SPEBH_THEKO
ID SPEBH_THEKO Reviewed; 288 AA.
AC Q5JI38;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=N(1)-aminopropylagmatine ureohydrolase;
DE EC=3.5.3.24;
DE AltName: Full=Agmatinase;
DE EC=3.5.3.11;
DE AltName: Full=Protein SpeB homolog;
GN OrderedLocusNames=TK0882;
OS Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS (Pyrococcus kodakaraensis (strain KOD1)).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=69014;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=15710748; DOI=10.1101/gr.3003105;
RA Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL Genome Res. 15:352-363(2005).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND SUBCELLULAR LOCATION.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=20675472; DOI=10.1128/jb.00279-10;
RA Morimoto N., Fukuda W., Nakajima N., Masuda T., Terui Y., Kanai T.,
RA Oshima T., Imanaka T., Fujiwara S.;
RT "Dual biosynthesis pathway for longer-chain polyamines in the
RT hyperthermophilic archaeon Thermococcus kodakarensis.";
RL J. Bacteriol. 192:4991-5001(2010).
CC -!- FUNCTION: Involved in the biosynthesis of polyamines which are thought
CC to support the growth of thermophilic microorganisms under high-
CC temperature conditions. It seems that long-chain and branched-chain of
CC polyamines effectively stabilize DNA and RNA, respectively. Catalyzes
CC the decarboxylation of N1-(3-aminopropyl)agmatine to yield spermidine
CC and urea. It can also use agmatine to yield putrescine.
CC {ECO:0000269|PubMed:20675472}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N(1)-aminopropylagmatine = spermidine + urea;
CC Xref=Rhea:RHEA:35827, ChEBI:CHEBI:15377, ChEBI:CHEBI:16199,
CC ChEBI:CHEBI:57834, ChEBI:CHEBI:64335; EC=3.5.3.24;
CC Evidence={ECO:0000269|PubMed:20675472};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=agmatine + H2O = putrescine + urea; Xref=Rhea:RHEA:13929,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:16199, ChEBI:CHEBI:58145,
CC ChEBI:CHEBI:326268; EC=3.5.3.11;
CC Evidence={ECO:0000269|PubMed:20675472};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00742};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000255|PROSITE-
CC ProRule:PRU00742};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=6.42 uM for N(1)-aminopropylagmatine (at pH 7.5 and 70 degrees
CC Celsius) {ECO:0000269|PubMed:20675472};
CC KM=486 uM for agmatine (at pH 7.5 and 70 degrees Celsius)
CC {ECO:0000269|PubMed:20675472};
CC Note=kcat is 1.86 sec(-1) for ureohydrolase activity with agmatine as
CC substrate (at pH 7.5 and 70 degrees Celsius). kcat is 1.01 sec(-1)
CC for ureohydrolase activity with N(1)-aminopropylagmatine as substrate
CC (at pH 7.5 and 70 degrees Celsius).;
CC Temperature dependence:
CC Optimum temperature is 90 degrees Celsius.
CC {ECO:0000269|PubMed:20675472};
CC -!- PATHWAY: Amine and polyamine biosynthesis; spermidine biosynthesis.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:20675472}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene show to a decreased
CC growth rate at 85 degrees Celsius and a severe growth defect at 93
CC degrees Celsius. This mutant accumulates N1-aminopropylagmatine and
CC agmatine at 85 degrees Celsius. {ECO:0000269|PubMed:20675472}.
CC -!- MISCELLANEOUS: In T.kodakarensis, two kinds of synthetic pathways from
CC agmatine to spermidine are predicted. One is the pathway via putrescine
CC (pathway I), and the other is that via N1-aminopropylagmatine (pathway
CC II) (PubMed:20675472). {ECO:0000305|PubMed:20675472}.
CC -!- SIMILARITY: Belongs to the arginase family. {ECO:0000255|PROSITE-
CC ProRule:PRU00742}.
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DR EMBL; AP006878; BAD85071.1; -; Genomic_DNA.
DR RefSeq; WP_011249833.1; NC_006624.1.
DR AlphaFoldDB; Q5JI38; -.
DR SMR; Q5JI38; -.
DR STRING; 69014.TK0882; -.
DR EnsemblBacteria; BAD85071; BAD85071; TK0882.
DR GeneID; 3234601; -.
DR KEGG; tko:TK0882; -.
DR PATRIC; fig|69014.16.peg.861; -.
DR eggNOG; arCOG01700; Archaea.
DR HOGENOM; CLU_039478_0_2_2; -.
DR InParanoid; Q5JI38; -.
DR OMA; YELTTIM; -.
DR OrthoDB; 52310at2157; -.
DR PhylomeDB; Q5JI38; -.
DR BioCyc; MetaCyc:MON-16735; -.
DR BRENDA; 3.5.3.24; 5246.
DR UniPathway; UPA00248; -.
DR Proteomes; UP000000536; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008783; F:agmatinase activity; IMP:UniProtKB.
DR GO; GO:0043920; F:aminopropylagmatine ureohydrolase activity; IEA:UniProtKB-EC.
DR GO; GO:0016813; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines; IMP:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0033389; P:putrescine biosynthetic process from arginine, using agmatinase; IBA:GO_Central.
DR GO; GO:0008295; P:spermidine biosynthetic process; IMP:UniProtKB.
DR InterPro; IPR005925; Agmatinase-rel.
DR InterPro; IPR006035; Ureohydrolase.
DR InterPro; IPR023696; Ureohydrolase_dom_sf.
DR PANTHER; PTHR11358; PTHR11358; 1.
DR Pfam; PF00491; Arginase; 1.
DR PIRSF; PIRSF036979; Arginase; 1.
DR SUPFAM; SSF52768; SSF52768; 1.
DR TIGRFAMs; TIGR01230; agmatinase; 1.
DR PROSITE; PS51409; ARGINASE_2; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Hydrolase; Manganese; Metal-binding; Polyamine biosynthesis;
KW Reference proteome; Spermidine biosynthesis.
FT CHAIN 1..288
FT /note="N(1)-aminopropylagmatine ureohydrolase"
FT /id="PRO_0000429862"
FT BINDING 114
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742"
FT BINDING 133
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742"
FT BINDING 133
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742"
FT BINDING 135
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742"
FT BINDING 137
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742"
FT BINDING 213
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742"
FT BINDING 213
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742"
FT BINDING 215
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742"
FT SITE 144
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000250"
SQ SEQUENCE 288 AA; 31979 MW; 83BD96B02438C1BF CRC64;
MEFLYTYETL KLEFPLVEPE KARFILLGVP FDGTTSYKAG ARFGPTLIRQ ATLNLESYIL
DYDLDIAELP IADIGDIAVV AGDPRKTADR VRETLEELKK ANPKAIPILL GGEHSQTLGA
VEALKPASYV VFDAHLDLRN SYEDNPYNHA CVARRISELG VKEAIFGIRS GTKEEVDFAR
ERDIPWVHAR DYSFDAFVDL VEALPEPVYL SIDIDVFDLS MVPSTGTPEA GGLRFWEVVE
AIEWLVEKKE IAGFDIMEVA GEKLGDPTAL TAAKLLFYSI GAMAKFGR
