RBSD_ECOLI
ID RBSD_ECOLI Reviewed; 139 AA.
AC P04982; Q2M866;
DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2004, sequence version 3.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=D-ribose pyranase;
DE EC=5.4.99.62 {ECO:0000269|PubMed:15060078};
GN Name=rbsD; OrderedLocusNames=b3748, JW5857;
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=K12;
RX PubMed=3011793; DOI=10.1016/s0021-9258(19)57448-8;
RA Bell A.W., Buckel S.D., Groarke J.M., Hope J.N., Kingsley D.H.,
RA Hermodson M.A.;
RT "The nucleotide sequences of the rbsD, rbsA, and rbsC genes of Escherichia
RT coli K12.";
RL J. Biol. Chem. 261:7652-7658(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7686882; DOI=10.1006/geno.1993.1230;
RA Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
RT "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome:
RT organizational symmetry around the origin of replication.";
RL Genomics 16:551-561(1993).
RN [3]
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 [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 PROTEIN SEQUENCE OF 1-8.
RC STRAIN=K12;
RX PubMed=17895580; DOI=10.1266/ggs.82.291;
RA Otsuka Y., Koga M., Iwamoto A., Yonesaki T.;
RT "A role of RnlA in the RNase LS activity from Escherichia coli.";
RL Genes Genet. Syst. 82:291-299(2007).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-41.
RC STRAIN=K12;
RX PubMed=8226635; DOI=10.1128/jb.175.21.6925-6931.1993;
RA Schleyer M., Bakker E.P.;
RT "Nucleotide sequence and 3'-end deletion studies indicate that the K(+)-
RT uptake protein kup from Escherichia coli is composed of a hydrophobic core
RT linked to a large and partially essential hydrophilic C-terminus.";
RL J. Bacteriol. 175:6925-6931(1993).
RN [7]
RP CRYSTALLIZATION.
RX PubMed=11320319; DOI=10.1107/s0907444901003109;
RA Kim M.-S., Oh H., Park C., Oh B.-H.;
RT "Crystallization and preliminary X-ray crystallographic analysis of
RT Escherichia coli RbsD, a component of the ribose-transport system with
RT unknown biochemical function.";
RL Acta Crystallogr. D 57:728-730(2001).
RN [8]
RP SUBUNIT.
RX PubMed=12738765; DOI=10.1074/jbc.m304523200;
RA Kim M.-S., Shin J., Lee W., Lee H.-S., Oh B.-H.;
RT "Crystal structures of RbsD leading to the identification of cytoplasmic
RT sugar-binding proteins with a novel folding architecture.";
RL J. Biol. Chem. 278:28173-28180(2003).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF HIS-20 AND HIS-106, AND
RP REACTION MECHANISM.
RX PubMed=15060078; DOI=10.1074/jbc.m402016200;
RA Ryu K.-S., Kim C., Kim I., Yoo S., Choi B.-S., Park C.;
RT "NMR application probes a novel and ubiquitous family of enzymes that alter
RT monosaccharide configuration.";
RL J. Biol. Chem. 279:25544-25548(2004).
RN [10]
RP SUBUNIT.
RX PubMed=16731978; DOI=10.1110/ps.062175806;
RA Feng Y., Jiao W., Fu X., Chang Z.;
RT "Stepwise disassembly and apparent nonstepwise reassembly for the
RT oligomeric RbsD protein.";
RL Protein Sci. 15:1441-1448(2006).
CC -!- FUNCTION: Catalyzes the interconversion of beta-pyran and beta-furan
CC forms of D-ribose. It also catalyzes the conversion between beta-
CC allofuranose and beta-allopyranose. {ECO:0000269|PubMed:15060078}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=beta-D-ribopyranose = beta-D-ribofuranose;
CC Xref=Rhea:RHEA:25432, ChEBI:CHEBI:27476, ChEBI:CHEBI:47002;
CC EC=5.4.99.62; Evidence={ECO:0000269|PubMed:15060078};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=beta-D-allofuranose = beta-D-allopyranose;
CC Xref=Rhea:RHEA:25609, ChEBI:CHEBI:40656, ChEBI:CHEBI:50256;
CC EC=5.4.99.62; Evidence={ECO:0000269|PubMed:15060078};
CC -!- PATHWAY: Carbohydrate metabolism; D-ribose degradation; D-ribose 5-
CC phosphate from beta-D-ribopyranose: step 1/2.
CC -!- SUBUNIT: Homodecamer. {ECO:0000269|PubMed:12738765,
CC ECO:0000269|PubMed:16731978}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the RbsD / FucU family. RbsD subfamily.
CC {ECO:0000305}.
CC -!- CAUTION: Was originally thought (PubMed:3011793) to be a high affinity
CC ribose transport protein, but further analysis (PubMed:15060078) shows
CC that it is a D-ribose pyranase. {ECO:0000305|PubMed:15060078,
CC ECO:0000305|PubMed:3011793}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA62101.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; M13169; AAA51472.1; -; Genomic_DNA.
DR EMBL; L10328; AAA62101.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC76771.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE77540.1; -; Genomic_DNA.
DR EMBL; X68551; CAA48556.1; -; Genomic_DNA.
DR PIR; E65178; E65178.
DR RefSeq; NP_418204.2; NC_000913.3.
DR RefSeq; WP_001301979.1; NZ_SSZK01000036.1.
DR AlphaFoldDB; P04982; -.
DR SMR; P04982; -.
DR BioGRID; 4261236; 14.
DR STRING; 511145.b3748; -.
DR jPOST; P04982; -.
DR PaxDb; P04982; -.
DR PRIDE; P04982; -.
DR EnsemblBacteria; AAC76771; AAC76771; b3748.
DR EnsemblBacteria; BAE77540; BAE77540; BAE77540.
DR GeneID; 948267; -.
DR KEGG; ecj:JW5857; -.
DR KEGG; eco:b3748; -.
DR PATRIC; fig|1411691.4.peg.2952; -.
DR EchoBASE; EB0810; -.
DR eggNOG; COG1869; Bacteria.
DR HOGENOM; CLU_135498_0_0_6; -.
DR InParanoid; P04982; -.
DR OMA; IIRTGEC; -.
DR PhylomeDB; P04982; -.
DR BioCyc; EcoCyc:EG10817-MON; -.
DR BioCyc; MetaCyc:EG10817-MON; -.
DR BRENDA; 5.4.99.62; 2026.
DR UniPathway; UPA00916; UER00888.
DR PRO; PR:P04982; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0062193; F:D-ribose pyranase activity; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0016872; F:intramolecular lyase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0016866; F:intramolecular transferase activity; IBA:GO_Central.
DR GO; GO:0048029; F:monosaccharide binding; IEA:InterPro.
DR GO; GO:0019303; P:D-ribose catabolic process; IMP:EcoCyc.
DR Gene3D; 3.40.1650.10; -; 1.
DR HAMAP; MF_01661; D_rib_pyranase; 1.
DR InterPro; IPR023064; D-ribose_pyranase.
DR InterPro; IPR023750; RbsD-like_sf.
DR InterPro; IPR007721; RbsD_FucU.
DR PANTHER; PTHR37831; PTHR37831; 1.
DR Pfam; PF05025; RbsD_FucU; 1.
DR SUPFAM; SSF102546; SSF102546; 1.
PE 1: Evidence at protein level;
KW Carbohydrate metabolism; Cytoplasm; Direct protein sequencing; Isomerase;
KW Reference proteome.
FT CHAIN 1..139
FT /note="D-ribose pyranase"
FT /id="PRO_0000097192"
FT ACT_SITE 20
FT /note="Proton donor"
FT /evidence="ECO:0000305"
FT BINDING 28
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 106
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 128..130
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MUTAGEN 20
FT /note="H->A: Loss of pyranase activity."
FT /evidence="ECO:0000269|PubMed:15060078"
FT MUTAGEN 106
FT /note="H->A: Retains one-third of the original activity."
FT /evidence="ECO:0000269|PubMed:15060078"
SQ SEQUENCE 139 AA; 15292 MW; D19A9D98CB79F611 CRC64;
MKKGTVLNSD ISSVISRLGH TDTLVVCDAG LPIPKSTTRI DMALTQGVPS FMQVLGVVTN
EMQVEAAIIA EEIKHHNPQL HETLLTHLEQ LQKHQGNTIE IRYTTHEQFK QQTAESQAVI
RSGECSPYAN IILCAGVTF
