RMLD_SHIFL
ID RMLD_SHIFL Reviewed; 299 AA.
AC P37778; Q54163;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 10-JAN-2003, sequence version 2.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=dTDP-4-dehydrorhamnose reductase {ECO:0000250|UniProtKB:P26392};
DE EC=1.1.1.133 {ECO:0000250|UniProtKB:P26392};
DE AltName: Full=dTDP-4-keto-L-rhamnose reductase {ECO:0000250|UniProtKB:P26392};
DE AltName: Full=dTDP-6-deoxy-L-lyxo-4-hexulose reductase {ECO:0000250|UniProtKB:P26392};
DE AltName: Full=dTDP-6-deoxy-L-mannose dehydrogenase {ECO:0000250|UniProtKB:P26392};
DE AltName: Full=dTDP-L-rhamnose synthase {ECO:0000250|UniProtKB:P26392};
GN Name=rfbD {ECO:0000303|PubMed:8170390}; OrderedLocusNames=SF2103, S2226;
OS Shigella flexneri.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Shigella.
OX NCBI_TaxID=623;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION IN DTDP-RHAMNOSE BIOSYNTHESIS,
RP AND PATHWAY.
RC STRAIN=PE577 / Serotype 2a;
RX PubMed=8170390; DOI=10.1111/j.1365-2958.1994.tb00308.x;
RA Macpherson D.F., Manning P.A., Morona R.;
RT "Characterization of the dTDP-rhamnose biosynthetic genes encoded in the
RT rfb locus of Shigella flexneri.";
RL Mol. Microbiol. 11:281-292(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=YSH6200 / Serotype 2a;
RX PubMed=8157605; DOI=10.1128/jb.176.8.2362-2373.1994;
RA Rajakumar K., Jost B.H., Sasakawa C., Okada N., Yoshikawa M., Adler B.;
RT "Nucleotide sequence of the rhamnose biosynthetic operon of Shigella
RT flexneri 2a and role of lipopolysaccharide in virulence.";
RL J. Bacteriol. 176:2362-2373(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=301 / Serotype 2a;
RX PubMed=12384590; DOI=10.1093/nar/gkf566;
RA Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J.,
RA Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L.,
RA Xue Y., Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H.,
RA Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.;
RT "Genome sequence of Shigella flexneri 2a: insights into pathogenicity
RT through comparison with genomes of Escherichia coli K12 and O157.";
RL Nucleic Acids Res. 30:4432-4441(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700930 / 2457T / Serotype 2a;
RX PubMed=12704152; DOI=10.1128/iai.71.5.2775-2786.2003;
RA Wei J., Goldberg M.B., Burland V., Venkatesan M.M., Deng W., Fournier G.,
RA Mayhew G.F., Plunkett G. III, Rose D.J., Darling A., Mau B., Perna N.T.,
RA Payne S.M., Runyen-Janecky L.J., Zhou S., Schwartz D.C., Blattner F.R.;
RT "Complete genome sequence and comparative genomics of Shigella flexneri
RT serotype 2a strain 2457T.";
RL Infect. Immun. 71:2775-2786(2003).
CC -!- FUNCTION: Involved in the biosynthesis of the dTDP-L-rhamnose which is
CC an important component of lipopolysaccharide (LPS) (PubMed:8170390).
CC Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield
CC dTDP-L-rhamnose (By similarity). RmlD uses NADH and NADPH nearly
CC equally well (By similarity). {ECO:0000250|UniProtKB:P26392,
CC ECO:0000269|PubMed:8170390}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dTDP-beta-L-rhamnose + NADP(+) = dTDP-4-dehydro-beta-L-
CC rhamnose + H(+) + NADPH; Xref=Rhea:RHEA:21796, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57510, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349,
CC ChEBI:CHEBI:62830; EC=1.1.1.133;
CC Evidence={ECO:0000250|UniProtKB:P26392};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P26392};
CC Note=Binds 1 Mg(2+) ion per monomer. {ECO:0000250|UniProtKB:P26392};
CC -!- PATHWAY: Carbohydrate biosynthesis; dTDP-L-rhamnose biosynthesis.
CC {ECO:0000305|PubMed:8170390}.
CC -!- PATHWAY: Bacterial outer membrane biogenesis; LPS O-antigen
CC biosynthesis. {ECO:0000250|UniProtKB:P37760}.
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:P26392}.
CC -!- SIMILARITY: Belongs to the dTDP-4-dehydrorhamnose reductase family.
CC {ECO:0000305}.
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DR EMBL; X71970; CAA50768.1; -; Genomic_DNA.
DR EMBL; L14842; AAA53680.1; -; Genomic_DNA.
DR EMBL; AE005674; AAN43642.1; -; Genomic_DNA.
DR EMBL; AE014073; AAP17471.1; -; Genomic_DNA.
DR PIR; C55213; C55213.
DR PIR; S41535; S41535.
DR RefSeq; NP_707935.1; NC_004337.2.
DR RefSeq; WP_001023623.1; NZ_WPGW01000076.1.
DR AlphaFoldDB; P37778; -.
DR SMR; P37778; -.
DR STRING; 198214.SF2103; -.
DR EnsemblBacteria; AAN43642; AAN43642; SF2103.
DR EnsemblBacteria; AAP17471; AAP17471; S2226.
DR GeneID; 1025316; -.
DR KEGG; sfl:SF2103; -.
DR KEGG; sfx:S2226; -.
DR PATRIC; fig|198214.7.peg.2511; -.
DR HOGENOM; CLU_045518_1_0_6; -.
DR OMA; AGETTWH; -.
DR OrthoDB; 1076083at2; -.
DR UniPathway; UPA00124; -.
DR UniPathway; UPA00281; -.
DR Proteomes; UP000001006; Chromosome.
DR Proteomes; UP000002673; Chromosome.
DR GO; GO:0008831; F:dTDP-4-dehydrorhamnose reductase activity; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019305; P:dTDP-rhamnose biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0045226; P:extracellular polysaccharide biosynthetic process; ISS:UniProtKB.
DR GO; GO:0009103; P:lipopolysaccharide biosynthetic process; ISS:UniProtKB.
DR GO; GO:0009243; P:O antigen biosynthetic process; IEA:UniProtKB-UniPathway.
DR InterPro; IPR005913; dTDP_dehydrorham_reduct.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR029903; RmlD-like-bd.
DR PANTHER; PTHR10491; PTHR10491; 1.
DR Pfam; PF04321; RmlD_sub_bind; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR01214; rmlD; 1.
PE 1: Evidence at protein level;
KW Carbohydrate metabolism; Lipopolysaccharide biosynthesis; Magnesium;
KW Metal-binding; NAD; NADP; Oxidoreductase; Reference proteome.
FT CHAIN 1..299
FT /note="dTDP-4-dehydrorhamnose reductase"
FT /id="PRO_0000207987"
FT ACT_SITE 128
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 10..12
FT /ligand="NADH"
FT /ligand_id="ChEBI:CHEBI:57945"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 11..12
FT /ligand="NADPH"
FT /ligand_id="ChEBI:CHEBI:57783"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 30
FT /ligand="NADH"
FT /ligand_id="ChEBI:CHEBI:57945"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 39..40
FT /ligand="NADH"
FT /ligand_id="ChEBI:CHEBI:57945"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 39..40
FT /ligand="NADPH"
FT /ligand_id="ChEBI:CHEBI:57783"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 63..65
FT /ligand="NADH"
FT /ligand_id="ChEBI:CHEBI:57945"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 63..65
FT /ligand="NADPH"
FT /ligand_id="ChEBI:CHEBI:57783"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 102
FT /ligand="NADPH"
FT /ligand_id="ChEBI:CHEBI:57783"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 104..105
FT /ligand="dTDP-beta-L-rhamnose"
FT /ligand_id="ChEBI:CHEBI:57510"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 128
FT /ligand="NADH"
FT /ligand_id="ChEBI:CHEBI:57945"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 128
FT /ligand="NADPH"
FT /ligand_id="ChEBI:CHEBI:57783"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 132
FT /ligand="NADH"
FT /ligand_id="ChEBI:CHEBI:57945"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 132
FT /ligand="NADPH"
FT /ligand_id="ChEBI:CHEBI:57783"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 153
FT /ligand="dTDP-beta-L-rhamnose"
FT /ligand_id="ChEBI:CHEBI:57510"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT SITE 104
FT /note="Could provide a fine-tuning to achieve optimal pKa
FT matching between active site and substrate"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT CONFLICT 89
FT /note="A -> I (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 115
FT /note="P -> A (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 130
FT /note="E -> G (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 135..136
FT /note="GE -> WG (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 141
FT /note="E -> D (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 144
FT /note="A -> G (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 172
FT /note="E -> D (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 175
FT /note="E -> T (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 180
FT /note="N -> T (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 190
FT /note="E -> LD (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 197
FT /note="A -> R (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 201..202
FT /note="RV -> WL (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 227
FT /note="A -> P (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 232
FT /note="E -> K (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 239
FT /note="I -> F (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 242
FT /note="A -> P (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 260
FT /note="R -> G (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
FT CONFLICT 264
FT /note="S -> F (in Ref. 1; CAA50768)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 299 AA; 32565 MW; F2C6EF7BA8BD54DE CRC64;
MNILLFGKTG QVGWELQRAL APLGNLIALD VHSTDYCGDF SNPEGVAETV KKIRPDVIVN
AAAHTAVDKA ESEPNFAQLL NATCVEAIAK AANEVGAWVI HYSTDYVFPG NGDTPWLETD
ATAPLNVYGE TKLAGEKALQ EHCAKHLIFR TSWVYAGKGN NFAKTMLRLA KEREELAVIN
DQFGAPTGAE LLADCTAHAI RVAANKPEVA GLYHLVAGGT TTWHDYAALV FEEARRAGIN
LALNKLNAVP TTAYPTPARR PHNSRLNTEK FQQNFALVLP DWQVGVKRML NELFTTTAI
