5ODC | pdb_00005odc

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus at 2.3 A resolution

PDB DOI: https://doi.org/10.2210/pdb5ODC/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: 2.30 Å
R-Value Free:
0.200 (Depositor), 0.214 (DCC)
R-Value Work:
0.178 (Depositor), 0.193 (DCC)
R-Value Observed:
0.179 (Depositor)

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: 465.76 kDa
Atom Count: 32,275
Modelled Residue Count: 4,011
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 EC: 1.8.98.1 (PDB Primary Data), 1.8 (UniProt)
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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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
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2D0TCB4
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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 EC: 1.8.98.1
UniProt
Find proteins for A0A2D0TC97 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A2D0TC97 Go to UniProtKB: A0A2D0TC97
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UniProt Group	A0A2D0TC97
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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 EC: 1.8.98.1
UniProt
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UniProt Group	A0A2D0TC98
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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: 1.12.99.6 (PDB Primary Data), 1.12.1.2 (UniProt)
UniProt
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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: 1.12.99.6 (PDB Primary Data), 1.12.1.2 (UniProt)
UniProt
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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 M [auth A] SDF format, chain SA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain SA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain SA [auth G]	M [auth A], SA [auth G]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain M [auth A] Focus chain SA [auth G] Interactions & Density Focus chain M [auth A] Focus chain SA [auth G]
PE3 Query on PE3 Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [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 P [auth A] Interactions & Density Focus chain P [auth A]
9S8 Query on 9S8 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain GB [auth H] SDF format, chain HB [auth H] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain GB [auth H] MOL2 format, chain HB [auth H] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain GB [auth H] mmCIF format, chain HB [auth H]	AA [auth B], BA [auth B], GB [auth H], HB [auth H]	Non-cubane [4Fe-4S]-cluster Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain GB [auth H] Focus chain HB [auth H] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain GB [auth H] Focus chain HB [auth H]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain BB [auth G] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain JB [auth I] SDF format, chain KA [auth E] SDF format, chain KB [auth I] SDF format, chain LA [auth E] SDF format, chain MA [auth E] SDF format, chain MB [auth K] SDF format, chain NB [auth K] SDF format, chain OB [auth K] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain WA [auth G] SDF format, chain XA [auth G] SDF format, chain YA [auth G] SDF format, chain ZA [auth G] MOL2 format, chain AB [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain JB [auth I] MOL2 format, chain KA [auth E] MOL2 format, chain KB [auth I] MOL2 format, chain LA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain MB [auth K] MOL2 format, chain NB [auth K] MOL2 format, chain OB [auth K] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth G] mmCIF format, chain AB [auth G] mmCIF format, chain BB [auth G] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain JB [auth I] mmCIF format, chain KA [auth E] mmCIF format, chain KB [auth I] mmCIF format, chain LA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain MB [auth K] mmCIF format, chain NB [auth K] mmCIF format, chain OB [auth K] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain WA [auth G] mmCIF format, chain XA [auth G] mmCIF format, chain YA [auth G] mmCIF format, chain ZA [auth G]	AB [auth G] BB [auth G] EA [auth C] FA [auth C] JB [auth I] AB [auth G], BB [auth G], EA [auth C], FA [auth C], JB [auth I], KA [auth E], KB [auth I], LA [auth E], MA [auth E], MB [auth K], NB [auth K], OB [auth K], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], WA [auth G], XA [auth G], YA [auth G], ZA [auth G]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain BB [auth G] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain JB [auth I] Focus chain KA [auth E] Focus chain KB [auth I] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain MB [auth K] Focus chain NB [auth K] Focus chain OB [auth K] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth G] Focus chain BB [auth G] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain JB [auth I] Focus chain KA [auth E] Focus chain KB [auth I] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain MB [auth K] Focus chain NB [auth K] Focus chain OB [auth K] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G]
NFU Query on NFU Download Ideal Coordinates CCD File SDF format, chain RA [auth F] SDF format, chain TB [auth L] MOL2 format, chain RA [auth F] MOL2 format, chain TB [auth L] mmCIF format, chain RA [auth F] mmCIF format, chain TB [auth L]	RA [auth F], TB [auth L]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C₃ H Fe N₂ Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N		Interactions Focus chain RA [auth F] Focus chain TB [auth L] Interactions & Density Focus chain RA [auth F] Focus chain TB [auth L]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain LB [auth J] MOL2 format, chain HA [auth D] MOL2 format, chain LB [auth J] mmCIF format, chain HA [auth D] mmCIF format, chain LB [auth J]	HA [auth D], LB [auth J]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain LB [auth J] Interactions & Density Focus chain HA [auth D] Focus chain LB [auth J]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain IA [auth D] MOL2 format, chain IA [auth D] mmCIF format, chain IA [auth D]	IA [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain IA [auth D] Interactions & Density Focus chain IA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CB [auth G] SDF format, chain DA [auth B] SDF format, chain DB [auth G] SDF format, chain EB [auth G] SDF format, chain FB [auth G] SDF format, chain GA [auth C] SDF format, chain JA [auth D] SDF format, chain NA [auth E] SDF format, chain PB [auth K] SDF format, chain QB [auth K] SDF format, chain RB [auth K] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain CB [auth G] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth G] MOL2 format, chain EB [auth G] MOL2 format, chain FB [auth G] MOL2 format, chain GA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain NA [auth E] MOL2 format, chain PB [auth K] MOL2 format, chain QB [auth K] MOL2 format, chain RB [auth K] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain CB [auth G] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth G] mmCIF format, chain EB [auth G] mmCIF format, chain FB [auth G] mmCIF format, chain GA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain NA [auth E] mmCIF format, chain PB [auth K] mmCIF format, chain QB [auth K] mmCIF format, chain RB [auth K] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	CB [auth G] DA [auth B] DB [auth G] EB [auth G] FB [auth G] CB [auth G], DA [auth B], DB [auth G], EB [auth G], FB [auth G], GA [auth C], JA [auth D], NA [auth E], PB [auth K], QB [auth K], RB [auth K], W [auth A], X [auth A], Y [auth A], Z [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CB [auth G] Focus chain DA [auth B] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain JA [auth D] Focus chain NA [auth E] Focus chain PB [auth K] Focus chain QB [auth K] Focus chain RB [auth K] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain CB [auth G] Focus chain DA [auth B] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain JA [auth D] Focus chain NA [auth E] Focus chain PB [auth K] Focus chain QB [auth K] Focus chain RB [auth K] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain O [auth A] SDF format, chain QA [auth F] SDF format, chain UA [auth G] SDF format, chain VA [auth G] MOL2 format, chain CA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain QA [auth F] MOL2 format, chain UA [auth G] MOL2 format, chain VA [auth G] mmCIF format, chain CA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain QA [auth F] mmCIF format, chain UA [auth G] mmCIF format, chain VA [auth G]	CA [auth B], O [auth A], QA [auth F], UA [auth G], VA [auth G]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth B] Focus chain O [auth A] Focus chain QA [auth F] Focus chain UA [auth G] Focus chain VA [auth G] Interactions & Density Focus chain CA [auth B] Focus chain O [auth A] Focus chain QA [auth F] Focus chain UA [auth G] Focus chain VA [auth G]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain OA [auth F] SDF format, chain SB [auth L] MOL2 format, chain OA [auth F] MOL2 format, chain SB [auth L] mmCIF format, chain OA [auth F] mmCIF format, chain SB [auth L]	OA [auth F], SB [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain OA [auth F] Focus chain SB [auth L] Interactions & Density Focus chain OA [auth F] Focus chain SB [auth L]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain IB [auth I] SDF format, chain PA [auth F] MOL2 format, chain IB [auth I] MOL2 format, chain PA [auth F] mmCIF format, chain IB [auth I] mmCIF format, chain PA [auth F]	IB [auth I], PA [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain IB [auth I] Focus chain PA [auth F] Interactions & Density Focus chain IB [auth I] Focus chain PA [auth F]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain TA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain TA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain TA [auth G]	N [auth A], TA [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain TA [auth G] Interactions & Density Focus chain N [auth A] Focus chain TA [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.200 (Depositor), 0.214 (DCC)
R-Value Work: 0.178 (Depositor), 0.193 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 378.047	α = 90
b = 98.446	β = 110.7
c = 137.884	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: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary