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Entry version 22 (26 Feb 2020)
Sequence version 1 (24 Jun 2015)
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Protein

Dihydromethanophenazine:CoB--CoM heterodisulfide reductase subunit D

Gene

hdrD

Organism
Methanosarcina thermophila (strain ATCC 43570 / DSM 1825 / OCM 12 / VKM B-1830 / TM-1)
Status
Reviewed-Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Part of a complex that catalyzes the reversible reduction of CoM-S-S-CoB to the thiol-coenzymes H-S-CoM (coenzyme M) and H-S-CoB (coenzyme B) (PubMed:9654152, PubMed:9665708, PubMed:11034998). Electrons probably transfer from phenazine to the high potential 4Fe cluster in HdrD subunit, then to the low potential heme in HdrE subunit and finally to CoM-S-S-CoB (PubMed:11034998).3 Publications

Miscellaneous

Methanophenazine seems to mediate electron transfer from F(420)H2 dehydrogenase to the dihydromethanophenazine:CoB--CoM heterodisulfide reductase.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

[4Fe-4S] clusterPROSITE-ProRule annotation1 PublicationNote: Binds 2 [4Fe-4S] cluster.PROSITE-ProRule annotation1 Publication

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

kcat is 74 sec(-1) at 25 degrees Celsius.1 Publication
  1. KM=92 µM for reduced 2-hydroxyphenazine1 Publication
  2. KM=144 µM for CoM-S-S-CoB1 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: coenzyme M-coenzyme B heterodisulfide reduction

    This protein is involved in step 1 of the subpathway that synthesizes coenzyme B and coenzyme M from coenzyme M-coenzyme B heterodisulfide.1 Publication
    Proteins known to be involved in this subpathway in this organism are:
    1. CoB--CoM heterodisulfide reductase iron-sulfur subunit A (MSTHT_2519), Dihydromethanophenazine:CoB--CoM heterodisulfide reductase subunit D (hdrD), Dihydromethanophenazine:CoB--CoM heterodisulfide reductase subunit E (hdrE), CoB--CoM heterodisulfide reductase iron-sulfur subunit A (MSTHT_0375)
    This subpathway is part of the pathway coenzyme M-coenzyme B heterodisulfide reduction, which is itself part of Cofactor metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes coenzyme B and coenzyme M from coenzyme M-coenzyme B heterodisulfide, the pathway coenzyme M-coenzyme B heterodisulfide reduction and in Cofactor metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi24Iron-sulfur 1 (4Fe-4S)PROSITE-ProRule annotation1
    Metal bindingi27Iron-sulfur 1 (4Fe-4S)PROSITE-ProRule annotation1
    Metal bindingi30Iron-sulfur 1 (4Fe-4S)PROSITE-ProRule annotation1
    Metal bindingi34Iron-sulfur 2 (4Fe-4S)PROSITE-ProRule annotation1
    Metal bindingi90Iron-sulfur 2 (4Fe-4S)PROSITE-ProRule annotation1
    Metal bindingi93Iron-sulfur 2 (4Fe-4S)PROSITE-ProRule annotation1
    Metal bindingi96Iron-sulfur 2 (4Fe-4S)PROSITE-ProRule annotation1
    Metal bindingi100Iron-sulfur 1 (4Fe-4S)PROSITE-ProRule annotation1

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionOxidoreductase
    Biological processMethanogenesis
    Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding

    Enzyme and pathway databases

    UniPathway: a resource for the exploration and annotation of metabolic pathways

    More...
    UniPathwayi
    UPA00647;UER00700

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
    Recommended name:
    Dihydromethanophenazine:CoB--CoM heterodisulfide reductase subunit DCurated (EC:1.8.98.11 Publication2 Publications)
    Alternative name(s):
    CoB--CoM heterodisulfide reductase iron-sulfur subunit DCurated
    Coenzyme B:coenzyme M:methanophenazine oxidoreductase subunit DCurated
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:hdrD
    ORF Names:MSTHT_2244Imported
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiMethanosarcina thermophila (strain ATCC 43570 / DSM 1825 / OCM 12 / VKM B-1830 / TM-1)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri523844 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiArchaeaEuryarchaeotaStenosarchaea groupMethanomicrobiaMethanosarcinalesMethanosarcinaceaeMethanosarcina
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000066529 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved
    <p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004438562 – 409Dihydromethanophenazine:CoB--CoM heterodisulfide reductase subunit DAdd BLAST408

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    The dihydromethanophenazine:CoB--CoM heterodisulfide reductase is composed of two subunits; HdrD and HdrE.

    1 Publication

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini14 – 444Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd BLAST31
    Domaini81 – 1104Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd BLAST30

    <p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Belongs to the HdrD family.Curated

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_023081_2_0_2

    KEGG Orthology (KO)

    More...
    KOi
    K08264

    Database of Orthologous Groups

    More...
    OrthoDBi
    21885at2157

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    1.10.1060.10, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR017896 4Fe4S_Fe-S-bd
    IPR017900 4Fe4S_Fe_S_CS
    IPR004017 Cys_rich_dom
    IPR009051 Helical_ferredxn

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF02754 CCG, 2 hits
    PF13183 Fer4_8, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF46548 SSF46548, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00198 4FE4S_FER_1, 2 hits
    PS51379 4FE4S_FER_2, 2 hits

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

    A0A0E3NEE1-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MAKRNPSIDT KNLTAVQLME LDACVRCGEC VKWCPTYAAS GEKPGLAPRD
    60 70 80 90 100
    KILRWRQYMN KSYGLKARLF GPQEIPISEL EEFKDDVHGC TTCGICSTVC
    110 120 130 140 150
    EAGINTVELW ESMRANLVKK GIGPYGKQNM FPKLIGQYRN PYMKDQKDRL
    160 170 180 190 200
    AWVPPDVKIE DKADIVYFTG CTAGYNQLAL AFATSRVLNK LGIKFAMLGE
    210 220 230 240 250
    DEWCCGSALI RTGQAHINNV PYELAKHNVE AIQKKGAKKV LFACAGCFRA
    260 270 280 290 300
    AKVDWPRLLG KELPFEVVHV SEFLAGLIKE GKIKWEKSIN KTVTYHDPCH
    310 320 330 340 350
    LGRHVGVFDA PRYVLSHIPG VKFVEMDRIK EFQRCCGAGG GVKAGLPDLA
    360 370 380 390 400
    MAVAESRVKD ALDTKADILS SCCPFCKRNL MDGRDSLKVD LVVEDVIELV

    AEALNLETK
    Length:409
    Mass (Da):45,454
    Last modified:June 24, 2015 - v1
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i3D93654EC149FF32
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    CP009501 Genomic DNA Translation: AKB14002.1

    NCBI Reference Sequences

    More...
    RefSeqi
    WP_048167969.1, NZ_CP009501.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AKB14002; AKB14002; MSTHT_2244

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    41602355

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    mthr:MSTHT_2244

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|523844.20.peg.2748

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP009501 Genomic DNA Translation: AKB14002.1
    RefSeqiWP_048167969.1, NZ_CP009501.1

    3D structure databases

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    SWISS-MODEL Interactive Workspace

    More...
    SWISS-MODEL-Workspacei
    Submit a new modelling project...

    Genome annotation databases

    EnsemblBacteriaiAKB14002; AKB14002; MSTHT_2244
    GeneIDi41602355
    KEGGimthr:MSTHT_2244
    PATRICifig|523844.20.peg.2748

    Phylogenomic databases

    HOGENOMiCLU_023081_2_0_2
    KOiK08264
    OrthoDBi21885at2157

    Enzyme and pathway databases

    UniPathwayiUPA00647;UER00700

    Family and domain databases

    Gene3Di1.10.1060.10, 1 hit
    InterProiView protein in InterPro
    IPR017896 4Fe4S_Fe-S-bd
    IPR017900 4Fe4S_Fe_S_CS
    IPR004017 Cys_rich_dom
    IPR009051 Helical_ferredxn
    PfamiView protein in Pfam
    PF02754 CCG, 2 hits
    PF13183 Fer4_8, 1 hit
    SUPFAMiSSF46548 SSF46548, 1 hit
    PROSITEiView protein in PROSITE
    PS00198 4FE4S_FER_1, 2 hits
    PS51379 4FE4S_FER_2, 2 hits

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiHDRD_METTT
    <p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: A0A0E3NEE1
    <p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 25, 2018
    Last sequence update: June 24, 2015
    Last modified: February 26, 2020
    This is version 22 of the entry and version 1 of the sequence. See complete history.
    <p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    Direct protein sequencing

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families
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