PDBsum entry 5odc

Oxidoreductase

PDB id

5odc

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Contents

			Protein chains

					653 a.a.


					291 a.a.


					184 a.a.


					138 a.a.


					298 a.a.


					447 a.a.


					173 a.a.

			Ligands

					FAD ×2


					ACT ×5


					PE3


					SF4 ×22


					GOL ×15


					9S8 ×4


					FES ×2


					TRS


					NFU ×2

			Metals

					_NA ×2


					_CA ×2


					_MG ×2

			Waters ×832

PDB id:

5odc

Links

Name:

Oxidoreductase

Title:

Heterodisulfide reductase / [nife]-hydrogenase complex from methanothermococcus thermolithotrophicus at 2.3 a resolution

Structure:

Heterodisulfide reductase, subunit a. Chain: a, g. Other_details: gb ref wp_018154264.1. Heterodisulfide reductase, subunit b. Chain: b, h. Other_details: gb ref wp_018154154.1, this subunit contains two pentacoordinated non cubane [4fe-4s] cluster. Heterodisulfide reductase, subunit c. Chain: c, i.

Source:

Methanothermococcus thermolithotrophicus dsm 2095. Organism_taxid: 523845. Cell_line: /. Atcc: /. Organ: /. Tissue: /. Tissue: /

Resolution:

2.30Å

R-factor:

0.179

R-free:

0.200

Authors:

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

Key ref:

T.Wagner et al. (2017). Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. Science, 357, 699-703. PubMed id: 28818947

Date:

05-Jul-17

Release date:

30-Aug-17

PROCHECK

	Headers

	References

Protein chains

A0A2D0TCB9 (A0A2D0TCB9_METTL) - CoB--CoM heterodisulfide reductase iron-sulfur subunit A from Methanothermococcus thermolithotrophicus DSM 2095

Seq: Struc:

Seq: Struc:					654 a.a. 653 a.a.

Protein chains

A0A2D0TCB4 (A0A2D0TCB4_METTL) - Heterodisulfide reductase, subunit B from Methanothermococcus thermolithotrophicus DSM 2095

Seq: Struc:					291 a.a. 291 a.a.

Protein chain

A0A2D0TC97 (A0A2D0TC97_METTL) - Heterodisulfide reductase, subunit C from Methanothermococcus thermolithotrophicus DSM 2095

Seq: Struc:					184 a.a. 184 a.a.

Protein chains

A0A2D0TC98 (A0A2D0TC98_METTL) - Methyl-viologen reducing hydrogenase subunit D from Methanothermococcus thermolithotrophicus DSM 2095

Seq: Struc:					140 a.a. 138 a.a.

Protein chains

A0A2D0TC99 (A0A2D0TC99_METTL) - Methyl-viologen reducing hydrogenase subunit G from Methanothermococcus thermolithotrophicus DSM 2095

Seq: Struc:					299 a.a. 298 a.a.

Protein chains

A0A2D0TCA6 (A0A2D0TCA6_METTL) - Methyl-viologen reducing hydrogenase subunit A from Methanothermococcus thermolithotrophicus DSM 2095

Seq: Struc:					473 a.a. 447 a.a.

Protein chain

A0A2D0TC97 (A0A2D0TC97_METTL) - Heterodisulfide reductase, subunit C from Methanothermococcus thermolithotrophicus DSM 2095

Seq: Struc:					184 a.a. 173 a.a.

Key:

PfamA domain

Secondary structure



		Enzyme reactions

Enzyme class 2:

Chains A, G: E.C.1.8.-.-

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Enzyme class 3:

Chains B, C, D, H, I, J: E.C.1.8.98.1 - dihydromethanophenazine:CoB--CoM heterodisulfide reductase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Pathway:

Reaction:

methanophenazine + coenzyme B + coenzyme M = dihydromethanophenazine + coenzyme M-coenzyme B heterodisulfide

methanophenazine	+	coenzyme B	+	coenzyme M	=	dihydromethanophenazine	+	coenzyme M-coenzyme B heterodisulfide

Cofactor:

Heme; Iron-sulfur

Heme	Iron-sulfur

Enzyme class 4:

Chains E, F, K, L: E.C.1.12.1.2 - hydrogen dehydrogenase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

H2 + NAD⁺ = NADH + H⁺

H2	+	NAD(+)	=	NADH	+	H(+)

Cofactor:

FAD or FMN; Iron-sulfur; Ni(2+)

FAD		FMN	Iron-sulfur	Ni(2+)

Enzyme class 5:

Chains E, F, K, L: E.C.1.12.99.6 - hydrogenase (acceptor).

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

H2 + A = AH2

Cofactor:

Iron-sulfur; Ni(2+)

Iron-sulfur

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

	Science 357:699-703 (2017)
PubMed id: 28818947

Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
T.Wagner, J.Koch, U.Ermler, S.Shima.

ABSTRACT

In methanogenic archaea, the carbon dioxide (CO₂) 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.