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Entry version 106 (02 Jun 2021)
Sequence version 3 (18 May 2010)
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Protein

(R)-2-hydroxyglutaryl-CoA dehydratase, subunit beta

Gene

hgdB

Organism
Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / VR4)
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

Involved in the fermentation of L-glutamate via the hydroxyglutarate pathway (PubMed:3691501).

Catalyzes the reversible syn-elimination of water from (R)-2-hydroxyglutaryl-CoA to yield (E)-glutaconyl-CoA (PubMed:3691501, PubMed:7398622, PubMed:7607244).

The dehydration mechanism involves a transient one electron reduction of the thioester from (R)-2-hydroxyglutaryl-CoA, generating a ketyl radical (PubMed:7607244).

Prior to (E)-glutaconyl-CoA formation, the ketyl radical is subsequently reoxidized by electron transfer back to the HgdA-HgdB complex (CompD) to avoid change in oxidation state of the substrate (PubMed:7607244).

The appropriate redox state of dehydratase HgdA-HgdB complex (CompD) is maintained by HgdC (CompA) via hydrolysis of ATP and ATP-dependent electron transfer (PubMed:7607244).

Since the electron is recycled, the dehydratase is able to perform several turnovers with only catalytic amounts of ATP and substoichiometric amounts of HgdC (CompA) (PubMed:7607244).

3 Publications

<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

Protein has several cofactor binding sites:

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Activated by the HgdC. Reversibly inactivated by oxidants such as 2-nitrophenol, 3-nitrophenol, 4-nitrophenol, 4-nitrobenzoate, carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP) and chloramphenicol. Irreversibly inactivated by oxidants such as hydroxylamine and nitrite.1 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: L-glutamate degradation via hydroxyglutarate pathway

This protein is involved in step 4 of the subpathway that synthesizes crotonoyl-CoA from L-glutamate.1 Publication This subpathway is part of the pathway L-glutamate degradation via hydroxyglutarate pathway, which is itself part of Amino-acid degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes crotonoyl-CoA from L-glutamate, the pathway L-glutamate degradation via hydroxyglutarate pathway and in Amino-acid degradation.

<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 functionLyase
Ligand4Fe-4S, Flavoprotein, FMN, Iron, Iron-sulfur, Magnesium, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
AFER591001:G1GH7-1877-MONOMER
MetaCyc:MONOMER-1044

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
4.2.1.167, 85

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

More...
UniPathwayi
UPA00533;UER00687

<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:
(R)-2-hydroxyglutaryl-CoA dehydratase, subunit beta1 Publication (EC:4.2.1.1673 Publications)
Alternative name(s):
(R)-2-hydroxyglutaryl-CoA dehydratase, component D1 Publication
<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:hgdB1 Publication
Ordered Locus Names:Acfer_1814
<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>OrganismiAcidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / VR4)
<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 identifieri591001 [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 lineageiBacteriaFirmicutesNegativicutesAcidaminococcalesAcidaminococcaceaeAcidaminococcus
<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
  • UP000001902 <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 provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Keywords - Cellular componenti

Cytoplasm

<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 methionineiRemoved2 Publications
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000839642 – 379(R)-2-hydroxyglutaryl-CoA dehydratase, subunit betaAdd BLAST378

<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 (R)-2-hydroxyglutaryl-CoA dehydratase enzyme system is a heterodimer composed of an alpha subunit (HgdA) and a beta subunit (HgdB).

1 Publication1 Publication

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
591001.Acfer_1814

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P11570

Database of comparative protein structure models

More...
ModBasei
Search...

<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

<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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG1775, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_053697_0_0_9

Identification of Orthologs from Complete Genome Data

More...
OMAi
SYICRIP

Database of Orthologous Groups

More...
OrthoDBi
1815612at2

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR010327, FldB/FldC_alpha/beta

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF06050, HGD-D, 1 hit

<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.

P11570-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAISALIEEF QKVSASPKTM LAKYKAQGKK AIGCLPYYVP EELVYAAGMV
60 70 80 90 100
PMGVWGCNGK QEVRSKEYCA SFYCTIAQQS LEMLLDGTLD GLDGIITPVL
110 120 130 140 150
CDTLRPMSQN FKVAMKDKMP VIFLAHPQVR QNAAGKQFTY DAYSEVKGHL
160 170 180 190 200
EEICGHEITN DAILDAIKVY NKSRAARREF CKLANEHPDL IPASVRATVL
210 220 230 240 250
RAAYFMLKDE YTEKLEELNK ELAAAPAGKF DGHKVVVSGI IYNMPGILKA
260 270 280 290 300
MDDNKLAIAA DDCAYESRSF AVDAPEDLDN GLQALAVQFS KQKNDVLLYD
310 320 330 340 350
PEFAKNTRSE HVCNLVKESG AEGLIVFMMQ FCDPEEMEYP DLKKALDAHH
360 370
IPHVKIGVDQ MTRDFGQAQT ALEAFAESL
Length:379
Mass (Da):42,028
Last modified:May 18, 2010 - v3
<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:iF9B9C0A633AB7809
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti244M → T in CAA32466 (PubMed:2659350).Curated1
Sequence conflicti283Q → H in CAA32466 (PubMed:2659350).Curated1
Sequence conflicti313C → G in CAA32466 (PubMed:2659350).Curated1

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
X14252 Genomic DNA Translation: CAA32466.1
CP001859 Genomic DNA Translation: ADB48168.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S04478, DWDXBF

NCBI Reference Sequences

More...
RefSeqi
WP_012939151.1, NC_013740.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ADB48168; ADB48168; Acfer_1814

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
afn:Acfer_1814

<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
X14252 Genomic DNA Translation: CAA32466.1
CP001859 Genomic DNA Translation: ADB48168.1
PIRiS04478, DWDXBF
RefSeqiWP_012939151.1, NC_013740.1

3D structure databases

SMRiP11570
ModBaseiSearch...

Protein-protein interaction databases

STRINGi591001.Acfer_1814

Genome annotation databases

EnsemblBacteriaiADB48168; ADB48168; Acfer_1814
KEGGiafn:Acfer_1814

Phylogenomic databases

eggNOGiCOG1775, Bacteria
HOGENOMiCLU_053697_0_0_9
OMAiSYICRIP
OrthoDBi1815612at2

Enzyme and pathway databases

UniPathwayiUPA00533;UER00687
BioCyciAFER591001:G1GH7-1877-MONOMER
MetaCyc:MONOMER-1044
BRENDAi4.2.1.167, 85

Family and domain databases

InterProiView protein in InterPro
IPR010327, FldB/FldC_alpha/beta
PfamiView protein in Pfam
PF06050, HGD-D, 1 hit

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 nameiHGDB_ACIFV
<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: P11570
Secondary accession number(s): D2RM66
<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: October 1, 1989
Last sequence update: May 18, 2010
Last modified: June 2, 2021
This is version 106 of the entry and version 3 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, Reference proteome

Documents

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