PDAD_METJA
ID PDAD_METJA Reviewed; 165 AA.
AC Q57764;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 25-MAY-2022, entry version 139.
DE RecName: Full=Pyruvoyl-dependent arginine decarboxylase;
DE Short=PvlArgDC;
DE EC=4.1.1.19;
DE Contains:
DE RecName: Full=Pyruvoyl-dependent arginine decarboxylase subunit beta;
DE Contains:
DE RecName: Full=Pyruvoyl-dependent arginine decarboxylase subunit alpha;
GN Name=pdaD; OrderedLocusNames=MJ0316;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP CHARACTERIZATION, MASS SPECTROMETRY, AND PYRUVATE FORMATION AT SER-53.
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=11980912; DOI=10.1074/jbc.m203467200;
RA Graham D.E., Xu H., White R.H.;
RT "Methanococcus jannaschii uses a pyruvoyl-dependent arginine decarboxylase
RT in polyamine biosynthesis.";
RL J. Biol. Chem. 277:23500-23507(2002).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + L-arginine = agmatine + CO2; Xref=Rhea:RHEA:17641,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:32682,
CC ChEBI:CHEBI:58145; EC=4.1.1.19;
CC -!- COFACTOR:
CC Name=pyruvate; Xref=ChEBI:CHEBI:15361;
CC Note=Binds 1 pyruvoyl group covalently per subunit.;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Thermostable.;
CC -!- SUBUNIT: Trimer of an alpha-beta dimer.
CC -!- MASS SPECTROMETRY: [Pyruvoyl-dependent arginine decarboxylase subunit
CC beta]: Mass=5436; Mass_error=11; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:11980912};
CC -!- MASS SPECTROMETRY: [Pyruvoyl-dependent arginine decarboxylase subunit
CC alpha]: Mass=12356; Mass_error=57; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:11980912};
CC -!- SIMILARITY: Belongs to the PdaD family. {ECO:0000305}.
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DR EMBL; L77117; AAB98302.1; -; Genomic_DNA.
DR PIR; E64339; E64339.
DR RefSeq; WP_010869814.1; NC_000909.1.
DR PDB; 1MT1; X-ray; 2.20 A; A/C/E/G/I/K=1-52, B/D/F/H/J/L=53-165.
DR PDB; 1N13; X-ray; 1.40 A; A/C/E/G/I/K=1-52, B/D/F/H/J/L=53-165.
DR PDB; 1N2M; X-ray; 1.90 A; A/B/C/D/E/F=1-165.
DR PDB; 2QQC; X-ray; 2.00 A; A/C/E/G/I/K=1-52, B/D/F/H/J/L=54-165.
DR PDB; 2QQD; X-ray; 2.00 A; A/D=1-52, B/E=54-165, C/F/G/H=1-165.
DR PDBsum; 1MT1; -.
DR PDBsum; 1N13; -.
DR PDBsum; 1N2M; -.
DR PDBsum; 2QQC; -.
DR PDBsum; 2QQD; -.
DR AlphaFoldDB; Q57764; -.
DR SMR; Q57764; -.
DR STRING; 243232.MJ_0316; -.
DR EnsemblBacteria; AAB98302; AAB98302; MJ_0316.
DR GeneID; 1451171; -.
DR KEGG; mja:MJ_0316; -.
DR eggNOG; arCOG04490; Archaea.
DR HOGENOM; CLU_114389_2_0_2; -.
DR InParanoid; Q57764; -.
DR OMA; AAALWYK; -.
DR OrthoDB; 98606at2157; -.
DR PhylomeDB; Q57764; -.
DR BRENDA; 4.1.1.19; 3260.
DR SABIO-RK; Q57764; -.
DR EvolutionaryTrace; Q57764; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0008792; F:arginine decarboxylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006527; P:arginine catabolic process; IEA:InterPro.
DR Gene3D; 3.50.20.10; -; 1.
DR HAMAP; MF_01404; PvlArgDC; 1.
DR InterPro; IPR016104; Pyr-dep_his/arg-deCO2ase.
DR InterPro; IPR016105; Pyr-dep_his/arg-deCO2ase_sand.
DR InterPro; IPR002724; Pyruvoyl-dep_arg_deCO2ase.
DR PANTHER; PTHR40438; PTHR40438; 1.
DR Pfam; PF01862; PvlArgDC; 1.
DR PIRSF; PIRSF005216; Pyruvoyl-dep_arg_deCO2ase; 1.
DR SFLD; SFLDG01170; Pyruvoyl-dependent_arginine_de; 1.
DR SUPFAM; SSF56271; SSF56271; 1.
DR TIGRFAMs; TIGR00286; TIGR00286; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Decarboxylase; Lyase; Pyruvate; Reference proteome.
FT CHAIN 1..52
FT /note="Pyruvoyl-dependent arginine decarboxylase subunit
FT beta"
FT /id="PRO_0000023314"
FT CHAIN 53..165
FT /note="Pyruvoyl-dependent arginine decarboxylase subunit
FT alpha"
FT /id="PRO_0000023315"
FT SITE 52..53
FT /note="Cleavage (non-hydrolytic)"
FT MOD_RES 53
FT /note="Pyruvic acid (Ser)"
FT /evidence="ECO:0000269|PubMed:11980912"
FT HELIX 10..12
FT /evidence="ECO:0007829|PDB:2QQD"
FT STRAND 17..26
FT /evidence="ECO:0007829|PDB:1N13"
FT HELIX 30..41
FT /evidence="ECO:0007829|PDB:1N13"
FT STRAND 46..51
FT /evidence="ECO:0007829|PDB:1N13"
FT STRAND 53..55
FT /evidence="ECO:0007829|PDB:2QQD"
FT STRAND 72..82
FT /evidence="ECO:0007829|PDB:1N13"
FT STRAND 88..100
FT /evidence="ECO:0007829|PDB:1N13"
FT STRAND 105..114
FT /evidence="ECO:0007829|PDB:1N13"
FT HELIX 116..134
FT /evidence="ECO:0007829|PDB:1N13"
FT STRAND 138..149
FT /evidence="ECO:0007829|PDB:1N13"
FT STRAND 151..163
FT /evidence="ECO:0007829|PDB:1N13"
SQ SEQUENCE 165 AA; 17708 MW; 04C7F8AB3AEC2342 CRC64;
MNAEINPLHA YFKLPNTVSL VAGSSEGETP LNAFDGALLN AGIGNVNLIR ISSIMPPEAE
IVPLPKLPMG ALVPTAYGYI ISDVPGETIS AAISVAIPKD KSLCGLIMEY EGKCSKKEAE
KTVREMAKIG FEMRGWELDR IESIAVEHTV EKLGCAFAAA ALWYK
