ADIA_ECOLI
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 03-AUG-2022, entry version 176.
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; Proteobacteria; 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; P28629; -.
DR PRIDE; P28629; -.
DR EnsemblBacteria; AAC77078; AAC77078; b4117.
DR EnsemblBacteria; BAE78119; BAE78119; BAE78119.
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 PhylomeDB; P28629; -.
DR BioCyc; EcoCyc:ARGDECARBOXDEG-MON; -.
DR BioCyc; MetaCyc:ARGDECARBOXDEG-MON; -.
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:0016831; F:carboxy-lyase activity; IBA:GO_Central.
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; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 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 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; SSF53383; SSF53383; 1.
DR SUPFAM; SSF55904; SSF55904; 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
