HDRD_METTT
ID HDRD_METTT Reviewed; 409 AA.
AC A0A0E3NEE1;
DT 25-APR-2018, integrated into UniProtKB/Swiss-Prot.
DT 24-JUN-2015, sequence version 1.
DT 03-AUG-2022, entry version 27.
DE RecName: Full=Dihydromethanophenazine:CoB--CoM heterodisulfide reductase subunit D {ECO:0000305};
DE EC=1.8.98.1 {ECO:0000269|PubMed:11034998, ECO:0000269|PubMed:9654152, ECO:0000305|PubMed:9665708};
DE AltName: Full=CoB--CoM heterodisulfide reductase iron-sulfur subunit D {ECO:0000305};
DE AltName: Full=Coenzyme B:coenzyme M:methanophenazine oxidoreductase subunit D {ECO:0000305};
GN Name=hdrD; ORFNames=MSTHT_2244 {ECO:0000312|EMBL:AKB14002.1};
OS Methanosarcina thermophila (strain ATCC 43570 / DSM 1825 / OCM 12 / VKM
OS B-1830 / TM-1).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanosarcinales; Methanosarcinaceae; Methanosarcina.
OX NCBI_TaxID=523844;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43570 / DSM 1825 / OCM 12 / VKM B-1830 / TM-1;
RA Henriksen J.R., Luke J., Reinhart S., Benedict M.N., Youngblut N.D.,
RA Metcalf M.E., Whitaker R.J., Metcalf W.W.;
RT "Methanogenic archaea and the global carbon cycle.";
RL Submitted (JUL-2014) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP PROTEIN SEQUENCE OF 2-21, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND
RP SUBUNIT.
RC STRAIN=ATCC 43570 / DSM 1825 / OCM 12 / VKM B-1830 / TM-1;
RX PubMed=9665708; DOI=10.1021/bi9726483;
RA Simianu M., Murakami E., Brewer J.M., Ragsdale S.W.;
RT "Purification and properties of the heme- and iron-sulfur-containing
RT heterodisulfide reductase from Methanosarcina thermophila.";
RL Biochemistry 37:10027-10039(1998).
RN [3]
RP FUNCTION, SOURCE OF ELECTRONS, AND CATALYTIC ACTIVITY.
RC STRAIN=ATCC 43570 / DSM 1825 / OCM 12 / VKM B-1830 / TM-1;
RX PubMed=9654152; DOI=10.1016/s0014-5793(98)00555-9;
RA Baeumer S., Murakami E., Brodersen J., Gottschalk G., Ragsdale S.W.,
RA Deppenmeier U.;
RT "The F420H2:heterodisulfide oxidoreductase system from Methanosarcina
RT species. 2-Hydroxyphenazine mediates electron transfer from F420H2
RT dehydrogenase to heterodisulfide reductase.";
RL FEBS Lett. 428:295-298(1998).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND PATHWAY.
RC STRAIN=ATCC 43570 / DSM 1825 / OCM 12 / VKM B-1830 / TM-1;
RX PubMed=11034998; DOI=10.1074/jbc.m004809200;
RA Murakami E., Deppenmeier U., Ragsdale S.W.;
RT "Characterization of the intramolecular electron transfer pathway from 2-
RT hydroxyphenazine to the heterodisulfide reductase from Methanosarcina
RT thermophila.";
RL J. Biol. Chem. 276:2432-2439(2001).
CC -!- FUNCTION: Part of a complex that catalyzes the reversible reduction of
CC CoM-S-S-CoB to the thiol-coenzymes H-S-CoM (coenzyme M) and H-S-CoB
CC (coenzyme B) (PubMed:9654152, PubMed:9665708, PubMed:11034998).
CC Electrons probably transfer from phenazine to the high potential 4Fe
CC cluster in HdrD subunit, then to the low potential heme in HdrE subunit
CC and finally to CoM-S-S-CoB (PubMed:11034998).
CC {ECO:0000269|PubMed:11034998, ECO:0000269|PubMed:9654152,
CC ECO:0000269|PubMed:9665708}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=coenzyme B + coenzyme M + methanophenazine = coenzyme M-
CC coenzyme B heterodisulfide + dihydromethanophenazine;
CC Xref=Rhea:RHEA:18085, ChEBI:CHEBI:29118, ChEBI:CHEBI:50375,
CC ChEBI:CHEBI:58319, ChEBI:CHEBI:58411, ChEBI:CHEBI:58596; EC=1.8.98.1;
CC Evidence={ECO:0000269|PubMed:11034998, ECO:0000269|PubMed:9654152,
CC ECO:0000305|PubMed:9665708};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00711,
CC ECO:0000269|PubMed:9665708};
CC Note=Binds 2 [4Fe-4S] cluster. {ECO:0000255|PROSITE-ProRule:PRU00711,
CC ECO:0000269|PubMed:9665708};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=92 uM for reduced 2-hydroxyphenazine
CC {ECO:0000269|PubMed:11034998};
CC KM=144 uM for CoM-S-S-CoB {ECO:0000269|PubMed:11034998};
CC Note=kcat is 74 sec(-1) at 25 degrees Celsius.
CC {ECO:0000269|PubMed:11034998};
CC -!- PATHWAY: Cofactor metabolism; coenzyme M-coenzyme B heterodisulfide
CC reduction; coenzyme B and coenzyme M from coenzyme M-coenzyme B
CC heterodisulfide: step 1/1. {ECO:0000305|PubMed:11034998}.
CC -!- SUBUNIT: The dihydromethanophenazine:CoB--CoM heterodisulfide reductase
CC is composed of two subunits; HdrD and HdrE.
CC {ECO:0000269|PubMed:9665708}.
CC -!- MISCELLANEOUS: Methanophenazine seems to mediate electron transfer from
CC F(420)H(2) dehydrogenase to the dihydromethanophenazine:CoB--CoM
CC heterodisulfide reductase. {ECO:0000305|PubMed:9654152}.
CC -!- SIMILARITY: Belongs to the HdrD family. {ECO:0000305}.
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DR EMBL; CP009501; AKB14002.1; -; Genomic_DNA.
DR RefSeq; WP_048167969.1; NZ_CP009501.1.
DR AlphaFoldDB; A0A0E3NEE1; -.
DR SMR; A0A0E3NEE1; -.
DR STRING; 523844.MSTHT_2244; -.
DR EnsemblBacteria; AKB14002; AKB14002; MSTHT_2244.
DR GeneID; 41602355; -.
DR KEGG; mthr:MSTHT_2244; -.
DR PATRIC; fig|523844.20.peg.2748; -.
DR HOGENOM; CLU_023081_2_0_2; -.
DR OrthoDB; 21885at2157; -.
DR UniPathway; UPA00647; UER00700.
DR Proteomes; UP000066529; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0051912; F:CoB--CoM heterodisulfide reductase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0015948; P:methanogenesis; IEA:UniProtKB-KW.
DR Gene3D; 1.10.1060.10; -; 1.
DR InterPro; IPR017896; 4Fe4S_Fe-S-bd.
DR InterPro; IPR017900; 4Fe4S_Fe_S_CS.
DR InterPro; IPR004017; Cys_rich_dom.
DR InterPro; IPR009051; Helical_ferredxn.
DR Pfam; PF02754; CCG; 2.
DR Pfam; PF13183; Fer4_8; 1.
DR PROSITE; PS00198; 4FE4S_FER_1; 2.
DR PROSITE; PS51379; 4FE4S_FER_2; 2.
PE 1: Evidence at protein level;
KW 4Fe-4S; Direct protein sequencing; Iron; Iron-sulfur; Metal-binding;
KW Methanogenesis; Oxidoreductase; Repeat.
FT INIT_MET 1
FT /note="Removed"
FT CHAIN 2..409
FT /note="Dihydromethanophenazine:CoB--CoM heterodisulfide
FT reductase subunit D"
FT /id="PRO_0000443856"
FT DOMAIN 14..44
FT /note="4Fe-4S ferredoxin-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT DOMAIN 81..110
FT /note="4Fe-4S ferredoxin-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 24
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 27
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 30
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 34
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 90
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 93
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 96
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 100
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
SQ SEQUENCE 409 AA; 45454 MW; 3D93654EC149FF32 CRC64;
MAKRNPSIDT KNLTAVQLME LDACVRCGEC VKWCPTYAAS GEKPGLAPRD KILRWRQYMN
KSYGLKARLF GPQEIPISEL EEFKDDVHGC TTCGICSTVC EAGINTVELW ESMRANLVKK
GIGPYGKQNM FPKLIGQYRN PYMKDQKDRL AWVPPDVKIE DKADIVYFTG CTAGYNQLAL
AFATSRVLNK LGIKFAMLGE DEWCCGSALI RTGQAHINNV PYELAKHNVE AIQKKGAKKV
LFACAGCFRA AKVDWPRLLG KELPFEVVHV SEFLAGLIKE GKIKWEKSIN KTVTYHDPCH
LGRHVGVFDA PRYVLSHIPG VKFVEMDRIK EFQRCCGAGG GVKAGLPDLA MAVAESRVKD
ALDTKADILS SCCPFCKRNL MDGRDSLKVD LVVEDVIELV AEALNLETK
