ID   ADIA_ECOLI              Reviewed;         755 AA.
AC   P28629; P78138; Q2M6I7;
DT   01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT   01-DEC-1992, sequence version 1.
DT   24-JAN-2024, entry version 182.
DE   RecName: Full=Biodegradative arginine decarboxylase;
DE            Short=ADC;
DE            EC=4.1.1.19 {ECO:0000269|PubMed:12867448};
GN   Name=adiA; Synonyms=adi; OrderedLocusNames=b4117, JW5731;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12;
RX   PubMed=8383109; DOI=10.1128/jb.175.5.1221-1234.1993;
RA   Stim K.P., Bennett G.N.;
RT   "Nucleotide sequence of the adi gene, which encodes the biodegradative
RT   acid-induced arginine decarboxylase of Escherichia coli.";
RL   J. Bacteriol. 175:1221-1234(1993).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA   Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT   "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT   from 92.8 through 100 minutes.";
RL   Nucleic Acids Res. 23:2105-2119(1995).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-78.
RX   PubMed=2830169; DOI=10.1016/0378-1119(87)90333-7;
RA   Webster C., Kempsell K., Booth I., Busby S.;
RT   "Organisation of the regulatory region of the Escherichia coli melibiose
RT   operon.";
RL   Gene 59:253-263(1987).
RN   [6]
RP   PROTEIN SEQUENCE OF 1-7.
RC   STRAIN=B;
RX   PubMed=4204273; DOI=10.1021/bi00701a006;
RA   Sabo D.L., Fischer E.H.;
RT   "Chemical properties of Escherichia coli lysine decarboxylase including a
RT   segment of its pyridoxal 5'-phosphate binding site.";
RL   Biochemistry 13:670-676(1974).
RN   [7]
RP   FUNCTION, CATALYTIC ACTIVITY, INDUCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=K12;
RX   PubMed=12867448; DOI=10.1128/jb.185.15.4402-4409.2003;
RA   Gong S., Richard H., Foster J.W.;
RT   "YjdE (AdiC) is the arginine:agmatine antiporter essential for arginine-
RT   dependent acid resistance in Escherichia coli.";
RL   J. Bacteriol. 185:4402-4409(2003).
RN   [8] {ECO:0007744|PDB:2VYC}
RP   X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS), ACTIVITY REGULATION, COFACTOR, AND
RP   PYRIDOXAL PHOSPHATE AT LYS-386.
RX   PubMed=19298070; DOI=10.1021/bi900075d;
RA   Andrell J., Hicks M.G., Palmer T., Carpenter E.P., Iwata S., Maher M.J.;
RT   "Crystal structure of the acid-induced arginine decarboxylase from
RT   Escherichia coli: reversible decamer assembly controls enzyme activity.";
RL   Biochemistry 48:3915-3927(2009).
CC   -!- FUNCTION: Component of the acid-resistance (AR) system allowing enteric
CC       pathogens to survive the acidic environment in the stomach (Probable).
CC       ADC can be found in two forms: biodegradative (this enzyme) and
CC       biosynthetic (speA). The biodegradative form plays a role in regulating
CC       pH by consuming proteins. Converts arginine imported by AdiC to
CC       agmatine which is then exported by AdiC (Probable).
CC       {ECO:0000305|PubMed:12867448, ECO:0000305|PubMed:19298070}.
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         Evidence={ECO:0000269|PubMed:12867448};
CC   -!- COFACTOR:
CC       Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC         Evidence={ECO:0000269|PubMed:19298070};
CC       Note=Binds one cofactor per subunit. {ECO:0000269|PubMed:19298070};
CC   -!- ACTIVITY REGULATION: Homodimers are probably inactive, their assembly
CC       into a homodecamer at low pH requires neutralization of negatively
CC       charged residues. This uses cytoplasmic protons, contributing pH
CC       regulation and stabilizes the homodecamer.
CC       {ECO:0000305|PubMed:19298070}.
CC   -!- SUBUNIT: Homodecamer. The basic unit is a homodimer, organized into a
CC       ring of giving a pentamer of five homodimers.
CC       {ECO:0000269|PubMed:19298070}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm.
CC   -!- INDUCTION: Under conditions of acidic pH, anaerobiosis and rich medium.
CC       Forms an operon with downstream adiY but not (further) downstream adiC.
CC       {ECO:0000269|PubMed:12867448}.
CC   -!- DISRUPTION PHENOTYPE: Loss of formation of agmatine, loss of arginine-
CC       dependent acid resistance. {ECO:0000269|PubMed:12867448}.
CC   -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-I family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA97017.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC       Sequence=BAE78119.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; M93362; AAA23481.1; -; Genomic_DNA.
DR   EMBL; U14003; AAA97017.1; ALT_INIT; Genomic_DNA.
DR   EMBL; U00096; AAC77078.2; -; Genomic_DNA.
DR   EMBL; AP009048; BAE78119.1; ALT_INIT; Genomic_DNA.
DR   EMBL; M18425; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   PIR; S56346; S56346.
DR   RefSeq; NP_418541.2; NC_000913.3.
DR   RefSeq; WP_001381593.1; NZ_SSZK01000018.1.
DR   PDB; 2VYC; X-ray; 2.40 A; A/B/C/D/E/F/G/H/I/J=1-755.
DR   PDBsum; 2VYC; -.
DR   AlphaFoldDB; P28629; -.
DR   SMR; P28629; -.
DR   BioGRID; 4263079; 16.
DR   DIP; DIP-2903N; -.
DR   IntAct; P28629; 6.
DR   STRING; 511145.b4117; -.
DR   PaxDb; 511145-b4117; -.
DR   EnsemblBacteria; AAC77078; AAC77078; b4117.
DR   GeneID; 948638; -.
DR   KEGG; ecj:JW5731; -.
DR   KEGG; eco:b4117; -.
DR   PATRIC; fig|511145.12.peg.4248; -.
DR   EchoBASE; EB1464; -.
DR   eggNOG; COG1982; Bacteria.
DR   HOGENOM; CLU_014292_3_0_6; -.
DR   InParanoid; P28629; -.
DR   OMA; RVDTWNL; -.
DR   OrthoDB; 9761189at2; -.
DR   PhylomeDB; P28629; -.
DR   BioCyc; EcoCyc:ARGDECARBOXDEG-MONOMER; -.
DR   BioCyc; MetaCyc:ARGDECARBOXDEG-MONOMER; -.
DR   BRENDA; 4.1.1.19; 2026.
DR   EvolutionaryTrace; P28629; -.
DR   PRO; PR:P28629; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005829; C:cytosol; HDA:UniProtKB.
DR   GO; GO:0008792; F:arginine decarboxylase activity; IDA:EcoliWiki.
DR   GO; GO:0030170; F:pyridoxal phosphate binding; IDA:EcoCyc.
DR   GO; GO:0006527; P:arginine catabolic process; IDA:EcoliWiki.
DR   GO; GO:0051454; P:intracellular pH elevation; IMP:EcoCyc.
DR   CDD; cd00615; Orn_deC_like; 1.
DR   Gene3D; 3.40.50.2300; -; 1.
DR   Gene3D; 3.90.1150.10; Aspartate Aminotransferase, domain 1; 1.
DR   Gene3D; 3.90.100.10; Orn/Lys/Arg decarboxylase, C-terminal domain; 1.
DR   Gene3D; 3.40.640.10; Type I PLP-dependent aspartate aminotransferase-like (Major domain); 1.
DR   InterPro; IPR005308; OKR_de-COase_N.
DR   InterPro; IPR011193; Orn/lys/arg_de-COase.
DR   InterPro; IPR000310; Orn/Lys/Arg_deCO2ase_major_dom.
DR   InterPro; IPR008286; Prn/Lys/Arg_de-COase_C.
DR   InterPro; IPR036633; Prn/Lys/Arg_de-COase_C_sf.
DR   InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR   InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR   InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR   PANTHER; PTHR45229:SF3; BIODEGRADATIVE ARGININE DECARBOXYLASE; 1.
DR   PANTHER; PTHR45229; CONSTITUTIVE ORNITHINE DECARBOXYLASE; 1.
DR   Pfam; PF01276; OKR_DC_1; 1.
DR   Pfam; PF03711; OKR_DC_1_C; 1.
DR   Pfam; PF03709; OKR_DC_1_N; 1.
DR   PIRSF; PIRSF009393; Orn_decarb; 1.
DR   SUPFAM; SSF55904; Ornithine decarboxylase C-terminal domain; 1.
DR   SUPFAM; SSF53383; PLP-dependent transferases; 1.
DR   PROSITE; PS00703; OKR_DC_1; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Decarboxylase; Direct protein sequencing; Lyase;
KW   Pyridoxal phosphate; Reference proteome.
FT   CHAIN           1..755
FT                   /note="Biodegradative arginine decarboxylase"
FT                   /id="PRO_0000201149"
FT   MOD_RES         386
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000269|PubMed:19298070,
FT                   ECO:0007744|PDB:2VYC"
FT   CONFLICT        75
FT                   /note="L -> P (in Ref. 5; M18425)"
FT                   /evidence="ECO:0000305"
FT   STRAND          2..6
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           15..30
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          34..40
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           41..48
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            49..51
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          55..60
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           66..82
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          88..92
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           94..99
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           103..108
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          110..114
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            115..117
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           120..136
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           141..150
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          156..160
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            161..166
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           167..170
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           172..181
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           183..187
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            194..197
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            200..203
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           205..218
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          221..228
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           229..241
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          247..253
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           256..265
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          268..272
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           287..290
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           292..301
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            303..305
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           306..308
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          316..321
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          325..328
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           330..337
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            338..340
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          342..347
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           354..356
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           358..360
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          363..366
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          374..383
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            384..386
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          387..389
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          395..400
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           408..417
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           425..438
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           441..469
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            470..472
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          477..480
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          482..485
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            487..489
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          492..494
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           495..497
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           500..505
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           507..509
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            517..519
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          528..531
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          535..539
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          547..549
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           556..564
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            565..567
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          571..573
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          575..581
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            588..591
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           592..607
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           611..614
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           616..621
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            623..625
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           631..645
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           647..656
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          661..663
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           665..673
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          677..681
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           682..684
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          689..692
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          694..696
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   TURN            697..699
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   HELIX           716..730
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          741..744
FT                   /evidence="ECO:0007829|PDB:2VYC"
FT   STRAND          747..753
FT                   /evidence="ECO:0007829|PDB:2VYC"
SQ   SEQUENCE   755 AA;  84425 MW;  0FCB715144649F8F CRC64;
     MKVLIVESEF LHQDTWVGNA VERLADALSQ QNVTVIKSTS FDDGFAILSS NEAIDCLMFS
     YQMEHPDEHQ NVRQLIGKLH ERQQNVPVFL LGDREKALAA MDRDLLELVD EFAWILEDTA
     DFIAGRAVAA MTRYRQQLLP PLFSALMKYS DIHEYSWAAP GHQGGVGFTK TPAGRFYHDY
     YGENLFRTDM GIERTSLGSL LDHTGAFGES EKYAARVFGA DRSWSVVVGT SGSNRTIMQA
     CMTDNDVVVV DRNCHKSIEQ GLMLTGAKPV YMVPSRNRYG IIGPIYPQEM QPETLQKKIS
     ESPLTKDKAG QKPSYCVVTN CTYDGVCYNA KEAQDLLEKT SDRLHFDEAW YGYARFNPIY
     ADHYAMRGEP GDHNGPTVFA THSTHKLLNA LSQASYIHVR EGRGAINFSR FNQAYMMHAT
     TSPLYAICAS NDVAVSMMDG NSGLSLTQEV IDEAVDFRQA MARLYKEFTA DGSWFFKPWN
     KEVVTDPQTG KTYDFADAPT KLLTTVQDCW VMHPGESWHG FKDIPDNWSM LDPIKVSILA
     PGMGEDGELE ETGVPAALVT AWLGRHGIVP TRTTDFQIMF LFSMGVTRGK WGTLVNTLCS
     FKRHYDANTP LAQVMPELVE QYPDTYANMG IHDLGDTMFA WLKENNPGAR LNEAYSGLPV
     AEVTPREAYN AIVDNNVELV SIENLPGRIA ANSVIPYPPG IPMLLSGENF GDKNSPQVSY
     LRSLQSWDHH FPGFEHETEG TEIIDGIYHV MCVKA
//