5ODI

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

Summary for 5ODI

• Entry DOI: 10.2210/pdb5odi/pdb
• Descriptor: Heterodisulfide reductase, subunit A, GLYCEROL, Non-cubane [4Fe-4S]-cluster, ... (18 entities in total)
• Functional Keywords: heterodisulfide reductase, [nife]-hydrogenase, fes cluster, ferredoxin, ccg motif, methanogenesis, flavoprotein, flavin-based electron bifurcation, [2fe-2s] cluster, macromolecular complex, anaerobic, thioredoxin, metabolism, oxydoreductase., oxidoreductase
• Biological source: Methanothermococcus thermolithotrophicus DSM 2095; More
• Total number of polymer chains: 12
• Total formula weight: 464945.48

Authors

Wagner, T.,Koch, J.,Ermler, U.,Shima, S. (deposition date: 2017-07-05, release date: 2017-08-30, Last modification date: 2025-10-01)

Primary citation

Wagner, T.,Koch, J.,Ermler, U.,Shima, S.
Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
Science, 357:699-703, 2017

PubMed Abstract: In methanogenic archaea, the carbon dioxide (CO) 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.

PubMed: 28818947
DOI: 10.1126/science.aan0425

Experimental method

X-RAY DIFFRACTION (2.4 Å)