5T61 | pdb_00005t61

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

• PDB DOI: https://doi.org/10.2210/pdb5T61/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanothermobacter wolfeii, Methanothermobacter sp. CaT2
• Mutation(s): No 


• Deposited: 2016-09-01 Released: 2016-10-19 
• Deposition Author(s): Wagner, T., Ermler, U., Shima, S.
• Funding Organization(s): Max Planck Society, PRESTO

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.259 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

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

• PubMed: 27846502 
• DOI: https://doi.org/10.1126/science.aaf9284
• Primary Citation 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.

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Organizational Affiliation: 
• Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany.
Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany.
Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany. [e-mail].
Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 332-0012 Saitama, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A4B4C4D4E4F4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A4B4C4D4E4F4 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 1,667.21 kDa 
• Atom Count: 114,321 
• Modeled Residue Count: 14,548 
• Deposited Residue Count: 14,656 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase subunit fwdA	A, EA [auth e], G, KA [auth k], M, QA [auth q], S, Y	569	Methanothermobacter wolfeii	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase subunit B	B, FA [auth f], H, LA [auth l], N, RA [auth r], T, Z	432	Methanothermobacter sp. CaT2	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C	AA [auth a], C, GA [auth g], I, MA [auth m], O, SA [auth s], U	270	Methanothermobacter wolfeii	Mutation(s): 0  EC: 1.2.99.5

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase subunit fwdD	BA [auth b], D, HA [auth h], J, NA [auth n], P, TA [auth t], V	130	Methanothermobacter wolfeii	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase subunit fwdG	CA [auth c], E, IA [auth i], K, OA [auth o], Q, UA [auth u], W	82	Methanothermobacter wolfeii	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase subunit fwdF	DA [auth d], F, JA [auth j], L, PA [auth p], R, VA [auth v], X	349	Methanothermobacter wolfeii	Mutation(s): 0

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MFN	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	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	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	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	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	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	ID [auth N]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
H2S	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	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	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
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, EA [auth e], G, KA [auth k], M, QA [auth q], S, Y	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.259 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.183	α = 89.98
b = 173.681	β = 95.42
c = 183.162	γ = 92.14

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Wagner, T., Ermler, U., Shima, S.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
PRESTO	Japan	--

Revision History  

• 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