RMLC_SALTY
ID RMLC_SALTY Reviewed; 183 AA.
AC P26394;
DT 01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1992, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=dTDP-4-dehydrorhamnose 3,5-epimerase {ECO:0000305|PubMed:17046787};
DE EC=5.1.3.13 {ECO:0000269|PubMed:17046787};
DE AltName: Full=Thymidine diphospho-4-keto-rhamnose 3,5-epimerase {ECO:0000305|PubMed:17046787};
DE AltName: Full=dTDP-4-keto-6-deoxyglucose 3,5-epimerase {ECO:0000305|PubMed:17046787};
DE AltName: Full=dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase {ECO:0000303|PubMed:17046787};
DE AltName: Full=dTDP-L-rhamnose synthase {ECO:0000305|PubMed:17046787};
GN Name=rfbC {ECO:0000303|PubMed:1710759}; Synonyms=rmlC;
GN OrderedLocusNames=STM2094;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PATHWAY.
RC STRAIN=LT2;
RX PubMed=1710759; DOI=10.1111/j.1365-2958.1991.tb00741.x;
RA Jiang X.-M., Neal B., Santiago F., Lee S.J., Romana L.K., Reeves P.R.;
RT "Structure and sequence of the rfb (O antigen) gene cluster of Salmonella
RT serovar typhimurium (strain LT2).";
RL Mol. Microbiol. 5:695-713(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [3]
RP MUTAGENESIS OF HIS-63; LYS-73 AND TYR-133, FUNCTION IN DTDP-RHAMNOSE
RP BIOSYNTHESIS, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, REACTION
RP MECHANISM, PATHWAY, AND ACTIVE SITE.
RX PubMed=17046787; DOI=10.1016/j.jmb.2006.09.063;
RA Dong C., Major L.L., Srikannathasan V., Errey J.C., Giraud M.F., Lam J.S.,
RA Graninger M., Messner P., McNeil M.R., Field R.A., Whitfield C.,
RA Naismith J.H.;
RT "RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an
RT intermediate with an unusual twist boat conformation.";
RL J. Mol. Biol. 365:146-159(2007).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.17 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS,
RP ACTIVE SITE, AND SUBUNIT.
RX PubMed=10802738; DOI=10.1038/75178;
RA Giraud M.-F., Leonard G.A., Field R.A., Berlind C., Naismith J.H.;
RT "RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of
RT epimerase.";
RL Nat. Struct. Biol. 7:398-402(2000).
CC -!- FUNCTION: Catalyzes the epimerization of the C3' and C5'positions of
CC dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose.
CC {ECO:0000269|PubMed:17046787}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-
CC L-rhamnose; Xref=Rhea:RHEA:16969, ChEBI:CHEBI:57649,
CC ChEBI:CHEBI:62830; EC=5.1.3.13;
CC Evidence={ECO:0000269|PubMed:17046787};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.71 mM for dTDP-6-deoxy-D-xylo-4-hexulose
CC {ECO:0000269|PubMed:17046787};
CC Note=kcat is 39 sec(-1) with dTDP-6-deoxy-D-xylo-4-hexulose as
CC substrate. {ECO:0000269|PubMed:17046787};
CC -!- PATHWAY: Carbohydrate biosynthesis; dTDP-L-rhamnose biosynthesis.
CC {ECO:0000305|PubMed:17046787}.
CC -!- PATHWAY: Bacterial outer membrane biogenesis; LPS O-antigen
CC biosynthesis. {ECO:0000305|PubMed:1710759}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10802738}.
CC -!- SIMILARITY: Belongs to the dTDP-4-dehydrorhamnose 3,5-epimerase family.
CC {ECO:0000305}.
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DR EMBL; X56793; CAA40118.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL20998.1; -; Genomic_DNA.
DR PIR; S15302; S15302.
DR RefSeq; NP_461039.1; NC_003197.2.
DR RefSeq; WP_000973708.1; NC_003197.2.
DR PDB; 1DZR; X-ray; 2.17 A; A/B=1-183.
DR PDB; 1DZT; X-ray; 2.20 A; A/B=1-183.
DR PDBsum; 1DZR; -.
DR PDBsum; 1DZT; -.
DR AlphaFoldDB; P26394; -.
DR SMR; P26394; -.
DR STRING; 99287.STM2094; -.
DR DrugBank; DB02549; 3'-O-Acetylthymidine-5'-diphosphate.
DR PaxDb; P26394; -.
DR EnsemblBacteria; AAL20998; AAL20998; STM2094.
DR GeneID; 1253615; -.
DR KEGG; stm:STM2094; -.
DR PATRIC; fig|99287.12.peg.2216; -.
DR HOGENOM; CLU_090940_1_1_6; -.
DR OMA; RGVFLEW; -.
DR PhylomeDB; P26394; -.
DR BioCyc; SENT99287:STM2094-MON; -.
DR SABIO-RK; P26394; -.
DR UniPathway; UPA00124; -.
DR UniPathway; UPA00281; -.
DR EvolutionaryTrace; P26394; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0008830; F:dTDP-4-dehydrorhamnose 3,5-epimerase activity; IDA:UniProtKB.
DR GO; GO:0016854; F:racemase and epimerase activity; IBA:GO_Central.
DR GO; GO:0033692; P:cellular polysaccharide biosynthetic process; IBA:GO_Central.
DR GO; GO:0019305; P:dTDP-rhamnose biosynthetic process; IBA:GO_Central.
DR GO; GO:0045226; P:extracellular polysaccharide biosynthetic process; IDA:UniProtKB.
DR GO; GO:0009103; P:lipopolysaccharide biosynthetic process; IDA:UniProtKB.
DR GO; GO:0009243; P:O antigen biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 2.60.120.10; -; 1.
DR InterPro; IPR000888; dTDP_sugar_isom.
DR InterPro; IPR014710; RmlC-like_jellyroll.
DR InterPro; IPR011051; RmlC_Cupin_sf.
DR PANTHER; PTHR21047; PTHR21047; 1.
DR Pfam; PF00908; dTDP_sugar_isom; 1.
DR SUPFAM; SSF51182; SSF51182; 1.
DR TIGRFAMs; TIGR01221; rmlC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Isomerase;
KW Lipopolysaccharide biosynthesis; Reference proteome.
FT CHAIN 1..183
FT /note="dTDP-4-dehydrorhamnose 3,5-epimerase"
FT /id="PRO_0000207979"
FT ACT_SITE 63
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:10802738,
FT ECO:0000269|PubMed:17046787, ECO:0007744|PDB:1DZR,
FT ECO:0007744|PDB:1DZT"
FT ACT_SITE 133
FT /note="Proton donor"
FT /evidence="ECO:0000269|PubMed:10802738,
FT ECO:0000269|PubMed:17046787, ECO:0007744|PDB:1DZT"
FT BINDING 24
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9HU21"
FT BINDING 29
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10802738,
FT ECO:0007744|PDB:1DZT"
FT BINDING 48..50
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:10802738,
FT ECO:0007744|PDB:1DZT"
FT BINDING 60
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10802738,
FT ECO:0007744|PDB:1DZR, ECO:0007744|PDB:1DZT"
FT BINDING 73
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10802738,
FT ECO:0007744|PDB:1DZR, ECO:0007744|PDB:1DZT"
FT BINDING 120
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10802738,
FT ECO:0007744|PDB:1DZR, ECO:0007744|PDB:1DZT"
FT BINDING 144
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9HU21"
FT BINDING 169
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10802738,
FT ECO:0007744|PDB:1DZT"
FT SITE 139
FT /note="Participates in a stacking interaction with the
FT thymidine ring of dTDP-4-oxo-6-deoxyglucose"
FT /evidence="ECO:0000250|UniProtKB:Q5SFD1"
FT MUTAGEN 63
FT /note="H->A: Loss of epimerase activity."
FT /evidence="ECO:0000269|PubMed:17046787"
FT MUTAGEN 73
FT /note="K->A: Reduces the epimerase activity by over 100-
FT fold."
FT /evidence="ECO:0000269|PubMed:17046787"
FT MUTAGEN 133
FT /note="Y->F: Reduces the epimerase activity by over 1000-
FT fold."
FT /evidence="ECO:0000269|PubMed:17046787"
FT STRAND 3..6
FT /evidence="ECO:0007829|PDB:1DZR"
FT STRAND 13..16
FT /evidence="ECO:0007829|PDB:1DZR"
FT STRAND 19..22
FT /evidence="ECO:0007829|PDB:1DZR"
FT STRAND 25..32
FT /evidence="ECO:0007829|PDB:1DZR"
FT HELIX 33..40
FT /evidence="ECO:0007829|PDB:1DZR"
FT STRAND 48..55
FT /evidence="ECO:0007829|PDB:1DZR"
FT STRAND 58..65
FT /evidence="ECO:0007829|PDB:1DZR"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:1DZR"
FT STRAND 73..88
FT /evidence="ECO:0007829|PDB:1DZR"
FT TURN 94..97
FT /evidence="ECO:0007829|PDB:1DZR"
FT STRAND 99..105
FT /evidence="ECO:0007829|PDB:1DZR"
FT TURN 106..108
FT /evidence="ECO:0007829|PDB:1DZR"
FT STRAND 111..114
FT /evidence="ECO:0007829|PDB:1DZR"
FT STRAND 118..124
FT /evidence="ECO:0007829|PDB:1DZR"
FT STRAND 126..137
FT /evidence="ECO:0007829|PDB:1DZR"
FT TURN 141..143
FT /evidence="ECO:0007829|PDB:1DZR"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:1DZR"
FT TURN 152..155
FT /evidence="ECO:0007829|PDB:1DZR"
FT HELIX 168..171
FT /evidence="ECO:0007829|PDB:1DZR"
FT HELIX 176..178
FT /evidence="ECO:0007829|PDB:1DZR"
SQ SEQUENCE 183 AA; 20663 MW; 0176B52C38038C77 CRC64;
MMIVIKTAIP DVLILEPKVF GDERGFFFES YNQQTFEELI GRKVTFVQDN HSKSKKNVLR
GLHFQRGENA QGKLVRCAVG EVFDVAVDIR KESPTFGQWV GVNLSAENKR QLWIPEGFAH
GFVTLSEYAE FLYKATNYYS PSSEGSILWN DEAIGIEWPF SQLPELSAKD AAAPLLDQAL
LTE
