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UniProtKB - Q5JI38 (SPEBH_THEKO)

Entry version 95 (23 Feb 2022)
Sequence version 1 (15 Feb 2005)
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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%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

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%5Fsection">'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 <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 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

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 functionHydrolase
Biological processPolyamine biosynthesis, Spermidine biosynthesis
LigandManganese, Metal-binding

Enzyme and pathway databases

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%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:
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%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
Ordered Locus Names:TK0882
<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>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%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 identifieri69014 [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 lineageiArchaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus ›
<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
  • UP000000536 <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 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 or proteolytic cleavage.<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

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

More...SMRi		Q5JI38

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

Belongs to the arginase family.PROSITE-ProRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		arCOG01700, Archaea

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_039478_0_2_2

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q5JI38

Identification of Orthologs from Complete Genome Data

More...OMAi		YELTTIM

Database of Orthologous Groups

More...OrthoDBi		52310at2157

Database for complete collections of gene phylogenies

More...PhylomeDBi		Q5JI38

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

The PANTHER Classification System

More...PANTHERi		PTHR11358, PTHR11358, 1 hit

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%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.

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

SMRiQ5JI38
ModBaseiSearch...

Protein-protein interaction databases

STRINGi69014.TK0882

Genome annotation databases

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

Phylogenomic databases

eggNOGiarCOG01700, Archaea
HOGENOMiCLU_039478_0_2_2
InParanoidiQ5JI38
OMAiYELTTIM
OrthoDBi52310at2157
PhylomeDBiQ5JI38

Enzyme and pathway databases

UniPathwayiUPA00248
BRENDAi3.5.3.24, 5246

Family and domain databases

InterProiView protein in InterPro
IPR005925, Agmatinase-rel
IPR006035, Ureohydrolase
IPR023696, Ureohydrolase_dom_sf
PANTHERiPTHR11358, PTHR11358, 1 hit
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

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 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%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: July 9, 2014
Last sequence update: February 15, 2005
Last modified: February 23, 2022
This is version 95 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

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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