UBID_ECOLI
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 03-AUG-2022, entry version 130.
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; Proteobacteria; 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;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01636,
CC 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;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01636,
CC ECO:0000269|PubMed:28057757, 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};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
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; P0AAB4; -.
DR PRIDE; P0AAB4; -.
DR EnsemblBacteria; AAC76846; AAC76846; b3843.
DR EnsemblBacteria; BAE77460; BAE77460; BAE77460.
DR GeneID; 66672251; -.
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; SYQQFWG; -.
DR PhylomeDB; P0AAB4; -.
DR BioCyc; EcoCyc:EG11396-MON; -.
DR BioCyc; MetaCyc:EG11396-MON; -.
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:0016831; F:carboxy-lyase activity; IBA:GO_Central.
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 HAMAP; MF_01636; UbiD; 1.
DR InterPro; IPR002830; UbiD.
DR InterPro; IPR023677; UbiD_bacteria.
DR PANTHER; PTHR30108; PTHR30108; 1.
DR Pfam; PF01977; UbiD; 1.
DR TIGRFAMs; TIGR00148; TIGR00148; 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
