5T61

TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANOTHERMOBACTER WOLFEII, TRICLINIC FORM AT 2.55 A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit B432Methanothermobacter sp. CaT2Mutation(s): 0 
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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
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdD130Methanothermobacter wolfeiiMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdG82Methanothermobacter wolfeiiMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Tungsten formylmethanofuran dehydrogenase subunit fwdF349Methanothermobacter wolfeiiMutation(s): 0 
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MFN
Query on MFN
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AC [auth G]
BG [auth e]
CE [auth S]
CF [auth Y]
GH [auth k]
AC [auth G],
BG [auth e],
CE [auth S],
CF [auth Y],
GH [auth k],
GI [auth q],
YA [auth A],
ZC [auth M]
N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE
C35 H44 N4 O16
RGBIJPWAWLXPOC-XRVZLLLRSA-N
MGD
Query on MGD
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DB [auth B]
EB [auth B]
FC [auth H]
FD [auth N]
GC [auth H]
DB [auth B],
EB [auth B],
FC [auth H],
FD [auth N],
GC [auth H],
GD [auth N],
GF [auth Z],
HF [auth Z],
IE [auth T],
JE [auth T],
JG [auth f],
KG [auth f],
LH [auth l],
MH [auth l],
MI [auth r],
NI [auth r]
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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AI [auth p]
AJ [auth v]
BB [auth B]
BJ [auth v]
DC [auth H]
AI [auth p],
AJ [auth v],
BB [auth B],
BJ [auth v],
DC [auth H],
DD [auth N],
EF [auth Z],
GE [auth T],
HG [auth f],
IB [auth E],
JB [auth E],
JC [auth K],
JH [auth l],
KC [auth K],
KI [auth r],
LB [auth F],
LD [auth Q],
LF [auth c],
MB [auth F],
MC [auth L],
MD [auth Q],
MF [auth c],
NB [auth F],
NC [auth L],
NE [auth W],
NG [auth i],
OB [auth F],
OC [auth L],
OD [auth R],
OE [auth W],
OF [auth d],
OG [auth i],
PB [auth F],
PC [auth L],
PD [auth R],
PE [auth X],
PF [auth d],
PH [auth o],
QB [auth F],
QC [auth L],
QD [auth R],
QE [auth X],
QF [auth d],
QG [auth j],
QH [auth o],
RB [auth F],
RC [auth L],
RD [auth R],
RE [auth X],
RF [auth d],
RG [auth j],
RI [auth u],
SB [auth F],
SC [auth L],
SD [auth R],
SE [auth X],
SF [auth d],
SG [auth j],
SH [auth p],
SI [auth u],
TB [auth F],
TC [auth L],
TD [auth R],
TE [auth X],
TF [auth d],
TG [auth j],
TH [auth p],
UD [auth R],
UE [auth X],
UF [auth d],
UG [auth j],
UH [auth p],
UI [auth v],
VD [auth R],
VE [auth X],
VF [auth d],
VG [auth j],
VH [auth p],
VI [auth v],
WD [auth R],
WE [auth X],
WF [auth d],
WG [auth j],
WH [auth p],
WI [auth v],
XG [auth j],
XH [auth p],
XI [auth v],
YH [auth p],
YI [auth v],
ZH [auth p],
ZI [auth v]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
W
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CB [auth B]
EC [auth H]
ED [auth N]
FF [auth Z]
HE [auth T]
CB [auth B],
EC [auth H],
ED [auth N],
FF [auth Z],
HE [auth T],
IG [auth f],
KH [auth l],
LI [auth r]
TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
ZN
Query on ZN
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AE [auth S]
AF [auth Y]
AG [auth e]
BE [auth S]
BF [auth Y]
AE [auth S],
AF [auth Y],
AG [auth e],
BE [auth S],
BF [auth Y],
EH [auth k],
EI [auth q],
FH [auth k],
FI [auth q],
WA [auth A],
XA [auth A],
XC [auth M],
YB [auth G],
YC [auth M],
ZB [auth G],
ZF [auth e]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K
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AB [auth A]
AH [auth j]
BD [auth M]
BH [auth j]
BI [auth p]
AB [auth A],
AH [auth j],
BD [auth M],
BH [auth j],
BI [auth p],
CC [auth G],
CD [auth M],
CH [auth j],
CI [auth p],
CJ [auth v],
DF [auth Y],
DG [auth e],
DH [auth j],
DI [auth p],
DJ [auth v],
EE [auth S],
EG [auth e],
EJ [auth v],
FE [auth S],
FG [auth e],
FJ [auth v],
GB [auth B],
GG [auth e],
GJ [auth v],
HJ [auth v],
IH [auth k],
II [auth q],
IJ [auth v],
JD [auth N],
JF [auth Z],
JI [auth q],
KB [auth E],
LC [auth K],
LE [auth T],
ND [auth Q],
NF [auth c],
PG [auth i],
PI [auth r],
RH [auth o],
TI [auth u],
UB [auth F],
UC [auth L],
VB [auth F],
VC [auth L],
WB [auth F],
WC [auth L],
XB [auth F],
XD [auth R],
XE [auth X],
XF [auth d],
YD [auth R],
YE [auth X],
YF [auth d],
YG [auth j],
ZD [auth R],
ZE [auth X],
ZG [auth j]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL
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ID [auth N]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
H2S
Query on H2S
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FB [auth B]
HC [auth H]
HD [auth N]
IF [auth Z]
KE [auth T]
FB [auth B],
HC [auth H],
HD [auth N],
IF [auth Z],
KE [auth T],
LG [auth f],
NH [auth l],
OI [auth r]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
MG
Query on MG
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HB [auth B]
IC [auth H]
KD [auth O]
KF [auth Z]
ME [auth T]
HB [auth B],
IC [auth H],
KD [auth O],
KF [auth Z],
ME [auth T],
MG [auth f],
OH [auth l],
QI [auth r]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA
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AD [auth M]
BC [auth G]
CG [auth e]
DE [auth S]
HH [auth k]
AD [auth M],
BC [auth G],
CG [auth e],
DE [auth S],
HH [auth k],
HI [auth q],
ZA [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
EA [auth e]
G
KA [auth k]
M
A,
EA [auth e],
G,
KA [auth k],
M,
QA [auth q],
S,
Y
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.183α = 89.98
b = 173.681β = 95.42
c = 183.162γ = 92.14
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

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
  • Version 1.2: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description