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 


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, 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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Protein Feature View
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  • Reference Sequence
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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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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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  • Reference Sequence
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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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  • Reference Sequence
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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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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdGF [auth G], L [auth P]82Methanothermobacter wolfeiiMutation(s): 0 
Gene Names: fwdGMWSIV6_0096
EC: 1.2.99.5
UniProt
Find proteins for Q1MVD4 (Methanothermobacter wolfeii)
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGD (Subject of Investigation/LOI)
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] , GA [auth F] , HA [auth F] , IA [auth F] , 
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 (Subject of Investigation/LOI)
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] , LB [auth J] , S [auth A] , T [auth A] , 
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] , OA [auth F] , P [auth A] , PA [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  



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