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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: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

L-arginine = agmatine + CO2.

Cofactori

pyruvateNote: Binds 1 pyruvoyl group covalently per subunit.

Temperature dependencei

Thermostable.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei52 – 532Cleavage (non-hydrolytic)

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

BRENDAi4.1.1.19. 3260.
SABIO-RKQ57764.

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
ProteomesiUP000000805 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5252Pyruvoyl-dependent arginine decarboxylase subunit betaPRO_0000023314Add
BLAST
Chaini53 – 165113Pyruvoyl-dependent arginine decarboxylase subunit alphaPRO_0000023315Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei53 – 531Pyruvic acid (Ser)

Interactioni

Subunit structurei

Trimer of an alpha-beta dimer.

Protein-protein interaction databases

STRINGi243232.MJ0316.

Structurei

Secondary structure

1
165
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi10 – 123Combined sources
Beta strandi17 – 2610Combined sources
Helixi30 – 4112Combined sources
Beta strandi46 – 516Combined sources
Beta strandi53 – 553Combined sources
Beta strandi72 – 8211Combined sources
Beta strandi88 – 10013Combined sources
Beta strandi105 – 11410Combined sources
Helixi116 – 13419Combined sources
Beta strandi138 – 14912Combined sources
Beta strandi151 – 16313Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 3-165.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ57764.

Family & Domainsi

Sequence similaritiesi

Belongs to the PdaD family.Curated

Phylogenomic databases

eggNOGiCOG1945.
InParanoidiQ57764.
KOiK02626.
OMAiISSIMPP.
PhylomeDBiQ57764.

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.

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.
RefSeqiNP_247289.1. NC_000909.1.

Genome annotation databases

EnsemblBacteriaiAAB98302; AAB98302; MJ_0316.
GeneIDi1451171.
KEGGimja:MJ_0316.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98302.1.
PIRiE64339.
RefSeqiNP_247289.1. NC_000909.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 3-165.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ0316.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB98302; AAB98302; MJ_0316.
GeneIDi1451171.
KEGGimja:MJ_0316.

Phylogenomic databases

eggNOGiCOG1945.
InParanoidiQ57764.
KOiK02626.
OMAiISSIMPP.
PhylomeDBiQ57764.

Enzyme and pathway databases

BRENDAi4.1.1.19. 3260.
SABIO-RKQ57764.

Miscellaneous databases

EvolutionaryTraceiQ57764.

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

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
  2. "Methanococcus jannaschii uses a pyruvoyl-dependent arginine decarboxylase in polyamine biosynthesis."
    Graham D.E., Xu H., White R.H.
    J. Biol. Chem. 277:23500-23507(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, MASS SPECTROMETRY.
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.

Entry informationi

Entry nameiPDAD_METJA
AccessioniPrimary (citable) accession number: Q57764
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: April 1, 2015
This is version 112 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

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

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.