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Protein

Pyruvoyl-dependent arginine decarboxylase

Gene

pdaD

Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

Functioni

Catalytic activityi

L-arginine = agmatine + CO2.UniRule annotation

Cofactori

pyruvateUniRule annotationNote: Binds 1 pyruvoyl group covalently per subunit.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei43 – 442Cleavage (non-hydrolytic)UniRule annotation

GO - Molecular functioni

  1. arginine decarboxylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. arginine catabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Ligandi

Pyruvate

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-16731.
TKOD69014:GH72-151-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyruvoyl-dependent arginine decarboxylaseUniRule annotation (EC:4.1.1.19UniRule annotation)
Short name:
PvlArgDCUniRule annotation
Cleaved into the following 2 chains:
Pyruvoyl-dependent arginine decarboxylase subunit betaUniRule annotation
Pyruvoyl-dependent arginine decarboxylase subunit alphaUniRule annotation
Gene namesi
Name:pdaDUniRule annotation
Ordered Locus Names:TK0149
OrganismiThermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Taxonomic identifieri69014 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
ProteomesiUP000000536: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4343Pyruvoyl-dependent arginine decarboxylase subunit betaUniRule annotationPRO_0000023334Add
BLAST
Chaini44 – 157114Pyruvoyl-dependent arginine decarboxylase subunit alphaUniRule annotationPRO_0000023335Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei44 – 441Pyruvic acid (Ser)UniRule annotation

Interactioni

Protein-protein interaction databases

IntActiQ5JFI4. 1 interaction.
MINTiMINT-8376658.
STRINGi69014.TK0149.

Structurei

3D structure databases

ProteinModelPortaliQ5JFI4.
SMRiQ5JFI4. Positions 3-43.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the PdaD family.UniRule annotation

Phylogenomic databases

eggNOGiCOG1945.
HOGENOMiHOG000012204.
InParanoidiQ5JFI4.
KOiK02626.
OMAiISSIMPP.

Family and domain databases

Gene3Di3.50.20.10. 1 hit.
HAMAPiMF_01404. PvlArgDC.
InterProiIPR016104. Pyr-dep_his/arg-deCO2ase.
IPR016105. Pyr-dep_his/arg-deCO2ase_sand.
IPR002724. Pyruvoyl-dep_arg_deCO2ase.
[Graphical view]
PfamiPF01862. PvlArgDC. 1 hit.
[Graphical view]
PIRSFiPIRSF005216. Pyruvoyl-dep_arg_deCO2ase. 1 hit.
ProDomiPD010449. Pyruvoyl-dep_arg_deCO2ase. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF56271. SSF56271. 1 hit.
TIGRFAMsiTIGR00286. TIGR00286. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q5JFI4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSWTTPKRAF IGAATAEGGT KLNAFDNALL KLGIGNVNLV KLSSVIPAHI
60 70 80 90 100
EWMEKVHDVP IGMLLPTVYA HIESDEPGMT ISAALGVGIS KNNEGGLIYE
110 120 130 140 150
YSGYCTKEEA EEMVRKMVEE GFRQRGWELG EFKVASAEIT VKDKPAAAIA

VVVMFPY
Length:157
Mass (Da):17,062
Last modified:February 15, 2005 - v1
Checksum:i9D91137305B1126E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006878 Genomic DNA. Translation: BAD84338.1.
RefSeqiYP_182562.1. NC_006624.1.

Genome annotation databases

EnsemblBacteriaiBAD84338; BAD84338; TK0149.
GeneIDi3234595.
KEGGitko:TK0149.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006878 Genomic DNA. Translation: BAD84338.1.
RefSeqiYP_182562.1. NC_006624.1.

3D structure databases

ProteinModelPortaliQ5JFI4.
SMRiQ5JFI4. Positions 3-43.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ5JFI4. 1 interaction.
MINTiMINT-8376658.
STRINGi69014.TK0149.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD84338; BAD84338; TK0149.
GeneIDi3234595.
KEGGitko:TK0149.

Phylogenomic databases

eggNOGiCOG1945.
HOGENOMiHOG000012204.
InParanoidiQ5JFI4.
KOiK02626.
OMAiISSIMPP.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-16731.
TKOD69014:GH72-151-MONOMER.

Family and domain databases

Gene3Di3.50.20.10. 1 hit.
HAMAPiMF_01404. PvlArgDC.
InterProiIPR016104. Pyr-dep_his/arg-deCO2ase.
IPR016105. Pyr-dep_his/arg-deCO2ase_sand.
IPR002724. Pyruvoyl-dep_arg_deCO2ase.
[Graphical view]
PfamiPF01862. PvlArgDC. 1 hit.
[Graphical view]
PIRSFiPIRSF005216. Pyruvoyl-dep_arg_deCO2ase. 1 hit.
ProDomiPD010449. Pyruvoyl-dep_arg_deCO2ase. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF56271. SSF56271. 1 hit.
TIGRFAMsiTIGR00286. TIGR00286. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes."
    Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.
    Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-918 / JCM 12380 / KOD1.

Entry informationi

Entry nameiPDAD_THEKO
AccessioniPrimary (citable) accession number: Q5JFI4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: February 15, 2005
Last modified: January 7, 2015
This is version 65 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.