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Protein

N(1)-aminopropylagmatine ureohydrolase

Gene

TK0882

Organism
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
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

Involved in the biosynthesis of polyamines which are thought to support the growth of thermophilic microorganisms under high-temperature conditions. It seems that long-chain and branched-chain of polyamines effectively stabilize DNA and RNA, respectively. Catalyzes the decarboxylation of N1-(3-aminopropyl)agmatine to yield spermidine and urea. It can also use agmatine to yield putrescine.1 Publication

Miscellaneous

In T.kodakarensis, two kinds of synthetic pathways from agmatine to spermidine are predicted. One is the pathway via putrescine (pathway I), and the other is that via N1-aminopropylagmatine (pathway II) (PubMed:20675472).1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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

Mn2+PROSITE-ProRule annotationNote: Binds 2 manganese ions per subunit.PROSITE-ProRule annotation

<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 1.86 sec(-1) for ureohydrolase activity with agmatine as substrate (at pH 7.5 and 70 degrees Celsius). Kcat is 1.01 sec(-1) for ureohydrolase activity with N1-aminopropylagmatine as substrate (at pH 7.5 and 70 degrees Celsius).
  1. KM=6.42 µM for N1-aminopropylagmatine (at pH 7.5 and 70 degrees Celsius)1 Publication
  2. KM=486 µM for agmatine (at pH 7.5 and 70 degrees Celsius)1 Publication

    Temperature dependencei

    Optimum temperature is 90 degrees Celsius.1 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: spermidine biosynthesis

    This protein is involved in the pathway spermidine biosynthesis, which is part of Amine and polyamine biosynthesis.
    View all proteins of this organism that are known to be involved in the pathway spermidine biosynthesis and in Amine and polyamine biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ 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 bindingi114Manganese 1PROSITE-ProRule annotation1
    Metal bindingi133Manganese 1PROSITE-ProRule annotation1
    Metal bindingi133Manganese 2PROSITE-ProRule annotation1
    Metal bindingi135Manganese 2PROSITE-ProRule annotation1
    Metal bindingi137Manganese 1PROSITE-ProRule annotation1
    <p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei144Important for catalytic activityBy similarity1
    Metal bindingi213Manganese 1PROSITE-ProRule annotation1
    Metal bindingi213Manganese 2PROSITE-ProRule annotation1
    Metal bindingi215Manganese 2PROSITE-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 functionHydrolase
    Biological processPolyamine biosynthesis, Spermidine biosynthesis
    LigandManganese, Metal-binding

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    MetaCyc:MONOMER-16735
    TKOD69014:G1G2A-875-MONOMER

    BRENDA Comprehensive Enzyme Information System

    More...
    BRENDAi
    3.5.3.24 5246

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

    More...
    UniPathwayi
    UPA00248

    <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_and_taxonomy_section">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:
    N(1)-aminopropylagmatine ureohydrolase (EC:3.5.3.24)
    Alternative name(s):
    Agmatinase (EC:3.5.3.11)
    Protein SpeB homolog
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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
    Ordered Locus Names:TK0882
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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>OrganismiThermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 identifieri69014 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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
    • UP000000536 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">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

    GO - Cellular componenti

    Keywords - Cellular componenti

    Cytoplasm

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    <p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

    Cells lacking this gene show to a decreased growth rate at 85 degrees Celsius and a severe growth defect at 93 degrees Celsius. This mutant accumulates N1-aminopropylagmatine and agmatine at 85 degrees Celsius.1 Publication

    <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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004298621 – 288N(1)-aminopropylagmatine ureohydrolaseAdd BLAST288

    <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

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    69014.TK0882

    <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

    Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

    More...
    ProteinModelPortali
    Q5JI38

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

    More...
    SMRi
    Q5JI38

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    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

    Belongs to the arginase family.PROSITE-ProRule annotation

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    arCOG01700 Archaea
    COG0010 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000204321

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    Q5JI38

    KEGG Orthology (KO)

    More...
    KOi
    K01480

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    SINHGTY

    Database of Orthologous Groups

    More...
    OrthoDBi
    POG093Z078T

    Family and domain databases

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR005925 Agmatinase-rel
    IPR006035 Ureohydrolase
    IPR023696 Ureohydrolase_dom_sf

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF00491 Arginase, 1 hit

    PIRSF; a whole-protein classification database

    More...
    PIRSFi
    PIRSF036979 Arginase, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF52768 SSF52768, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR01230 agmatinase, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS51409 ARGINASE_2, 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_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

    Q5JI38-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MEFLYTYETL KLEFPLVEPE KARFILLGVP FDGTTSYKAG ARFGPTLIRQ
    60 70 80 90 100
    ATLNLESYIL DYDLDIAELP IADIGDIAVV AGDPRKTADR VRETLEELKK
    110 120 130 140 150
    ANPKAIPILL GGEHSQTLGA VEALKPASYV VFDAHLDLRN SYEDNPYNHA
    160 170 180 190 200
    CVARRISELG VKEAIFGIRS GTKEEVDFAR ERDIPWVHAR DYSFDAFVDL
    210 220 230 240 250
    VEALPEPVYL SIDIDVFDLS MVPSTGTPEA GGLRFWEVVE AIEWLVEKKE
    260 270 280
    IAGFDIMEVA GEKLGDPTAL TAAKLLFYSI GAMAKFGR
    Length:288
    Mass (Da):31,979
    Last modified:February 15, 2005 - 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:i83BD96B02438C1BF
    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
    AP006878 Genomic DNA Translation: BAD85071.1

    NCBI Reference Sequences

    More...
    RefSeqi
    WP_011249833.1, NC_006624.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    BAD85071; BAD85071; TK0882

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    3234601

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    tko:TK0882

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|69014.16.peg.861

    <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
    AP006878 Genomic DNA Translation: BAD85071.1
    RefSeqiWP_011249833.1, NC_006624.1

    3D structure databases

    ProteinModelPortaliQ5JI38
    SMRiQ5JI38
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi69014.TK0882

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAD85071; BAD85071; TK0882
    GeneIDi3234601
    KEGGitko:TK0882
    PATRICifig|69014.16.peg.861

    Phylogenomic databases

    eggNOGiarCOG01700 Archaea
    COG0010 LUCA
    HOGENOMiHOG000204321
    InParanoidiQ5JI38
    KOiK01480
    OMAiSINHGTY
    OrthoDBiPOG093Z078T

    Enzyme and pathway databases

    UniPathwayi
    UPA00248

    BioCyciMetaCyc:MONOMER-16735
    TKOD69014:G1G2A-875-MONOMER
    BRENDAi3.5.3.24 5246

    Family and domain databases

    InterProiView protein in InterPro
    IPR005925 Agmatinase-rel
    IPR006035 Ureohydrolase
    IPR023696 Ureohydrolase_dom_sf
    PfamiView protein in Pfam
    PF00491 Arginase, 1 hit
    PIRSFiPIRSF036979 Arginase, 1 hit
    SUPFAMiSSF52768 SSF52768, 1 hit
    TIGRFAMsiTIGR01230 agmatinase, 1 hit
    PROSITEiView protein in PROSITE
    PS51409 ARGINASE_2, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    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 nameiSPEBH_THEKO
    <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: Q5JI38
    <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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 9, 2014
    Last sequence update: February 15, 2005
    Last modified: December 5, 2018
    This is version 84 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

    Complete proteome, Reference proteome

    Documents

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