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UniProtKB - A0A031WDE4 (HYPD_CLODI)

Entry version 40 (07 Apr 2021)
Sequence version 1 (09 Jul 2014)
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Protein

Trans-4-hydroxy-L-proline dehydratase

Gene

pflD

Organism
Clostridioides difficile (Peptoclostridium difficile)
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

Glycine radical enzyme that catalyzes the dehydration of the non-proteinogenic amino acid trans-4-hydroxy-L-proline (Hyp) to produce delta1-pyrroline-5-carboxylate (P5C). Is involved in the anaerobic degradation of 4-hydroxyproline.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 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 45 sec(-1) for trans-4-hydroxy-L-proline as substrate.1 Publication
  1. KM=1.2 mM for trans-4-hydroxy-L-proline1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <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 sitei434Cysteine radical intermediateBy similarity1
    Active sitei436Proton acceptorBy 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

    Complete GO annotation on QuickGO ...

    GO - Biological processi

    Complete GO annotation on QuickGO ...

    <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

    <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:
    Trans-4-hydroxy-L-proline dehydratase1 Publication (EC:4.2.1.1721 Publication)
    Alternative name(s):
    Glycyl radical enzymeCurated
    Hyp dehydratase1 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:pflD1 Publication
    Synonyms:csdB_2Imported
    ORF Names:BGU81_07860Imported, BN1095_640054Imported, BN1096_740112Imported, BN1097_360077Imported, SAMEA3375004_02654Imported
    <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 lineageiBacteria › Firmicutes › Clostridia › Clostridiales › Peptostreptococcaceae › Clostridioides

    <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 '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_00004450271 – 789Trans-4-hydroxy-L-proline dehydrataseAdd BLAST789

    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 residuei765Glycine radicalPROSITE-ProRule annotation1 Publication1

    <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

    Requires the activating protein PflE to generate the key active site glycyl radical on Gly-765 that is involved in catalysis.1 Publication

    Keywords - PTMi

    Organic radical

    <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

    Secondary structure

    1789
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

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

    More...    SMRi    		A0A031WDE4

    Database of comparative protein structure models

    More...    ModBasei    		Search...

    Protein Data Bank in Europe - Knowledge Base

    More...    PDBe-KBi    		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>Domaini7 – 663PFLPROSITE-ProRule annotationAdd BLAST657
    Domaini670 – 789Glycine radicalPROSITE-ProRule annotationAdd BLAST120

    <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 glycyl radical enzyme (GRE) family. HYPD subfamily.Curated

    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.

    A0A031WDE4-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MARGTFERTK KLREESINAE PHISIERAVL MTEAYKKYEG SVEIPVLRAL 
            60         70         80         90        100
    SFKHYIENRT LSINDGELIV GEKGDSPNGA PTYPEICCHT MEDLEVMHNR 
           110        120        130        140        150
    DIINFSVSEE ARKIHKEEII PFWKKRQTRD KIINAMTPEW LAAYEAGMFT 
           160        170        180        190        200
    EFMEQRAPGH TVCGDTIYKK GFLDLKKDIE ARLKELDFLN DLDAYNKKAD 
           210        220        230        240        250
    LEAMAIACDA MVILGKRYAE KARQMAEEET DEAKKKDLLL IAETCDVVPA 
           260        270        280        290        300
    HKPETYHQAI QMYWFVHIGV TTELNIWDAF TPGRLDQHLN PFYERDVENG 
           310        320        330        340        350
    ILDRDRAQEL LECLWVKFNN QPAPPKVGIT LKESSTYTDF ANINTGGINP 
           360        370        380        390        400
    DGQDGVNEVS YIILDVMDEM KLIQPSSNVQ ISKKTPQKFL KRACEISRKG 
           410        420        430        440        450
    WGQPAFYNTE AIVQELMEAG KTIEDARLGG TSGCVETGCF GKEAYVLTGY 
           460        470        480        490        500
    MNIPKILELT LNNGYDPISK KQIGIETGDP RNFQSYEELF EAFKKQLHYM 
           510        520        530        540        550
    IDIKIEGNAV IENICAKHMP CPLMSTIVDD CIEKGKDYQR GGARYNTRYI 
           560        570        580        590        600
    QGVGIGTITD SLTAIKYNVF DKKKFDMDTL LKALDANFEG YEAILNLVSN 
           610        620        630        640        650
    KTPKYGNDDD YADEIMQEIF NAYYNEVTGR PTVCGGEYRV DMLPTTCHIY 
           660        670        680        690        700
    FGEIMGASPN GRLCAKPVSE GISPEKGGDT NGPTAVIKSC AKMDHIKTGG 
           710        720        730        740        750
    TLLNQRFAPS VVQGEKGLDN MANLVRAYFN MDGHHIQFNV FDKNVLLEAQ 
           760        770        780 
    KNPQDYKDLI VRVAGYSDHF NNLSRTLQDE IIGRTEQTF
    Length:789
    Mass (Da):89,175
    Last modified:July 9, 2014 - 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:i9CC72891AE3505E5
    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
    		LK932372 Genomic DNA Translation: CDS85123.1
    LK932529 Genomic DNA Translation: CDS89454.1
    LK933338 Genomic DNA Translation: CDT68933.1
    MPEQ01000010 Genomic DNA Translation: PBG28510.1
    FURH01000003 Genomic DNA Translation: SJT80202.1

    NCBI Reference Sequences

    More...    RefSeqi    		WP_021363977.1, NZ_VINA01000003.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...    EnsemblBacteriai    		PBG28510; PBG28510; BGU81_07860

    Database of genes from NCBI RefSeq genomes

    More...    GeneIDi    		57296828

    <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
    		LK932372 Genomic DNA Translation: CDS85123.1
    LK932529 Genomic DNA Translation: CDS89454.1
    LK933338 Genomic DNA Translation: CDT68933.1
    MPEQ01000010 Genomic DNA Translation: PBG28510.1
    FURH01000003 Genomic DNA Translation: SJT80202.1
    RefSeqiWP_021363977.1, NZ_VINA01000003.1

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...    PDBei

    Protein Data Bank RCSB

    More...    RCSB PDBi

    Protein Data Bank Japan

    More...    PDBji
    Links Updated
    		PDB entryMethodResolution (Å)ChainPositionsPDBsum
    6VXCX-ray2.05A/B/C/D/E/F/G/H1-789[»]
    6VXEX-ray2.46A/B/C/D/E/F/G/H1-789[»]
    SMRiA0A031WDE4
    ModBaseiSearch...
    PDBe-KBiSearch...

    Genome annotation databases

    EnsemblBacteriaiPBG28510; PBG28510; BGU81_07860
    GeneIDi57296828

    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 nameiHYPD_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: A0A031WDE4
    <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: September 12, 2018
    Last sequence update: July 9, 2014
    Last modified: April 7, 2021
    This is version 40 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

    3D-structure

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
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