5ODI

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus cocrystallized with CoM-SH

PDB DOI: https://doi.org/10.2210/pdb5ODI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanothermococcus thermolithotrophicus DSM 2095
Mutation(s): No

Deposited: 2017-07-05 Released: 2017-08-30
Deposition Author(s): Wagner, T., Koch, J., Ermler, U., Shima, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.241
R-Value Work: 0.202
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.

Wagner, T., Koch, J., Ermler, U., Shima, S.

(2017) Science 357: 699-703

PubMed: 28818947 Search on PubMed
DOI: https://doi.org/10.1126/science.aan0425
Primary Citation of Related Structures:
5ODC, 5ODH, 5ODI, 5ODQ, 5ODR

PubMed Abstract:
In methanogenic archaea, the carbon dioxide (CO ₂) fixation and methane-forming steps are linked through the heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhAGD) complex that uses flavin-based electron bifurcation to reduce ferredoxin and the heterodisulfide of coenzymes M and B. Here, we present the structure of the native heterododecameric HdrABC-MvhAGD complex at 2.15-angstrom resolution. HdrB contains two noncubane [4Fe-4S] clusters composed of fused [3Fe-4S]-[2Fe-2S] units sharing 1 iron (Fe) and 1 sulfur (S), which were coordinated at the CCG motifs. Soaking experiments showed that the heterodisulfide is clamped between the two noncubane [4Fe-4S] clusters and homolytically cleaved, forming coenzyme M and B bound to each iron. Coenzymes are consecutively released upon one-by-one electron transfer. The HdrABC-MvhAGD atomic model serves as a structural template for numerous HdrABC homologs involved in diverse microbial metabolic pathways.

Organizational Affiliation

Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 464.95 kDa
Atom Count: 31,986
Modelled Residue Count: 4,015
Deposited Residue Count: 4,082
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterodisulfide reductase, subunit A	A, G	654	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0
UniProt
Find proteins for A0A2D0TCB9 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A2D0TCB9 Go to UniProtKB: A0A2D0TCB9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2D0TCB9
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterodisulfide reductase, subunit B	B, H	291	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0 EC: 1.8.98.1
UniProt
Find proteins for A0A2D0TCB4 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A2D0TCB4 Go to UniProtKB: A0A2D0TCB4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2D0TCB4
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterodisulfide reductase, subunit C	C, I	184	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0
UniProt
Find proteins for A0A2D0TC97 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A2D0TC97 Go to UniProtKB: A0A2D0TC97
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2D0TC97
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-viologen reducing hydrogenase, subunit D	D, J	140	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0
UniProt
Find proteins for A0A2D0TC98 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A2D0TC98 Go to UniProtKB: A0A2D0TC98
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2D0TC98
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-viologen reducing hydrogenase, subunit G	E, K	299	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0 EC: 1.12.1.2
UniProt
Find proteins for A0A2D0TC99 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A2D0TC99 Go to UniProtKB: A0A2D0TC99
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2D0TC99
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-viologen reducing hydrogenase, subunit A	F, L	473	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0 EC: 1.12.1.2
UniProt
Find proteins for A0A2D0TCA6 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A2D0TCA6 Go to UniProtKB: A0A2D0TCA6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2D0TCA6
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Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain LA [auth G] SDF format, chain N [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain N [auth A]	LA [auth G], N [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain LA [auth G] Focus chain N [auth A] Interactions & Density Focus chain LA [auth G] Focus chain N [auth A]
PE3 Query on PE3 Download Ideal Coordinates CCD File SDF format, chain JA [auth G] MOL2 format, chain JA [auth G]	JA [auth G]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C₂₈ H₅₈ O₁₅ ILLKMACMBHTSHP-UHFFFAOYSA-N		Interactions Focus chain JA [auth G] Interactions & Density Focus chain JA [auth G]
9S8 Query on 9S8 Download Ideal Coordinates CCD File SDF format, chain UA [auth H] SDF format, chain TA [auth H] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain TA [auth H] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	TA [auth H], UA [auth H], W [auth B], X [auth B]	Non-cubane [4Fe-4S]-cluster Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain TA [auth H] Focus chain UA [auth H] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain TA [auth H] Focus chain UA [auth H] Focus chain W [auth B] Focus chain X [auth B]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain PA [auth G] SDF format, chain Q [auth A] SDF format, chain AA [auth C] SDF format, chain AB [auth K] SDF format, chain BB [auth K] SDF format, chain CB [auth K] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain O [auth A] SDF format, chain OA [auth G] SDF format, chain P [auth A] SDF format, chain QA [auth G] SDF format, chain R [auth A] SDF format, chain RA [auth G] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain XA [auth I] SDF format, chain YA [auth I] SDF format, chain Z [auth C] MOL2 format, chain PA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth K] MOL2 format, chain BB [auth K] MOL2 format, chain CB [auth K] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth G] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth G] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain XA [auth I] MOL2 format, chain YA [auth I] MOL2 format, chain Z [auth C]	AA [auth C] AB [auth K] BB [auth K] CB [auth K] EA [auth E] AA [auth C], AB [auth K], BB [auth K], CB [auth K], EA [auth E], FA [auth E], GA [auth E], MA [auth G], NA [auth G], O [auth A], OA [auth G], P [auth A], PA [auth G], Q [auth A], QA [auth G], R [auth A], RA [auth G], S [auth A], T [auth A], XA [auth I], YA [auth I], Z [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth K] Focus chain BB [auth K] Focus chain CB [auth K] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain O [auth A] Focus chain OA [auth G] Focus chain P [auth A] Focus chain PA [auth G] Focus chain Q [auth A] Focus chain QA [auth G] Focus chain R [auth A] Focus chain RA [auth G] Focus chain S [auth A] Focus chain T [auth A] Focus chain XA [auth I] Focus chain YA [auth I] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth K] Focus chain BB [auth K] Focus chain CB [auth K] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain O [auth A] Focus chain OA [auth G] Focus chain P [auth A] Focus chain PA [auth G] Focus chain Q [auth A] Focus chain QA [auth G] Focus chain R [auth A] Focus chain RA [auth G] Focus chain S [auth A] Focus chain T [auth A] Focus chain XA [auth I] Focus chain YA [auth I] Focus chain Z [auth C]
NFU Query on NFU Download Ideal Coordinates CCD File SDF format, chain EB [auth L] SDF format, chain HA [auth F] MOL2 format, chain EB [auth L] MOL2 format, chain HA [auth F]	EB [auth L], HA [auth F]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C₃ H Fe N₂ Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N		Interactions Focus chain EB [auth L] Focus chain HA [auth F] Interactions & Density Focus chain EB [auth L] Focus chain HA [auth F]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain ZA [auth J] MOL2 format, chain BA [auth D] MOL2 format, chain ZA [auth J]	BA [auth D], ZA [auth J]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain ZA [auth J] Interactions & Density Focus chain BA [auth D] Focus chain ZA [auth J]
COM Query on COM Download Ideal Coordinates CCD File SDF format, chain VA [auth H] SDF format, chain Y [auth B] MOL2 format, chain VA [auth H] MOL2 format, chain Y [auth B]	VA [auth H], Y [auth B]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain VA [auth H] Focus chain Y [auth B] Interactions & Density Focus chain VA [auth H] Focus chain Y [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain DA [auth D] MOL2 format, chain DA [auth D]	DA [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain DA [auth D] Interactions & Density Focus chain DA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain DB [auth K] SDF format, chain SA [auth G] SDF format, chain V [auth A] SDF format, chain WA [auth H] MOL2 format, chain U [auth A] MOL2 format, chain DB [auth K] MOL2 format, chain SA [auth G] MOL2 format, chain V [auth A] MOL2 format, chain WA [auth H]	DB [auth K], SA [auth G], U [auth A], V [auth A], WA [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DB [auth K] Focus chain SA [auth G] Focus chain U [auth A] Focus chain V [auth A] Focus chain WA [auth H] Interactions & Density Focus chain DB [auth K] Focus chain SA [auth G] Focus chain U [auth A] Focus chain V [auth A] Focus chain WA [auth H]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain KA [auth G] SDF format, chain M [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain KA [auth G] MOL2 format, chain M [auth A]	CA [auth D], KA [auth G], M [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth D] Focus chain KA [auth G] Focus chain M [auth A] Interactions & Density Focus chain CA [auth D] Focus chain KA [auth G] Focus chain M [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain FB [auth L] SDF format, chain IA [auth F] MOL2 format, chain FB [auth L] MOL2 format, chain IA [auth F]	FB [auth L], IA [auth F]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain FB [auth L] Focus chain IA [auth F] Interactions & Density Focus chain FB [auth L] Focus chain IA [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.241
R-Value Work: 0.202
R-Value Observed: 0.203
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 370.528	α = 90
b = 97.077	β = 109.43
c = 135.149	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-08-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-08-30
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.

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5ODI

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus cocrystallized with CoM-SH

Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.

Entity ID: 1

UniProt

Entity Groups

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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

UniProt

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Entity ID: 6

UniProt

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)