KB [auth J],
MA [auth F],
NA [auth F],
OA [auth F],
P [auth A],
PA [auth F],
Q [auth A],
QA [auth F],
TA [auth G],
UA [auth G],
WB [auth N],
XB [auth N],
YA [auth I],
YB [auth N],
ZA [auth I],
ZB [auth N]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
H2S
Query on H2S
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AA [auth B],
JB [auth J]		HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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O [auth A],
XA [auth I]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
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		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • 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

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Ligand Structure Quality Assessment 


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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