5ODH | pdb_00005odh

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with heterodisulfide for 3.5 minutes

PDB DOI: https://doi.org/10.2210/pdb5ODH/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: 2.20 Å
R-Value Free:
0.245 (Depositor), 0.247 (DCC)
R-Value Work:
0.214 (Depositor), 0.218 (DCC)
R-Value Observed:
0.215 (Depositor)

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

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 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: 467.28 kDa
Atom Count: 32,106
Modeled Residue Count: 4,019
Deposited Residue Count: 4,082
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterodisulfide reductase, subunit A	A, G	654	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0 EC: 1.8
UniProt
Find proteins for A0A2D0TCB9 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A2D0TCB9 Go to UniProtKB: A0A2D0TCB9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2D0TCB9
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Reference Sequence

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| 3D Structure

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2D0TCB4
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterodisulfide reductase, subunit C	C, I	184	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0 EC: 1.8.98.1
UniProt
Find proteins for A0A2D0TC97 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A2D0TC97 Go to UniProtKB: A0A2D0TC97
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2D0TC97
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Reference Sequence

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| 3D Structure

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 EC: 1.8.98.1
UniProt
Find proteins for A0A2D0TC98 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A2D0TC98 Go to UniProtKB: A0A2D0TC98
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2D0TC98
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Reference Sequence

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| 3D Structure

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 (PDB Primary Data), 1.12.99.6 (UniProt)
UniProt
Find proteins for A0A2D0TC99 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A2D0TC99 Go to UniProtKB: A0A2D0TC99
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2D0TC99
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Reference Sequence

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| 3D Structure

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 (PDB Primary Data), 1.12.99.6 (UniProt)
UniProt
Find proteins for A0A2D0TCA6 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A2D0TCA6 Go to UniProtKB: A0A2D0TCA6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2D0TCA6
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Reference Sequence

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain WA [auth G] MOL2 format, chain U [auth A] MOL2 format, chain WA [auth G] mmCIF format, chain U [auth A] mmCIF format, chain WA [auth G]	U [auth A], WA [auth G]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain U [auth A] Focus chain WA [auth G] Interactions & Density Focus chain U [auth A] Focus chain WA [auth G]
PE3 Query on PE3 Download:Ideal Coordinates CCD File SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain T [auth A] SDF format, chain IB [auth L] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain T [auth A] MOL2 format, chain IB [auth L] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth F] mmCIF format, chain T [auth A] mmCIF format, chain IB [auth L]	IA [auth F], IB [auth L], JA [auth F], T [auth A]	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 IA [auth F] Focus chain IB [auth L] Focus chain JA [auth F] Focus chain T [auth A] Interactions & Density Focus chain IA [auth F] Focus chain IB [auth L] Focus chain JA [auth F] Focus chain T [auth A]
9S8 Query on 9S8 Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain XA [auth H] SDF format, chain YA [auth H] SDF format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain XA [auth H] MOL2 format, chain YA [auth H] MOL2 format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain XA [auth H] mmCIF format, chain YA [auth H] mmCIF format, chain W [auth B]	V [auth B], W [auth B], XA [auth H], YA [auth H]	Non-cubane [4Fe-4S]-cluster Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Focus chain W [auth B] Focus chain XA [auth H] Focus chain YA [auth H] Interactions & Density Focus chain V [auth B] Focus chain W [auth B] Focus chain XA [auth H] Focus chain YA [auth H]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BB [auth I] SDF format, chain CB [auth I] SDF format, chain EA [auth E] SDF format, chain FB [auth K] SDF format, chain GA [auth E] SDF format, chain GB [auth K] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain P [auth A] SDF format, chain PA [auth G] SDF format, chain QA [auth G] SDF format, chain R [auth A] SDF format, chain RA [auth G] SDF format, chain Q [auth A] SDF format, chain OA [auth G] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain FA [auth E] SDF format, chain EB [auth K] SDF format, chain BA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BB [auth I] MOL2 format, chain CB [auth I] MOL2 format, chain EA [auth E] MOL2 format, chain FB [auth K] MOL2 format, chain GA [auth E] MOL2 format, chain GB [auth K] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth G] MOL2 format, chain QA [auth G] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain EB [auth K] MOL2 format, chain BA [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BB [auth I] mmCIF format, chain CB [auth I] mmCIF format, chain EA [auth E] mmCIF format, chain FB [auth K] mmCIF format, chain GA [auth E] mmCIF format, chain GB [auth K] mmCIF format, chain MA [auth G] mmCIF format, chain NA [auth G] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth G] mmCIF format, chain QA [auth G] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain OA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain FA [auth E] mmCIF format, chain EB [auth K] mmCIF format, chain BA [auth C]	AA [auth C] BA [auth C] BB [auth I] CB [auth I] EA [auth E] AA [auth C], BA [auth C], BB [auth I], CB [auth I], EA [auth E], EB [auth K], FA [auth E], FB [auth K], GA [auth E], GB [auth K], M [auth A], MA [auth G], N [auth A], 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]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain BB [auth I] Focus chain CB [auth I] Focus chain EA [auth E] Focus chain EB [auth K] Focus chain FA [auth E] Focus chain FB [auth K] Focus chain GA [auth E] Focus chain GB [auth K] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] 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] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain BB [auth I] Focus chain CB [auth I] Focus chain EA [auth E] Focus chain EB [auth K] Focus chain FA [auth E] Focus chain FB [auth K] Focus chain GA [auth E] Focus chain GB [auth K] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] 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]
TP7 Query on TP7 Download:Ideal Coordinates CCD File SDF format, chain AB [auth H] MOL2 format, chain AB [auth H] mmCIF format, chain AB [auth H]	AB [auth H]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain AB [auth H] Interactions & Density Focus chain AB [auth H]
NFU Query on NFU Download:Ideal Coordinates CCD File SDF format, chain JB [auth L] SDF format, chain KA [auth F] MOL2 format, chain JB [auth L] MOL2 format, chain KA [auth F] mmCIF format, chain JB [auth L] mmCIF format, chain KA [auth F]	JB [auth L], KA [auth F]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C₃ H Fe N₂ Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N		Interactions Focus chain JB [auth L] Focus chain KA [auth F] Interactions & Density Focus chain JB [auth L] Focus chain KA [auth F]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain DB [auth J] SDF format, chain CA [auth D] MOL2 format, chain DB [auth J] MOL2 format, chain CA [auth D] mmCIF format, chain DB [auth J] mmCIF format, chain CA [auth D]	CA [auth D], DB [auth J]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DB [auth J] Interactions & Density Focus chain CA [auth D] Focus chain DB [auth J]
COM Query on COM Download:Ideal Coordinates CCD File SDF format, chain ZA [auth H] SDF format, chain X [auth B] MOL2 format, chain ZA [auth H] MOL2 format, chain X [auth B] mmCIF format, chain ZA [auth H] mmCIF format, chain X [auth B]	X [auth B], ZA [auth H]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain X [auth B] Focus chain ZA [auth H] Interactions & Density Focus chain X [auth B] Focus chain ZA [auth H]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] MOL2 format, chain DA [auth D] mmCIF 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 HA [auth E] SDF format, chain SA [auth G] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain S [auth A] SDF format, chain HB [auth K] MOL2 format, chain HA [auth E] MOL2 format, chain SA [auth G] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain S [auth A] MOL2 format, chain HB [auth K] mmCIF format, chain HA [auth E] mmCIF format, chain SA [auth G] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain S [auth A] mmCIF format, chain HB [auth K]	HA [auth E] HB [auth K] S [auth A] SA [auth G] Y [auth B] HA [auth E], HB [auth K], S [auth A], SA [auth G], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain HA [auth E] Focus chain HB [auth K] Focus chain S [auth A] Focus chain SA [auth G] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain HA [auth E] Focus chain HB [auth K] Focus chain S [auth A] Focus chain SA [auth G] Focus chain Y [auth B] Focus chain Z [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain UA [auth G] SDF format, chain VA [auth G] MOL2 format, chain UA [auth G] MOL2 format, chain VA [auth G] mmCIF format, chain UA [auth G] mmCIF format, chain VA [auth G]	UA [auth G], VA [auth G]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain UA [auth G] Focus chain VA [auth G] Interactions & Density Focus chain UA [auth G] Focus chain VA [auth G]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain LA [auth F] SDF format, chain TA [auth G] SDF format, chain KB [auth L] MOL2 format, chain LA [auth F] MOL2 format, chain TA [auth G] MOL2 format, chain KB [auth L] mmCIF format, chain LA [auth F] mmCIF format, chain TA [auth G] mmCIF format, chain KB [auth L]	KB [auth L], LA [auth F], TA [auth G]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain KB [auth L] Focus chain LA [auth F] Focus chain TA [auth G] Interactions & Density Focus chain KB [auth L] Focus chain LA [auth F] Focus chain TA [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.245 (Depositor), 0.247 (DCC)
R-Value Work: 0.214 (Depositor), 0.218 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 366.381	α = 90
b = 97.104	β = 108.43
c = 133.974	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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
Version 1.2: 2024-10-23
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

5ODH | pdb_00005odh

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with heterodisulfide for 3.5 minutes

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)