ULAD_ECOLI
ID ULAD_ECOLI Reviewed; 216 AA.
AC P39304; Q2M6A9;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=3-keto-L-gulonate-6-phosphate decarboxylase UlaD;
DE EC=4.1.1.85 {ECO:0000269|PubMed:11741871};
DE AltName: Full=3-dehydro-L-gulonate-6-phosphate decarboxylase;
DE AltName: Full=KGPDC;
DE AltName: Full=L-ascorbate utilization protein D;
GN Name=ulaD; Synonyms=sgaH, yjfV; OrderedLocusNames=b4196, JW4154;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
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 [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 DISCUSSION OF SEQUENCE.
RA Reizer J., Charbit A., Reizer A., Saier M.H. Jr.;
RT "Novel phosphotransferases system genes revealed by bacterial genome
RT analysis: operons encoding homologues of sugar-specific permease domains of
RT the phosphotransferase system and pentose catabolic enzymes.";
RL Genome Sci. Technol. 1:53-75(1996).
RN [5]
RP DISCUSSION OF SEQUENCE.
RX PubMed=9274005; DOI=10.1099/00221287-143-8-2519;
RA Reizer J., Reizer A., Saier M.H. Jr.;
RT "Is the ribulose monophosphate pathway widely distributed in bacteria?";
RL Microbiology 143:2519-2520(1997).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, AND ROLE IN L-ASCORBATE UTILIZATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=11741871; DOI=10.1128/jb.184.1.302-306.2002;
RA Yew W.S., Gerlt J.A.;
RT "Utilization of L-ascorbate by Escherichia coli K-12: assignments of
RT functions to products of the yjf-sga and yia-sgb operons.";
RL J. Bacteriol. 184:302-306(2002).
RN [7]
RP TRANSCRIPTIONAL REGULATION.
RX PubMed=12374842; DOI=10.1128/jb.184.21.6065-6068.2002;
RA Campos E., Aguilar J., Baldoma L., Badia J.;
RT "The gene yjfQ encodes the repressor of the yjfR-X regulon (ula), which is
RT involved in L-ascorbate metabolism in Escherichia coli.";
RL J. Bacteriol. 184:6065-6068(2002).
RN [8]
RP TRANSCRIPTIONAL REGULATION.
RX PubMed=14996803; DOI=10.1128/jb.186.6.1720-1728.2004;
RA Campos E., Baldoma L., Aguilar J., Badia J.;
RT "Regulation of expression of the divergent ulaG and ulaABCDEF operons
RT involved in L-ascorbate dissimilation in Escherichia coli.";
RL J. Bacteriol. 186:1720-1728(2004).
RN [9]
RP MUTAGENESIS OF GLU-33; LYS-64; ASP-67; GLU-112; HIS-136 AND ARG-139,
RP KINETIC PARAMETERS, AND REACTION STEREOCHEMISTRY.
RX PubMed=15157077; DOI=10.1021/bi049741t;
RA Yew W.S., Wise E.L., Rayment I., Gerlt J.A.;
RT "Evolution of enzymatic activities in the orotidine 5'-monophosphate
RT decarboxylase suprafamily: mechanistic evidence for a proton relay system
RT in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase.";
RL Biochemistry 43:6427-6437(2004).
RN [10]
RP MUTAGENESIS.
RX PubMed=15697206; DOI=10.1021/bi047815v;
RA Yew W.S., Akana J., Wise E.L., Rayment I., Gerlt J.A.;
RT "Evolution of enzymatic activities in the orotidine 5'-monophosphate
RT decarboxylase suprafamily: enhancing the promiscuous D-arabino-hex-3-ulose
RT 6-phosphate synthase reaction catalyzed by 3-keto-L-gulonate 6-phosphate
RT decarboxylase.";
RL Biochemistry 44:1807-1815(2005).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.62 ANGSTROMS) OF COMPLEXES WITH MAGNESIUM;
RP PHOSPHATE AND L-GULONATE-6-PHOSPHATE, AND SUBUNIT.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=11900527; DOI=10.1021/bi012174e;
RA Wise E., Yew W.S., Babbitt P.C., Gerlt J.A., Rayment I.;
RT "Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions:
RT orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate
RT decarboxylase.";
RL Biochemistry 41:3861-3869(2002).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS) OF COMPLEXES WITH L-GULONATE
RP 6-PHOSPHATE; L-THREONOHYDROXAMATE 4-PHOSPHATE; L-XYLITOL 5-PHOSPHATE AND
RP L-XYLULOSE 5-PHOSPHATE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=14567674; DOI=10.1021/bi0348819;
RA Wise E.L., Yew W.S., Gerlt J.A., Rayment I.;
RT "Structural evidence for a 1,2-enediolate intermediate in the reaction
RT catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the
RT orotidine 5'-monophosphate decarboxylase suprafamily.";
RL Biochemistry 42:12133-12142(2003).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF MUTANTS ALA-64; ALA-136; GLN-112
RP AND GLN-112/ALA-136 IN COMPLEX WITH L-THREONOHYDROXAMATE 4-PHOSPHATE, AND
RP REACTION MECHANISM.
RX PubMed=15157078; DOI=10.1021/bi0497392;
RA Wise E.L., Yew W.S., Gerlt J.A., Rayment I.;
RT "Evolution of enzymatic activities in the orotidine 5'-monophosphate
RT decarboxylase suprafamily: crystallographic evidence for a proton relay
RT system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase.";
RL Biochemistry 43:6438-6446(2004).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF NATIVE PROTEIN IN COMPLEX WITH
RP D-RIBULOSE 5-PHOSPHATE; MUTANTS ASP-112/ALA-169 AND ASP-11/VAL-139/ALA-169
RP IN COMPLEX WITH D-RIBULOSE 5-PHOSPHATE AND MUTANT ASP-11/VAL-139/ALA-169 IN
RP COMPLEX WITH L-XYLULOSE 5-PHOSPHATE.
RX PubMed=15697207; DOI=10.1021/bi0478143;
RA Wise E.L., Yew W.S., Akana J., Gerlt J.A., Rayment I.;
RT "Evolution of enzymatic activities in the orotidine 5'-monophosphate
RT decarboxylase suprafamily: structural basis for catalytic promiscuity in
RT wild-type and designed mutants of 3-keto-L-gulonate 6-phosphate
RT decarboxylase.";
RL Biochemistry 44:1816-1823(2005).
CC -!- FUNCTION: Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into
CC L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization.
CC {ECO:0000269|PubMed:11741871}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-dehydro-L-gulonate 6-phosphate + H(+) = CO2 + L-xylulose 5-
CC phosphate; Xref=Rhea:RHEA:14353, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:57829, ChEBI:CHEBI:58774; EC=4.1.1.85;
CC Evidence={ECO:0000269|PubMed:11741871};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14354;
CC Evidence={ECO:0000269|PubMed:11741871};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Note=Binds 1 Mg(2+) ion per subunit.;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.67 mM for 3-keto-L-gulonate-6-P {ECO:0000269|PubMed:15157077};
CC -!- PATHWAY: Cofactor degradation; L-ascorbate degradation; D-xylulose 5-
CC phosphate from L-ascorbate: step 2/4.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11900527,
CC ECO:0000269|PubMed:15157078, ECO:0000269|PubMed:15697207}.
CC -!- INDUCTION: Induced by L-ascorbate. Repressed by UlaR.
CC {ECO:0000269|PubMed:12374842, ECO:0000269|PubMed:14996803}.
CC -!- MISCELLANEOUS: The reaction mechanism proceeds via the formation of a
CC Mg(2+) ion-stabilized 1,2-cis-enediolate intermediate. Water molecules
CC competitively shuttle protons from the side chains of His-136 and Arg-
CC 139 to alternate faces of this intermediate. The active site is located
CC at the interface of the component polypeptides.
CC -!- SIMILARITY: Belongs to the HPS/KGPDC family. KGPDC subfamily.
CC {ECO:0000305}.
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DR EMBL; U14003; AAA97092.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77153.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78197.1; -; Genomic_DNA.
DR PIR; S56421; S56421.
DR RefSeq; NP_418617.1; NC_000913.3.
DR RefSeq; WP_000056749.1; NZ_LN832404.1.
DR PDB; 1KV8; X-ray; 1.62 A; A/B=1-216.
DR PDB; 1KW1; X-ray; 2.20 A; A/B=1-216.
DR PDB; 1Q6L; X-ray; 1.80 A; A/B=1-216.
DR PDB; 1Q6O; X-ray; 1.20 A; A/B=1-216.
DR PDB; 1Q6Q; X-ray; 1.70 A; A/B=1-216.
DR PDB; 1Q6R; X-ray; 1.76 A; A/B=1-216.
DR PDB; 1SO3; X-ray; 1.90 A; A/B=1-216.
DR PDB; 1SO4; X-ray; 1.70 A; A/B=1-216.
DR PDB; 1SO5; X-ray; 1.80 A; A/B=1-216.
DR PDB; 1SO6; X-ray; 1.90 A; A/B=1-216.
DR PDB; 1XBV; X-ray; 1.66 A; A/B=1-216.
DR PDB; 1XBX; X-ray; 1.81 A; A/B=1-216.
DR PDB; 1XBY; X-ray; 1.58 A; A/B=1-216.
DR PDB; 1XBZ; X-ray; 1.80 A; A/B=1-216.
DR PDBsum; 1KV8; -.
DR PDBsum; 1KW1; -.
DR PDBsum; 1Q6L; -.
DR PDBsum; 1Q6O; -.
DR PDBsum; 1Q6Q; -.
DR PDBsum; 1Q6R; -.
DR PDBsum; 1SO3; -.
DR PDBsum; 1SO4; -.
DR PDBsum; 1SO5; -.
DR PDBsum; 1SO6; -.
DR PDBsum; 1XBV; -.
DR PDBsum; 1XBX; -.
DR PDBsum; 1XBY; -.
DR PDBsum; 1XBZ; -.
DR AlphaFoldDB; P39304; -.
DR SMR; P39304; -.
DR BioGRID; 4262000; 15.
DR DIP; DIP-10869N; -.
DR IntAct; P39304; 1.
DR STRING; 511145.b4196; -.
DR DrugBank; DB01655; L-gulonic acid 6-phosphate.
DR DrugBank; DB03855; L-Threonohydroxamate 4-Phosphate.
DR DrugBank; DB02630; L-xylitol 5-phosphate.
DR DrugBank; DB01923; L-Xylulose 5-Phosphate.
DR DrugBank; DB04034; Ribulose-5-Phosphate.
DR SWISS-2DPAGE; P39304; -.
DR PaxDb; P39304; -.
DR PRIDE; P39304; -.
DR EnsemblBacteria; AAC77153; AAC77153; b4196.
DR EnsemblBacteria; BAE78197; BAE78197; BAE78197.
DR GeneID; 67414814; -.
DR GeneID; 948714; -.
DR KEGG; ecj:JW4154; -.
DR KEGG; eco:b4196; -.
DR PATRIC; fig|1411691.4.peg.2505; -.
DR EchoBASE; EB2389; -.
DR eggNOG; COG0269; Bacteria.
DR HOGENOM; CLU_081825_0_0_6; -.
DR InParanoid; P39304; -.
DR OMA; WEQAQEW; -.
DR PhylomeDB; P39304; -.
DR BioCyc; EcoCyc:G7858-MON; -.
DR BioCyc; MetaCyc:G7858-MON; -.
DR BRENDA; 4.1.1.85; 2026.
DR SABIO-RK; P39304; -.
DR UniPathway; UPA00263; UER00378.
DR EvolutionaryTrace; P39304; -.
DR PRO; PR:P39304; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0033982; F:3-dehydro-L-gulonate-6-phosphate decarboxylase activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0004590; F:orotidine-5'-phosphate decarboxylase activity; IEA:InterPro.
DR GO; GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IEA:InterPro.
DR GO; GO:0019854; P:L-ascorbic acid catabolic process; IEP:EcoCyc.
DR CDD; cd04726; KGPDC_HPS; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_01267; UlaD; 1.
DR InterPro; IPR023942; 3-keto-L-gulonate6Pdecase_UlaD.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR041710; HPS/KGPDC.
DR InterPro; IPR001754; OMPdeCOase_dom.
DR InterPro; IPR011060; RibuloseP-bd_barrel.
DR Pfam; PF00215; OMPdecase; 1.
DR SMART; SM00934; OMPdecase; 1.
DR SUPFAM; SSF51366; SSF51366; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Decarboxylase; Lyase; Magnesium;
KW Metal-binding; Reference proteome.
FT CHAIN 1..216
FT /note="3-keto-L-gulonate-6-phosphate decarboxylase UlaD"
FT /id="PRO_0000212103"
FT BINDING 11
FT /ligand="substrate"
FT BINDING 33
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 62
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 192
FT /ligand="substrate"
FT SITE 64
FT /note="Transition state stabilizer"
FT SITE 67
FT /note="Transition state stabilizer"
FT MUTAGEN 33
FT /note="E->K: Loss of activity."
FT /evidence="ECO:0000269|PubMed:15157077"
FT MUTAGEN 64
FT /note="K->A: 16% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15157077"
FT MUTAGEN 67
FT /note="D->A: 5% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15157077"
FT MUTAGEN 112
FT /note="E->A: 0.5% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15157077"
FT MUTAGEN 136
FT /note="H->A: 5% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15157077"
FT MUTAGEN 139
FT /note="R->V: 17% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15157077"
FT STRAND 5..10
FT /evidence="ECO:0007829|PDB:1Q6O"
FT HELIX 15..25
FT /evidence="ECO:0007829|PDB:1Q6O"
FT HELIX 26..28
FT /evidence="ECO:0007829|PDB:1Q6O"
FT STRAND 30..34
FT /evidence="ECO:0007829|PDB:1Q6O"
FT HELIX 36..42
FT /evidence="ECO:0007829|PDB:1Q6O"
FT HELIX 45..53
FT /evidence="ECO:0007829|PDB:1Q6O"
FT STRAND 57..65
FT /evidence="ECO:0007829|PDB:1Q6O"
FT HELIX 69..78
FT /evidence="ECO:0007829|PDB:1Q6O"
FT STRAND 82..87
FT /evidence="ECO:0007829|PDB:1Q6O"
FT HELIX 92..104
FT /evidence="ECO:0007829|PDB:1Q6O"
FT STRAND 108..113
FT /evidence="ECO:0007829|PDB:1Q6O"
FT HELIX 119..127
FT /evidence="ECO:0007829|PDB:1Q6O"
FT STRAND 132..136
FT /evidence="ECO:0007829|PDB:1Q6O"
FT HELIX 139..143
FT /evidence="ECO:0007829|PDB:1Q6O"
FT HELIX 150..161
FT /evidence="ECO:0007829|PDB:1Q6O"
FT STRAND 165..171
FT /evidence="ECO:0007829|PDB:1Q6O"
FT HELIX 174..180
FT /evidence="ECO:0007829|PDB:1Q6O"
FT STRAND 186..191
FT /evidence="ECO:0007829|PDB:1Q6O"
FT HELIX 192..195
FT /evidence="ECO:0007829|PDB:1Q6O"
FT STRAND 197..199
FT /evidence="ECO:0007829|PDB:1KV8"
FT HELIX 200..214
FT /evidence="ECO:0007829|PDB:1Q6O"
SQ SEQUENCE 216 AA; 23578 MW; EC8490DA1D02D824 CRC64;
MSLPMLQVAL DNQTMDSAYE TTRLIAEEVD IIEVGTILCV GEGVRAVRDL KALYPHKIVL
ADAKIADAGK ILSRMCFEAN ADWVTVICCA DINTAKGALD VAKEFNGDVQ IELTGYWTWE
QAQQWRDAGI GQVVYHRSRD AQAAGVAWGE ADITAIKRLS DMGFKVTVTG GLALEDLPLF
KGIPIHVFIA GRSIRDAASP VEAARQFKRS IAELWG
