YCJR_ECOLI
ID YCJR_ECOLI Reviewed; 262 AA.
AC P76044; Q2MBF7;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 13-NOV-2007, sequence version 2.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=3-dehydro-D-guloside 4-epimerase {ECO:0000305|PubMed:30742415};
DE EC=5.1.3.- {ECO:0000269|PubMed:30742415};
DE AltName: Full=3-keto-D-guloside 4-epimerase {ECO:0000305|PubMed:30742415};
GN Name=ycjR; OrderedLocusNames=b1314, JW5202;
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=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 [2]
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 [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBSTRATE SPECIFICITY, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=K12;
RX PubMed=30742415; DOI=10.1021/acs.biochem.8b01278;
RA Mukherjee K., Huddleston J.P., Narindoshvili T., Nemmara V.V.,
RA Raushel F.M.;
RT "Functional Characterization of the ycjQRS Gene Cluster from Escherichia
RT coli: A Novel Pathway for the Transformation of D-Gulosides to D-
RT Glucosides.";
RL Biochemistry 58:1388-1399(2019).
CC -!- FUNCTION: Catalyzes the epimerization at C4 of 3-dehydro-D-gulosides
CC leading to 3-dehydro-D-glucosides. Probably functions in a metabolic
CC pathway that transforms D-gulosides to D-glucosides. Can use methyl
CC alpha-3-dehydro-D-glucoside and methyl beta-3-dehydro-D-glucoside as
CC substrates in vitro. However, the actual specific physiological
CC substrates for this metabolic pathway are unknown. Cannot act on D-
CC psicose, D-fructose, D-tagatose, D-sorbose, L-xylulose, or L-ribulose.
CC {ECO:0000269|PubMed:30742415}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 3-dehydro-D-guloside = a 3-dehydro-D-glucoside;
CC Xref=Rhea:RHEA:61728, ChEBI:CHEBI:145016, ChEBI:CHEBI:145017;
CC Evidence={ECO:0000269|PubMed:30742415};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:30742415};
CC Note=Binds 1 Mn(2+) ion per subunit. {ECO:0000269|PubMed:30742415};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=37 mM for methyl alpha-3-dehydro-D-glucoside (at pH 8.0 and 30
CC degrees Celsius) {ECO:0000269|PubMed:30742415};
CC KM=34.5 mM for methyl beta-3-dehydro-D-glucoside (at pH 7.0 and 30
CC degrees Celsius) {ECO:0000269|PubMed:30742415};
CC KM=31 mM for methyl beta-3-dehydro-D-glucoside (at pH 8.0 and 30
CC degrees Celsius) {ECO:0000269|PubMed:30742415};
CC Note=kcat is 19.2 sec(-1) for the epimerization of methyl alpha-3-
CC dehydro-D-glucoside (at pH 8.0 and 30 degrees Celsius). kcat is 2.2
CC sec(-1) for the epimerization of methyl beta-3-dehydro-D-glucoside
CC (at pH 7.0 and 30 degrees Celsius). kcat is 4.0 sec(-1) for the
CC epimerization of methyl beta-3-dehydro-D-glucoside (at pH 8.0 and 30
CC degrees Celsius). {ECO:0000269|PubMed:30742415};
CC -!- SIMILARITY: Belongs to the hyi family. {ECO:0000305}.
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DR EMBL; U00096; AAC74396.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE76399.1; -; Genomic_DNA.
DR PIR; E64880; E64880.
DR RefSeq; NP_415830.2; NC_000913.3.
DR RefSeq; WP_000690229.1; NZ_SSZK01000012.1.
DR PDB; 6WN6; X-ray; 1.86 A; A/B/C/D=1-262.
DR PDBsum; 6WN6; -.
DR AlphaFoldDB; P76044; -.
DR SMR; P76044; -.
DR BioGRID; 4263192; 21.
DR STRING; 511145.b1314; -.
DR PaxDb; P76044; -.
DR PRIDE; P76044; -.
DR DNASU; 947427; -.
DR EnsemblBacteria; AAC74396; AAC74396; b1314.
DR EnsemblBacteria; BAE76399; BAE76399; BAE76399.
DR GeneID; 947427; -.
DR KEGG; ecj:JW5202; -.
DR KEGG; eco:b1314; -.
DR PATRIC; fig|1411691.4.peg.965; -.
DR EchoBASE; EB3674; -.
DR eggNOG; COG1082; Bacteria.
DR HOGENOM; CLU_050006_9_0_6; -.
DR InParanoid; P76044; -.
DR OMA; ECFAHAQ; -.
DR PhylomeDB; P76044; -.
DR BioCyc; EcoCyc:G6652-MON; -.
DR BioCyc; MetaCyc:G6652-MON; -.
DR PRO; PR:P76044; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; 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:0016857; F:racemase and epimerase activity, acting on carbohydrates and derivatives; IDA:EcoCyc.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:UniProtKB-KW.
DR InterPro; IPR036237; Xyl_isomerase-like_sf.
DR InterPro; IPR013022; Xyl_isomerase-like_TIM-brl.
DR Pfam; PF01261; AP_endonuc_2; 1.
DR SUPFAM; SSF51658; SSF51658; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Isomerase; Manganese; Metal-binding;
KW Reference proteome.
FT CHAIN 1..262
FT /note="3-dehydro-D-guloside 4-epimerase"
FT /id="PRO_0000209108"
FT ACT_SITE 146
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q9WYP7"
FT ACT_SITE 240
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q9WYP7"
FT BINDING 146
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:Q9WYP7"
FT BINDING 179
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:Q9WYP7"
FT BINDING 182
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9WYP7"
FT BINDING 205
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:Q9WYP7"
FT BINDING 211
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9WYP7"
FT BINDING 240
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:Q9WYP7"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:6WN6"
FT HELIX 15..25
FT /evidence="ECO:0007829|PDB:6WN6"
FT STRAND 28..33
FT /evidence="ECO:0007829|PDB:6WN6"
FT HELIX 34..39
FT /evidence="ECO:0007829|PDB:6WN6"
FT HELIX 41..51
FT /evidence="ECO:0007829|PDB:6WN6"
FT STRAND 55..59
FT /evidence="ECO:0007829|PDB:6WN6"
FT HELIX 71..91
FT /evidence="ECO:0007829|PDB:6WN6"
FT STRAND 95..100
FT /evidence="ECO:0007829|PDB:6WN6"
FT STRAND 102..104
FT /evidence="ECO:0007829|PDB:6WN6"
FT STRAND 109..111
FT /evidence="ECO:0007829|PDB:6WN6"
FT HELIX 118..139
FT /evidence="ECO:0007829|PDB:6WN6"
FT STRAND 142..146
FT /evidence="ECO:0007829|PDB:6WN6"
FT TURN 150..152
FT /evidence="ECO:0007829|PDB:6WN6"
FT HELIX 159..168
FT /evidence="ECO:0007829|PDB:6WN6"
FT STRAND 172..179
FT /evidence="ECO:0007829|PDB:6WN6"
FT HELIX 180..186
FT /evidence="ECO:0007829|PDB:6WN6"
FT HELIX 190..196
FT /evidence="ECO:0007829|PDB:6WN6"
FT TURN 197..200
FT /evidence="ECO:0007829|PDB:6WN6"
FT STRAND 201..206
FT /evidence="ECO:0007829|PDB:6WN6"
FT STRAND 211..213
FT /evidence="ECO:0007829|PDB:6WN6"
FT HELIX 221..230
FT /evidence="ECO:0007829|PDB:6WN6"
FT STRAND 235..239
FT /evidence="ECO:0007829|PDB:6WN6"
FT STRAND 245..247
FT /evidence="ECO:0007829|PDB:6WN6"
FT HELIX 248..259
FT /evidence="ECO:0007829|PDB:6WN6"
SQ SEQUENCE 262 AA; 29832 MW; 5E19C6FA47E14DF6 CRC64;
MKIGTQNQAF FPENILEKFR YIKEMGFDGF EIDGKLLVNN IEEVKAAIKE TGLPVTTACG
GYDGWIGDFI EERRLNGLKQ IERILEALAE VGGKGIVVPA AWGMFTFRLP PMTSPRSLDG
DRKMVSDSLR VLEQVAARTG TVVYLEPLNR YQDHMINTLA DARRYIVEND LKHVQIIGDF
YHMNIEEDNL AQALHDNRDL LGHVHIADNH RYQPGSGTLD FHALFEQLRA DNYQGYVVYE
GRIRAEDPAQ AYRDSLAWLR TC
