YGID_ECOLI
ID YGID_ECOLI Reviewed; 271 AA.
AC P24197; Q2M9G1;
DT 01-MAR-1992, integrated into UniProtKB/Swiss-Prot.
DT 02-NOV-2016, sequence version 4.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=4,5-DOPA dioxygenase extradiol {ECO:0000305};
DE EC=1.13.11.29 {ECO:0000269|PubMed:23666480};
GN Name=ygiD; OrderedLocusNames=b3039, JW3007;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1314093; DOI=10.1016/0167-4781(92)90535-8;
RA Yang T.-P., Depew R.E.;
RT "Nucleotide sequence of a region duplicated in Escherichia coli toc
RT mutants.";
RL Biochim. Biophys. Acta 1130:227-228(1992).
RN [2]
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 [3]
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 [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND
RP SUBCELLULAR LOCATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=23666480; DOI=10.1007/s00253-013-4961-3;
RA Gandia-Herrero F., Garcia-Carmona F.;
RT "Escherichia coli protein YgiD produces the structural unit of plant
RT pigments betalains: characterization of a prokaryotic enzyme with DOPA-
RT extradiol-dioxygenase activity.";
RL Appl. Microbiol. Biotechnol. 98:1165-1174(2014).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.27 ANGSTROMS), AND ZINC BINDING.
RG Southeast collaboratory for structural genomics (SECSG);
RT "Crystal structure of uncharacterized protein JW3007 from Escherichia coli
RT K12.";
RL Submitted (JUN-2007) to the PDB data bank.
CC -!- FUNCTION: In vitro, opens the cyclic ring of dihydroxy-phenylalanine
CC (DOPA) between carbons 4 and 5, thus producing an unstable seco-DOPA
CC that rearranges nonenzymatically to betalamic acid. The physiological
CC substrate is unknown. {ECO:0000269|PubMed:23666480}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-dopa + O2 = 4-(L-alanin-3-yl)-2-hydroxy-cis,cis-muconate 6-
CC semialdehyde + H(+); Xref=Rhea:RHEA:21220, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:57504, ChEBI:CHEBI:57639;
CC EC=1.13.11.29; Evidence={ECO:0000269|PubMed:23666480};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=7.9 mM for L-DOPA {ECO:0000269|PubMed:23666480};
CC Note=kcat is 0.17 min(-1) with L-DOPA. {ECO:0000269|PubMed:23666480};
CC pH dependence:
CC Optimum pH is 8.0. {ECO:0000269|PubMed:23666480};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:23666480}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:23666480}.
CC -!- MISCELLANEOUS: Betalamic acid is the structural unit of the betalains,
CC natural nitrogen-containing water-soluble pigments with high colorant
CC and bioactive properties, characteristic of plants of the order
CC Caryophyllales. {ECO:0000305|PubMed:23666480}.
CC -!- SIMILARITY: Belongs to the DODA-type extradiol aromatic ring-opening
CC dioxygenase family. {ECO:0000305}.
CC -!- CAUTION: It is uncertain whether Met-1 or Met-10 is the initiator.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC76075.2; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; M77129; AAA71877.1; -; Genomic_DNA.
DR EMBL; U28377; AAA69207.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76075.2; ALT_INIT; Genomic_DNA.
DR EMBL; AP009048; BAE77095.1; -; Genomic_DNA.
DR PIR; E65091; E65091.
DR RefSeq; NP_417511.2; NC_000913.3.
DR RefSeq; WP_000188362.1; NZ_CP011343.2.
DR PDB; 2PW6; X-ray; 2.27 A; A=1-271.
DR PDBsum; 2PW6; -.
DR AlphaFoldDB; P24197; -.
DR SMR; P24197; -.
DR BioGRID; 4263035; 3.
DR IntAct; P24197; 3.
DR STRING; 511145.b3039; -.
DR PaxDb; P24197; -.
DR PRIDE; P24197; -.
DR EnsemblBacteria; AAC76075; AAC76075; b3039.
DR EnsemblBacteria; BAE77095; BAE77095; BAE77095.
DR GeneID; 946447; -.
DR KEGG; ecj:JW3007; -.
DR KEGG; eco:b3039; -.
DR PATRIC; fig|1411691.4.peg.3693; -.
DR EchoBASE; EB1154; -.
DR eggNOG; COG3384; Bacteria.
DR HOGENOM; CLU_046582_2_0_6; -.
DR InParanoid; P24197; -.
DR BioCyc; EcoCyc:EG11166-MON; -.
DR BioCyc; MetaCyc:EG11166-MON; -.
DR EvolutionaryTrace; P24197; -.
DR PRO; PR:P24197; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0046566; F:DOPA dioxygenase activity; IDA:EcoCyc.
DR GO; GO:0008198; F:ferrous iron binding; IEA:InterPro.
DR GO; GO:0050297; F:stizolobate synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006725; P:cellular aromatic compound metabolic process; IEA:InterPro.
DR CDD; cd07363; 45_DOPA_Dioxygenase; 1.
DR InterPro; IPR014436; Extradiol_dOase_DODA.
DR InterPro; IPR004183; Xdiol_dOase_suB.
DR Pfam; PF02900; LigB; 1.
DR PIRSF; PIRSF006157; Doxgns_DODA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Dioxygenase; Metal-binding; Oxidoreductase;
KW Reference proteome; Zinc.
FT CHAIN 1..271
FT /note="4,5-DOPA dioxygenase extradiol"
FT /id="PRO_0000169405"
FT BINDING 22
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|Ref.5"
FT BINDING 57
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|Ref.5"
FT BINDING 177
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|Ref.5"
FT BINDING 234
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|Ref.5"
FT CONFLICT 243..270
FT /note="GAWDGQEPITIPVEGIEMGSLSMLSVQI -> RYVGWAGANYHS (in
FT Ref. 1; AAA71877)"
FT /evidence="ECO:0000305"
FT STRAND 17..21
FT /evidence="ECO:0007829|PDB:2PW6"
FT HELIX 33..44
FT /evidence="ECO:0007829|PDB:2PW6"
FT STRAND 49..66
FT /evidence="ECO:0007829|PDB:2PW6"
FT HELIX 95..105
FT /evidence="ECO:0007829|PDB:2PW6"
FT STRAND 110..115
FT /evidence="ECO:0007829|PDB:2PW6"
FT HELIX 121..130
FT /evidence="ECO:0007829|PDB:2PW6"
FT STRAND 138..144
FT /evidence="ECO:0007829|PDB:2PW6"
FT HELIX 149..159
FT /evidence="ECO:0007829|PDB:2PW6"
FT HELIX 160..165
FT /evidence="ECO:0007829|PDB:2PW6"
FT STRAND 167..173
FT /evidence="ECO:0007829|PDB:2PW6"
FT STRAND 184..186
FT /evidence="ECO:0007829|PDB:2PW6"
FT HELIX 192..202
FT /evidence="ECO:0007829|PDB:2PW6"
FT TURN 203..206
FT /evidence="ECO:0007829|PDB:2PW6"
FT HELIX 211..213
FT /evidence="ECO:0007829|PDB:2PW6"
FT TURN 215..217
FT /evidence="ECO:0007829|PDB:2PW6"
FT HELIX 219..221
FT /evidence="ECO:0007829|PDB:2PW6"
FT HELIX 225..228
FT /evidence="ECO:0007829|PDB:2PW6"
FT STRAND 230..232
FT /evidence="ECO:0007829|PDB:2PW6"
FT TURN 233..235
FT /evidence="ECO:0007829|PDB:2PW6"
FT HELIX 236..243
FT /evidence="ECO:0007829|PDB:2PW6"
FT STRAND 247..249
FT /evidence="ECO:0007829|PDB:2PW6"
FT TURN 260..262
FT /evidence="ECO:0007829|PDB:2PW6"
FT STRAND 268..270
FT /evidence="ECO:0007829|PDB:2PW6"
SQ SEQUENCE 271 AA; 29903 MW; A74E9035BAF6EB0F CRC64;
MTPLVKDIIM SSTRMPALFL GHGSPMNVLE DNLYTRSWQK LGMTLPRPQA IVVVSAHWFT
RGTGVTAMET PPTIHDFGGF PQALYDTHYP APGSPALAQR LVELLAPIPV TLDKEAWGFD
HGSWGVLIKM YPDADIPMVQ LSIDSSKPAA WHFEMGRKLA ALRDEGIMLV ASGNVVHNLR
TVKWHGDSSP YPWATSFNEY VKANLTWQGP VEQHPLVNYL DHEGGTLSNP TPEHYLPLLY
VLGAWDGQEP ITIPVEGIEM GSLSMLSVQI G
