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Protein

Pyruvoyl-dependent arginine decarboxylase

Gene

pdaD

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalytic activityi

L-arginine = agmatine + CO2.

Cofactori

pyruvateNote: Binds 1 pyruvoyl group covalently per subunit.

Temperature dependencei

Thermostable.

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDecarboxylase, Lyase
LigandPyruvate

Enzyme and pathway databases

BioCyciMJAN243232:G1GKE-339-MONOMER
BRENDAi4.1.1.19 3260
SABIO-RKiQ57764

Names & Taxonomyi

Protein namesi
Recommended name:
Pyruvoyl-dependent arginine decarboxylase (EC:4.1.1.19)
Short name:
PvlArgDC
Cleaved into the following 2 chains:
Gene namesi
Name:pdaD
Ordered Locus Names:MJ0316
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000233141 – 52Pyruvoyl-dependent arginine decarboxylase subunit betaAdd BLAST52
ChainiPRO_000002331553 – 165Pyruvoyl-dependent arginine decarboxylase subunit alphaAdd BLAST113

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei53Pyruvic acid (Ser)1 Publication1

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei52 – 53Cleavage (non-hydrolytic)2

Interactioni

Subunit structurei

Trimer of an alpha-beta dimer.

Protein-protein interaction databases

STRINGi243232.MJ_0316

Structurei

Secondary structure

1165
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi10 – 12Combined sources3
Beta strandi17 – 26Combined sources10
Helixi30 – 41Combined sources12
Beta strandi46 – 51Combined sources6
Beta strandi53 – 55Combined sources3
Beta strandi72 – 82Combined sources11
Beta strandi88 – 100Combined sources13
Beta strandi105 – 114Combined sources10
Helixi116 – 134Combined sources19
Beta strandi138 – 149Combined sources12
Beta strandi151 – 163Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1MT1X-ray2.20A/C/E/G/I/K1-52[»]
B/D/F/H/J/L53-165[»]
1N13X-ray1.40A/C/E/G/I/K1-52[»]
B/D/F/H/J/L53-165[»]
1N2MX-ray1.90A/B/C/D/E/F1-165[»]
2QQCX-ray2.00A/C/E/G/I/K1-52[»]
B/D/F/H/J/L54-165[»]
2QQDX-ray2.00A/D1-52[»]
B/E54-165[»]
C/F/G/H1-165[»]
ProteinModelPortaliQ57764
SMRiQ57764
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ57764

Family & Domainsi

Sequence similaritiesi

Belongs to the PdaD family.Curated

Phylogenomic databases

eggNOGiarCOG04490 Archaea
COG1945 LUCA
InParanoidiQ57764
KOiK02626
OMAiAAALWYK
OrthoDBiPOG093Z0D0B
PhylomeDBiQ57764

Family and domain databases

Gene3Di3.50.20.10, 1 hit
HAMAPiMF_01404 PvlArgDC, 1 hit
InterProiView protein in InterPro
IPR016104 Pyr-dep_his/arg-deCO2ase
IPR016105 Pyr-dep_his/arg-deCO2ase_sand
IPR002724 Pyruvoyl-dep_arg_deCO2ase
PANTHERiPTHR40438 PTHR40438, 1 hit
PfamiView protein in Pfam
PF01862 PvlArgDC, 1 hit
PIRSFiPIRSF005216 Pyruvoyl-dep_arg_deCO2ase, 1 hit
ProDomiView protein in ProDom or Entries sharing at least one domain
PD010449 Pyruvoyl-dep_arg_deCO2ase, 1 hit
SFLDiSFLDG01170 Pyruvoyl-dependent_arginine_de, 1 hit
SUPFAMiSSF56271 SSF56271, 1 hit
TIGRFAMsiTIGR00286 TIGR00286, 1 hit

Sequencei

Sequence statusi: Complete.

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

Q57764-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNAEINPLHA YFKLPNTVSL VAGSSEGETP LNAFDGALLN AGIGNVNLIR
60 70 80 90 100
ISSIMPPEAE IVPLPKLPMG ALVPTAYGYI ISDVPGETIS AAISVAIPKD
110 120 130 140 150
KSLCGLIMEY EGKCSKKEAE KTVREMAKIG FEMRGWELDR IESIAVEHTV
160
EKLGCAFAAA ALWYK
Length:165
Mass (Da):17,708
Last modified:November 1, 1996 - v1
Checksum:i04C7F8AB3AEC2342
GO

Mass spectrometryi

Molecular mass is 5436±11 Da from positions 1 - 52. Determined by MALDI. 1 Publication
Molecular mass is 12356±57 Da from positions 53 - 165. Determined by MALDI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA Translation: AAB98302.1
PIRiE64339
RefSeqiWP_010869814.1, NC_000909.1

Genome annotation databases

EnsemblBacteriaiAAB98302; AAB98302; MJ_0316
GeneIDi1451171
KEGGimja:MJ_0316

Similar proteinsi

Entry informationi

Entry nameiPDAD_METJA
AccessioniPrimary (citable) accession number: Q57764
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: May 23, 2018
This is version 125 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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