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Protein

Biosynthetic arginine decarboxylase

Gene

speA

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the biosynthesis of agmatine from arginine.UniRule annotation

Catalytic activityi

L-arginine = agmatine + CO2.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+UniRule annotation
  • pyridoxal 5'-phosphateUniRule annotation

GO - Molecular functioni

  1. arginine decarboxylase activity Source: UniProtKB-HAMAP
  2. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. arginine catabolic process Source: InterPro
  2. spermidine biosynthetic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Polyamine biosynthesis, Spermidine biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding, Pyridoxal phosphate

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-3401-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Biosynthetic arginine decarboxylaseUniRule annotation (EC:4.1.1.19UniRule annotation)
Short name:
ADCUniRule annotation
Gene namesi
Name:speAUniRule annotation
Ordered Locus Names:VPA0170
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002493 Componenti: Chromosome 2

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 640640Biosynthetic arginine decarboxylasePRO_0000149984Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei105 – 1051N6-(pyridoxal phosphate)lysineUniRule annotation

Interactioni

Protein-protein interaction databases

STRINGi223926.VPA0170.

Structurei

3D structure databases

ProteinModelPortaliQ87JS8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni290 – 30011Substrate-bindingUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the Orn/Lys/Arg decarboxylase class-II family. SpeA subfamily.UniRule annotation

Phylogenomic databases

eggNOGiCOG1166.
HOGENOMiHOG000029191.
KOiK01585.
OMAiIDHYVDG.
OrthoDBiEOG676Z0R.

Family and domain databases

Gene3Di2.40.37.10. 2 hits.
3.20.20.10. 1 hit.
HAMAPiMF_01417. SpeA.
InterProiIPR009006. Ala_racemase/Decarboxylase_C.
IPR002985. Arg_decrbxlase.
IPR022643. De-COase2_C.
IPR022644. De-COase2_N.
IPR000183. Orn/DAP/Arg_de-COase.
IPR029066. PLP-binding_barrel.
[Graphical view]
PfamiPF02784. Orn_Arg_deC_N. 1 hit.
PF00278. Orn_DAP_Arg_deC. 1 hit.
[Graphical view]
PIRSFiPIRSF001336. Arg_decrbxlase. 1 hit.
PRINTSiPR01180. ARGDCRBXLASE.
PR01179. ODADCRBXLASE.
SUPFAMiSSF51419. SSF51419. 1 hit.
TIGRFAMsiTIGR01273. speA. 1 hit.

Sequencei

Sequence statusi: Complete.

Q87JS8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRIELEKATK LDRIRADYNV HYWSQGFYGI DDQGEVYVSP RSDRAHQIPF
60 70 80 90 100
SAIVNELEAQ QLNLPVLVRF PQIVHQRVHG ICHAFNQAIE EYQYPNKYLL
110 120 130 140 150
VYPIKVNQQR EVVDEILASQ AQLETKQLGL EAGSKPELLA VLALAQQGSS
160 170 180 190 200
VIVCNGYKDR EYVRLALIGE KLGHKVFIVL EKLSELDLVL EEAKSLGVKP
210 220 230 240 250
RLGLRIRLAS QGAGKWQASG GEKSKFGLSA SQVLSVIERL KREGSLDAMQ
260 270 280 290 300
LVHFHLGSQM ANIRDVRNGV NESARFYCEL RALGANIEYF DVGGGLAVDY
310 320 330 340 350
DGTRSQSSNS MNYGLAEYAR NIVNTVGDVC QQYEQPMPVI ISESGRSLTA
360 370 380 390 400
HHAVLISNVI GTETYQPEEV HELGVDAPLL LQNMWRNWEN LQDGTDARAL
410 420 430 440 450
IEIYNDTQSD LAEVHSQFAT GVLNLEQRAW AEQLSLRIYF ELSRKMSTKN
460 470 480 490 500
RFHRPILDEL SERLADKFFV NFSLFQSLPD AWGIDQVFPV LPLSGLGDAE
510 520 530 540 550
ERRAVMLDIT CDSDGAIDHY VDGQGIESTL PVPAWSKDKP YLMGFFLVGA
560 570 580 590 600
YQEILGDMHN LFGDTHSAVV NVDEHGQFEI SYINEGDSVE DMMRYVHIDV
610 620 630 640
DAIRDNYKQL VSQRVEANEQ AQILAELEQG LAGYTYLEDF
Length:640
Mass (Da):72,065
Last modified:June 1, 2003 - v1
Checksum:i17371F21185F27A7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000032 Genomic DNA. Translation: BAC61513.1.
RefSeqiNP_799680.1. NC_004605.1.

Genome annotation databases

EnsemblBacteriaiBAC61513; BAC61513; BAC61513.
GeneIDi1190857.
KEGGivpa:VPA0170.
PATRICi20144787. VBIVibPar50997_3128.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000032 Genomic DNA. Translation: BAC61513.1.
RefSeqiNP_799680.1. NC_004605.1.

3D structure databases

ProteinModelPortaliQ87JS8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223926.VPA0170.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC61513; BAC61513; BAC61513.
GeneIDi1190857.
KEGGivpa:VPA0170.
PATRICi20144787. VBIVibPar50997_3128.

Phylogenomic databases

eggNOGiCOG1166.
HOGENOMiHOG000029191.
KOiK01585.
OMAiIDHYVDG.
OrthoDBiEOG676Z0R.

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-3401-MONOMER.

Family and domain databases

Gene3Di2.40.37.10. 2 hits.
3.20.20.10. 1 hit.
HAMAPiMF_01417. SpeA.
InterProiIPR009006. Ala_racemase/Decarboxylase_C.
IPR002985. Arg_decrbxlase.
IPR022643. De-COase2_C.
IPR022644. De-COase2_N.
IPR000183. Orn/DAP/Arg_de-COase.
IPR029066. PLP-binding_barrel.
[Graphical view]
PfamiPF02784. Orn_Arg_deC_N. 1 hit.
PF00278. Orn_DAP_Arg_deC. 1 hit.
[Graphical view]
PIRSFiPIRSF001336. Arg_decrbxlase. 1 hit.
PRINTSiPR01180. ARGDCRBXLASE.
PR01179. ODADCRBXLASE.
SUPFAMiSSF51419. SSF51419. 1 hit.
TIGRFAMsiTIGR01273. speA. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae."
    Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.
    Lancet 361:743-749(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RIMD 2210633.

Entry informationi

Entry nameiSPEA_VIBPA
AccessioniPrimary (citable) accession number: Q87JS8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2004
Last sequence update: June 1, 2003
Last modified: January 7, 2015
This is version 71 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.