ID   UBID_ECOLI              Reviewed;         497 AA.
AC   P0AAB4; P26615; P27861; P76767; Q2M8E6; Q47265; Q47714;
DT   13-SEP-2005, integrated into UniProtKB/Swiss-Prot.
DT   13-SEP-2005, sequence version 1.
DT   27-MAR-2024, entry version 138.
DE   RecName: Full=3-octaprenyl-4-hydroxybenzoate carboxy-lyase {ECO:0000255|HAMAP-Rule:MF_01636, ECO:0000303|PubMed:782527};
DE            EC=4.1.1.98 {ECO:0000255|HAMAP-Rule:MF_01636, ECO:0000269|PubMed:782527};
DE   AltName: Full=Polyprenyl p-hydroxybenzoate decarboxylase {ECO:0000255|HAMAP-Rule:MF_01636};
GN   Name=ubiD {ECO:0000255|HAMAP-Rule:MF_01636}; Synonyms=yigC, yigY;
GN   OrderedLocusNames=b3843, JW3819;
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=5KC;
RX   PubMed=1584020; DOI=10.1111/j.1365-2958.1992.tb02166.x;
RA   Bailey M.J.A., Koronakis V., Schmoll T., Hughes C.;
RT   "Escherichia coli HlyT protein, a transcriptional activator of haemolysin
RT   synthesis and secretion, is encoded by the rfaH (sfrB) locus required for
RT   expression of sex factor and lipopolysaccharide genes.";
RL   Mol. Microbiol. 6:1003-1012(1992).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=1379743; DOI=10.1126/science.1379743;
RA   Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.;
RT   "Analysis of the Escherichia coli genome: DNA sequence of the region from
RT   84.5 to 86.5 minutes.";
RL   Science 257:771-778(1992).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND SEQUENCE REVISION.
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   FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, PATHWAY,
RP   SUBUNIT, AND SUBCELLULAR LOCATION.
RC   STRAIN=K12;
RX   PubMed=782527; DOI=10.1016/0005-2736(76)90407-7;
RA   Leppik R.A., Young I.G., Gibson F.;
RT   "Membrane-associated reactions in ubiquinone biosynthesis in Escherichia
RT   coli. 3-Octaprenyl-4-hydroxybenzoate carboxy-lyase.";
RL   Biochim. Biophys. Acta 436:800-810(1976).
RN   [6]
RP   IDENTIFICATION AS UBID, AND VARIANT AN66 ARG-452.
RC   STRAIN=K12;
RX   PubMed=11029449; DOI=10.1128/jb.182.21.6243-6246.2000;
RA   Zhang H., Javor G.T.;
RT   "Identification of the ubiD gene on the Escherichia coli chromosome.";
RL   J. Bacteriol. 182:6243-6246(2000).
RN   [7]
RP   X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS), AND SUBUNIT.
RA   Zhou W., Forouhar F., Seetharaman J., Fang Y., Xiao R., Cunningham K.,
RA   Ma L.-C., Chen C.X., Acton T.B., Montelione G.T., Hunt J.F., Tong L.;
RT   "Crystal structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (UbiD)
RT   from Escherichia coli, Northeast structural genomics target ER459.";
RL   Submitted (SEP-2006) to the PDB data bank.
RN   [8]
RP   X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH PRENYL-FMN ANALOG
RP   AND MANGANESE ION, ACTIVE SITE, COFACTOR, AND SUBUNIT.
RX   PubMed=28057757; DOI=10.1074/jbc.m116.762732;
RA   Marshall S.A., Fisher K., Ni Cheallaigh A., White M.D., Payne K.A.,
RA   Parker D.A., Rigby S.E., Leys D.;
RT   "Oxidative maturation and structural characterization of prenylated FMN
RT   binding by UbiD, a decarboxylase involved in bacterial ubiquinone
RT   biosynthesis.";
RL   J. Biol. Chem. 292:4623-4637(2017).
CC   -!- FUNCTION: Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy
CC       benzoate to 2-octaprenylphenol, an intermediate step in ubiquinone
CC       biosynthesis. {ECO:0000255|HAMAP-Rule:MF_01636,
CC       ECO:0000269|PubMed:782527}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a 4-hydroxy-3-all-trans-polyprenylbenzoate + H(+) = a 2-all-
CC         trans-polyprenylphenol + CO2; Xref=Rhea:RHEA:41680, Rhea:RHEA-
CC         COMP:9514, Rhea:RHEA-COMP:9516, ChEBI:CHEBI:1269, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:16526, ChEBI:CHEBI:78396; EC=4.1.1.98;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01636,
CC         ECO:0000269|PubMed:782527};
CC   -!- COFACTOR:
CC       Name=prenyl-FMN; Xref=ChEBI:CHEBI:87746; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_01636, ECO:0000269|PubMed:28057757};
CC       Note=Binds 1 prenylated FMN (prenyl-FMN) per subunit.
CC       {ECO:0000255|HAMAP-Rule:MF_01636, ECO:0000269|PubMed:28057757};
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_01636, ECO:0000269|PubMed:28057757,
CC         ECO:0000269|PubMed:782527};
CC   -!- ACTIVITY REGULATION: Requires phospholipid, a metal ion, dithiothreitol
CC       and at least one other so far unidentified soluble cofactor for maximal
CC       activity. Inhibited by EDTA. {ECO:0000269|PubMed:782527}.
CC   -!- PATHWAY: Cofactor biosynthesis; ubiquinone biosynthesis.
CC       {ECO:0000255|HAMAP-Rule:MF_01636, ECO:0000269|PubMed:782527}.
CC   -!- SUBUNIT: Homohexamer. {ECO:0000255|HAMAP-Rule:MF_01636,
CC       ECO:0000269|PubMed:28057757, ECO:0000305|PubMed:782527,
CC       ECO:0000305|Ref.7}.
CC   -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000255|HAMAP-Rule:MF_01636,
CC       ECO:0000305|PubMed:782527}; Peripheral membrane protein
CC       {ECO:0000255|HAMAP-Rule:MF_01636, ECO:0000305|PubMed:782527}.
CC   -!- SIMILARITY: Belongs to the UbiD family. {ECO:0000255|HAMAP-
CC       Rule:MF_01636}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA67639.1; Type=Frameshift; Evidence={ECO:0000305};
CC       Sequence=CAA46146.1; Type=Frameshift; Evidence={ECO:0000305};
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DR   EMBL; X65013; CAA46146.1; ALT_FRAME; Genomic_DNA.
DR   EMBL; M87049; AAA67639.1; ALT_FRAME; Genomic_DNA.
DR   EMBL; M87049; AAA67640.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC76846.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE77460.1; -; Genomic_DNA.
DR   PIR; D65189; D65189.
DR   PIR; S20905; S20905.
DR   PIR; S30734; S30734.
DR   RefSeq; NP_418285.1; NC_000913.3.
DR   RefSeq; WP_000339804.1; NZ_STEB01000021.1.
DR   PDB; 2IDB; X-ray; 2.90 A; A/B/C=1-497.
DR   PDB; 5M1B; X-ray; 3.15 A; A/B/C=1-497.
DR   PDB; 5M1C; X-ray; 2.75 A; A/B/C=1-497.
DR   PDB; 5M1D; X-ray; 2.70 A; A/B/C=1-497.
DR   PDB; 5M1E; X-ray; 2.62 A; A/B/C=1-497.
DR   PDBsum; 2IDB; -.
DR   PDBsum; 5M1B; -.
DR   PDBsum; 5M1C; -.
DR   PDBsum; 5M1D; -.
DR   PDBsum; 5M1E; -.
DR   AlphaFoldDB; P0AAB4; -.
DR   SMR; P0AAB4; -.
DR   BioGRID; 4261466; 338.
DR   BioGRID; 852623; 1.
DR   DIP; DIP-48249N; -.
DR   IntAct; P0AAB4; 4.
DR   STRING; 511145.b3843; -.
DR   jPOST; P0AAB4; -.
DR   PaxDb; 511145-b3843; -.
DR   EnsemblBacteria; AAC76846; AAC76846; b3843.
DR   GeneID; 75204835; -.
DR   GeneID; 948326; -.
DR   KEGG; ecj:JW3819; -.
DR   KEGG; eco:b3843; -.
DR   PATRIC; fig|1411691.4.peg.2867; -.
DR   EchoBASE; EB1369; -.
DR   eggNOG; COG0043; Bacteria.
DR   HOGENOM; CLU_023348_4_1_6; -.
DR   InParanoid; P0AAB4; -.
DR   OMA; DWKDVIW; -.
DR   OrthoDB; 9809841at2; -.
DR   PhylomeDB; P0AAB4; -.
DR   BioCyc; EcoCyc:EG11396-MONOMER; -.
DR   BioCyc; MetaCyc:EG11396-MONOMER; -.
DR   BRENDA; 4.1.1.98; 2026.
DR   UniPathway; UPA00232; -.
DR   EvolutionaryTrace; P0AAB4; -.
DR   PRO; PR:P0AAB4; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR   GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR   GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0008694; F:3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity; IDA:EcoCyc.
DR   GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR   GO; GO:0030145; F:manganese ion binding; IDA:EcoCyc.
DR   GO; GO:0120233; F:prenyl-FMNH2 binding; IDA:EcoCyc.
DR   GO; GO:0034214; P:protein hexamerization; IDA:EcoCyc.
DR   GO; GO:0006744; P:ubiquinone biosynthetic process; IMP:EcoCyc.
DR   GO; GO:0032150; P:ubiquinone biosynthetic process from chorismate; IMP:EcoCyc.
DR   Gene3D; 1.20.5.570; Single helix bin; 1.
DR   Gene3D; 3.40.1670.10; UbiD C-terminal domain-like; 1.
DR   HAMAP; MF_01636; UbiD; 1.
DR   InterPro; IPR002830; UbiD.
DR   InterPro; IPR049381; UbiD-like_C.
DR   InterPro; IPR049383; UbiD-like_N.
DR   InterPro; IPR023677; UbiD_bacteria.
DR   InterPro; IPR048304; UbiD_Rift_dom.
DR   NCBIfam; TIGR00148; UbiD family decarboxylase; 1.
DR   PANTHER; PTHR30108; 3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE-RELATED; 1.
DR   PANTHER; PTHR30108:SF17; FERULIC ACID DECARBOXYLASE 1; 1.
DR   Pfam; PF01977; UbiD; 1.
DR   Pfam; PF20696; UbiD_C; 1.
DR   Pfam; PF20695; UbiD_N; 1.
DR   SUPFAM; SSF50475; FMN-binding split barrel; 1.
DR   SUPFAM; SSF143968; UbiD C-terminal domain-like; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cell membrane; Decarboxylase; Flavoprotein; FMN; Lyase;
KW   Manganese; Membrane; Metal-binding; Reference proteome;
KW   Ubiquinone biosynthesis.
FT   CHAIN           1..497
FT                   /note="3-octaprenyl-4-hydroxybenzoate carboxy-lyase"
FT                   /id="PRO_0000157357"
FT   ACT_SITE        290
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01636,
FT                   ECO:0000305|PubMed:28057757"
FT   BINDING         175
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01636,
FT                   ECO:0000269|PubMed:28057757, ECO:0007744|PDB:5M1D,
FT                   ECO:0007744|PDB:5M1E"
FT   BINDING         178..180
FT                   /ligand="prenyl-FMN"
FT                   /ligand_id="ChEBI:CHEBI:87746"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01636,
FT                   ECO:0000269|PubMed:28057757, ECO:0007744|PDB:5M1D,
FT                   ECO:0007744|PDB:5M1E"
FT   BINDING         192..194
FT                   /ligand="prenyl-FMN"
FT                   /ligand_id="ChEBI:CHEBI:87746"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01636,
FT                   ECO:0000269|PubMed:28057757, ECO:0007744|PDB:5M1D,
FT                   ECO:0007744|PDB:5M1E"
FT   BINDING         197..198
FT                   /ligand="prenyl-FMN"
FT                   /ligand_id="ChEBI:CHEBI:87746"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01636,
FT                   ECO:0000269|PubMed:28057757, ECO:0007744|PDB:5M1D,
FT                   ECO:0007744|PDB:5M1E"
FT   BINDING         241
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01636,
FT                   ECO:0000269|PubMed:28057757, ECO:0007744|PDB:5M1D,
FT                   ECO:0007744|PDB:5M1E"
FT   VARIANT         452
FT                   /note="G -> R (in AN66; inactive protein)"
FT                   /evidence="ECO:0000269|PubMed:11029449"
FT   HELIX           9..18
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          22..25
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           34..44
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          49..53
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          62..64
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           70..75
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   TURN            76..78
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           84..94
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           116..118
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          123..127
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           129..131
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          132..136
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           137..139
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           142..144
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          161..167
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          174..178
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          180..185
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          188..190
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          195..197
FT                   /evidence="ECO:0007829|PDB:2IDB"
FT   HELIX           198..209
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          215..222
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           225..232
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          237..239
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           241..249
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          254..257
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          259..262
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          264..266
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          270..285
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          293..296
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          299..311
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          324..326
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           328..337
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   TURN            338..340
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           341..347
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          351..355
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           358..360
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   TURN            361..363
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          364..370
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           377..387
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           390..392
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          397..402
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           410..420
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           423..426
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          427..434
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          442..444
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          447..454
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   STRAND          463..465
FT                   /evidence="ECO:0007829|PDB:5M1D"
FT   HELIX           475..488
FT                   /evidence="ECO:0007829|PDB:5M1D"
SQ   SEQUENCE   497 AA;  55604 MW;  5432A3BEBE81ECC5 CRC64;
     MDAMKYNDLR DFLTLLEQQG ELKRITLPVD PHLEITEIAD RTLRAGGPAL LFENPKGYSM
     PVLCNLFGTP KRVAMGMGQE DVSALREVGK LLAFLKEPEP PKGFRDLFDK LPQFKQVLNM
     PTKRLRGAPC QQKIVSGDDV DLNRIPIMTC WPEDAAPLIT WGLTVTRGPH KERQNLGIYR
     QQLIGKNKLI MRWLSHRGGA LDYQEWCAAH PGERFPVSVA LGADPATILG AVTPVPDTLS
     EYAFAGLLRG TKTEVVKCIS NDLEVPASAE IVLEGYIEQG ETAPEGPYGD HTGYYNEVDS
     FPVFTVTHIT QREDAIYHST YTGRPPDEPA VLGVALNEVF VPILQKQFPE IVDFYLPPEG
     CSYRLAVVTI KKQYAGHAKR VMMGVWSFLR QFMYTKFVIV CDDDVNARDW NDVIWAITTR
     MDPARDTVLV ENTPIDYLDF ASPVSGLGSK MGLDATNKWP GETQREWGRP IKKDPDVVAH
     IDAIWDELAI FNNGKSA
//