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Entry version 63 (02 Dec 2020)
Sequence version 1 (01 Jun 2003)
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Protein

4-hydroxyphenylacetate decarboxylase glycyl radical subunit

Gene

hpdB

Organism
Clostridioides difficile (Peptoclostridium difficile)
Status
Reviewed-Annotation score:

Annotation score:5 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

Glycyl radical subunit of the HPA decarboxylase that decarboxylates phenylacetates with a hydroxyl group in the p-position. Active toward 4-hydroxyphenylacetate, 3,4-dihydroxyphenylacetate and to a lesser extent p-hydroxymandelate (2-hydroxy-2-(4-hydroxyphenyl)acetate), forming 4-methylphenol, 4-methylcatechol and 4-hydroxybenzylalcohol, respectively. Is likely involved in the catabolism of aromatic amino acids such as tyrosine fermentation. 4-methylphenol (p-cresol) formation provides metabolic toxicity, which may benefit the pathogen C.difficile by suppression of the endogenous gastrointestinal microflora, allowing the development of gastrointestinal infections (PubMed:11231288, PubMed:16878993). The large subunit is the catalytic subunit that binds the substrate (By similarity).By similarity2 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 <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

Enzyme activity catalyzed by the HPA decarboxylase complex is rapidly and irreversibly inactivated by oxygen. Competitively inhibited by p-hydroxyphenylacetamide. Not inhibited by m- or o-hydroxyphenyl-acetate, p-hydroxybenzoate or p-hydroxyphenylpropionate.1 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 110 sec(-1) for the decarboxylation of 4-hydroxyphenylacetate. kcat is 65 sec(-1) for the decarboxylation of 3,4-hydroxyphenylacetate.1 Publication
  1. KM=649 µM for 4-hydroxyphenylacetate1 Publication
  2. KM=410 µM for 3,4-dihydroxyphenylacetate1 Publication
  1. Vmax=14.97 µmol/min/mg enzyme for the decarboxylation of 4-hydroxyphenylacetate1 Publication
  2. Vmax=8.82 µmol/min/mg enzyme for the decarboxylation of 3,4-hydroxyphenylacetate1 Publication

pH dependencei

Optimum pH is 7.0.1 Publication

Temperature dependencei

Has a half-life of 15 minutes at 30 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei3484-hydroxyphenylacetateBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei507Cysteine radical intermediateBy similarity1
Binding sitei5074-hydroxyphenylacetateBy similarity1
Active sitei509Proton donorBy similarity1
Binding sitei5404-hydroxyphenylacetateBy similarity1
Binding sitei6414-hydroxyphenylacetateBy similarity1

<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

<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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

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BioCyci
MetaCyc:MONOMER-18507

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
4.1.1.83, 1473

SABIO-RK: Biochemical Reaction Kinetics Database

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SABIO-RKi
Q84F16

<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:
4-hydroxyphenylacetate decarboxylase glycyl radical subunit1 Publication (EC:4.1.1.832 Publications)
Short name:
HPA decarboxylase glycyl radical subunit
Alternative name(s):
4-hydroxyphenylacetate decarboxylase catalytic beta subunitBy similarity
4-hydroxyphenylacetate decarboxylase large subunit1 Publication
p-hydroxyphenylacetate decarboxylase large subunit1 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:hpdBImported
<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>OrganismiClostridioides difficile (Peptoclostridium difficile)
<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 identifieri1496 [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 lineageiBacteriaFirmicutesClostridiaClostridialesPeptostreptococcaceaeClostridioides

<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 methionineiRemoved1 Publication
<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_50000705262 – 9024-hydroxyphenylacetate decarboxylase glycyl radical subunit1 PublicationAdd BLAST901

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei877Glycine radicalPROSITE-ProRule annotation1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Phosphorylated on serine. Phosphorylation may trigger the formation of the active heterooctamers and thereby regulates enzyme activity.1 Publication
Requires the activating protein HpdA to generate the key active site glycyl radical that is involved in catalysis.2 Publications

Keywords - PTMi

Organic radical, Phosphoprotein

<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

Heterooctamer consisting of 4 large (HpdB) subunits and 4 small (HpdC) subunits. Also forms a catalytically inactive homodimer.

2 Publications

<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
Q84F16

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

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>Domaini38 – 774PFLPROSITE-ProRule annotationAdd BLAST737
Domaini782 – 902Glycine radicalPROSITE-ProRule annotationAdd BLAST121

<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

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001150, Gly_radical
IPR004184, PFL_dom

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01228, Gly_radical, 1 hit
PF02901, PFL-like, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51149, GLY_RADICAL_2, 1 hit
PS51554, PFL, 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.

Q84F16-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSQSKEDKIR SILEAKNIKS NFQNKENLSE FNEKKASKRA EDLLDVYYNT
60 70 80 90 100
LSTADMEFPY WYNREYRKSD GDIPVVRRAK ALKAAFSHMT PNIIPGEKIV
110 120 130 140 150
MQKTRHYRGS FPMPWVSESF FVAQGEQMRE EAKKLASNTA DELTKFGSGG
160 170 180 190 200
GNVTESFGNV VSIAGKFGMR KEEVPVLVKM AKEWVGKSVE DLGFHYEKMM
210 220 230 240 250
PDYDLKENLM STLICMFDSG YTLPQGREVI NYFYPLNYGL DGIIEMAKEC
260 270 280 290 300
KKAVAGNASG DGLIGMDRLY FYEAVIQVIE GLQTWILNYA KHAKYLESIE
310 320 330 340 350
TDLEAKKEYS DLVEILEHIA HKQPRTFREA LQLTYTIHIA SVNEDAISGM
360 370 380 390 400
SIGRFGQILY PWYEQDIEKG LITKEEVIEL LELYRIKITC IDCFASAGVN
410 420 430 440 450
GGVLSGNTFN TLSIGGLKED GSTGANELEE LLLEASMRCR TPQPSLTMLY
460 470 480 490 500
DEKLPEDFLM KAAECTKLGS GYPAWVNNSN GTTFMMKQFA DEGMTVEEAR
510 520 530 540 550
AFALGGCLET SPGCWKQLTL NGKTYSIAGG AGQSAGSGVH FIANPKILEL
560 570 580 590 600
VLMNGKDYRM NIQVFEPHNK PLDTYEEVIE VFKDYYKQAI NVLERANNIE
610 620 630 640 650
LDIWRKFDTS IINSLLKPDC LDKGQHIGNM GYRYNATLNV ETCGTVTMVN
660 670 680 690 700
SFAALKKLVY DDKAFTIEEI KDAILNNFGF KDALEVGNYS MADQVKVDKT
710 720 730 740 750
GKYDAIYKAC LDAPKYGNND LYADNILKNY EVWLSKVCEE AQSLYAKKMY
760 770 780 790 800
PCQISVSTHG PQGAATLATP DGRLSGTTYS DGSVSAYAGT DKNGVYALFE
810 820 830 840 850
SATIWDQAVV QNSQMNLKLH PTTIKGQQGT KKLLDLTRSY LRKGGFHIQY
860 870 880 890 900
NVVDSETLKD AQKNPDNYRQ LMVRVAGFTQ YWCELGKPIQ DEVIARTEYE

GV
Length:902
Mass (Da):101,276
Last modified:June 1, 2003 - 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:i07F152C7CEBDF87C
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AJ543425 Genomic DNA Translation: CAD65889.1

NCBI Reference Sequences

More...
RefSeqi
WP_009895226.1, NZ_RRAL01000038.1

Genome annotation databases

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ag:CAD65889

<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
AJ543425 Genomic DNA Translation: CAD65889.1
RefSeqiWP_009895226.1, NZ_RRAL01000038.1

3D structure databases

SMRiQ84F16
ModBaseiSearch...

Genome annotation databases

KEGGiag:CAD65889

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-18507
BRENDAi4.1.1.83, 1473
SABIO-RKiQ84F16

Family and domain databases

InterProiView protein in InterPro
IPR001150, Gly_radical
IPR004184, PFL_dom
PfamiView protein in Pfam
PF01228, Gly_radical, 1 hit
PF02901, PFL-like, 1 hit
PROSITEiView protein in PROSITE
PS51149, GLY_RADICAL_2, 1 hit
PS51554, PFL, 1 hit

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 nameiHPDL_CLODI
<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: Q84F16
<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: January 11, 2011
Last sequence update: June 1, 2003
Last modified: December 2, 2020
This is version 63 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. SIMILARITY comments
    Index of protein domains and families
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