5T5M

TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANOTHERMOBACTER WOLFEII, TRIGONAL FORM AT 2.5 A.

PDB DOI: https://doi.org/10.2210/pdb5T5M/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanothermobacter wolfeii
Mutation(s): No

Deposited: 2016-08-31 Released: 2016-10-19
Deposition Author(s): Wagner, T., Ermler, U., Shima, S.
Funding Organization(s): Max Planck Society, PRESTO

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 ?
R-Value Free: 0.182
R-Value Work: 0.158
R-Value Observed: 0.159

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 27846502 Search on PubMed
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-Stra?e 10, 35043 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 207.51 kDa
Atom Count: 14,415
Modelled Residue Count: 1,815
Deposited Residue Count: 1,832
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase subunit fwdA	A	569	Methanothermobacter wolfeii	Mutation(s): 0 EC: 1.2.99.5
UniProt
Find proteins for O74030 (Methanothermobacter wolfeii) Explore O74030 Go to UniProtKB: O74030
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O74030
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase subunit fwdB	B	432	Methanothermobacter wolfeii	Mutation(s): 0 EC: 1.2.99.5
UniProt
Find proteins for O74032 (Methanothermobacter wolfeii) Explore O74032 Go to UniProtKB: O74032
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O74032
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C	C	270	Methanothermobacter wolfeii	Mutation(s): 0 EC: 1.2.99.5 (PDB Primary Data), 1.2.7.12 (UniProt)
UniProt
Find proteins for O74031 (Methanothermobacter wolfeii) Explore O74031 Go to UniProtKB: O74031
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O74031
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase subunit fwdD	D	130	Methanothermobacter wolfeii	Mutation(s): 0 EC: 1.2.99.5
UniProt
Find proteins for O74029 (Methanothermobacter wolfeii) Explore O74029 Go to UniProtKB: O74029
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O74029
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase subunit fwdF	E [auth F]	349	Methanothermobacter wolfeii	Mutation(s): 0
UniProt
Find proteins for O74028 (Methanothermobacter wolfeii) Explore O74028 Go to UniProtKB: O74028
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O74028
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase subunit fwdG	F [auth G]	82	Methanothermobacter wolfeii	Mutation(s): 0
UniProt
Find proteins for Q1MVD4 (Methanothermobacter wolfeii) Explore Q1MVD4 Go to UniProtKB: Q1MVD4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1MVD4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD Query on MGD Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	P [auth B], Q [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		Interactions Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain P [auth B] Focus chain Q [auth B]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain CA [auth G] SDF format, chain DA [auth G] SDF format, chain N [auth B] SDF format, chain U [auth F] SDF format, chain V [auth F] SDF format, chain W [auth F] SDF format, chain X [auth F] SDF format, chain Y [auth F] SDF format, chain Z [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain N [auth B] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth F]	AA [auth F] BA [auth F] CA [auth G] DA [auth G] N [auth B] AA [auth F], BA [auth F], CA [auth G], DA [auth G], N [auth B], U [auth F], V [auth F], W [auth F], X [auth F], Y [auth F], Z [auth F]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain N [auth B] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain N [auth B] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F]
W Query on W Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain T [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain T [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain T [auth D]	K [auth A], L [auth A], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth D] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
H2S Query on H2S Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain S [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain S [auth C]	G [auth A], J [auth A], S [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth A] Focus chain S [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 ?
R-Value Free: 0.182
R-Value Work: 0.158
R-Value Observed: 0.159
Space Group: P 3₂ 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 105.543	α = 90
b = 105.543	β = 90
c = 340.549	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-10-19

Deposition Author(s):

Wagner, T.

Ermler, U.

Shima, S.

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

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: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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5T5M

TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANOTHERMOBACTER WOLFEII, TRIGONAL FORM AT 2.5 A.

The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

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Entity ID: 3

UniProt

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Entity ID: 4

UniProt

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Entity ID: 5

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Entity ID: 6

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)