RMLB_SALTY
ID RMLB_SALTY Reviewed; 361 AA.
AC P26391;
DT 01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1992, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=dTDP-glucose 4,6-dehydratase {ECO:0000303|PubMed:11796113};
DE EC=4.2.1.46 {ECO:0000269|PubMed:11796113};
GN Name=rfbB {ECO:0000303|PubMed:1710759}; OrderedLocusNames=STM2097;
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].
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 X-RAY CRYSTALLOGRAPHY (2.47 ANGSTROMS) IN COMPLEX WITH NAD, COFACTOR, AND
RP SUBUNIT.
RX PubMed=11243820; DOI=10.1006/jmbi.2000.4470;
RA Allard S.T., Giraud M.F., Whitfield C., Graninger M., Messner P.,
RA Naismith J.H.;
RT "The crystal structure of dTDP-D-Glucose 4,6-dehydratase (RmlB) from
RT Salmonella enterica serovar Typhimurium, the second enzyme in the dTDP-l-
RT rhamnose pathway.";
RL J. Mol. Biol. 307:283-295(2001).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND NAD,
RP FUNCTION AS A DEHYDRATASE, CATALYTIC ACTIVITY, COFACTOR, ACTIVE SITE,
RP REACTION MECHANISM, AND SUBUNIT.
RX PubMed=11796113; DOI=10.1016/s0969-2126(01)00694-3;
RA Allard S.T., Beis K., Giraud M.-F., Hegeman A.D., Gross J.W.,
RA Wilmouth R.C., Whitfield C., Graninger M., Messner P., Allen A.G.,
RA Maskell D.J., Naismith J.H.;
RT "Toward a structural understanding of the dehydratase mechanism.";
RL Structure 10:81-92(2002).
CC -!- FUNCTION: Catalyzes the dehydration of dTDP-D-glucose to form dTDP-6-
CC deoxy-D-xylo-4-hexulose via a three-step process involving oxidation,
CC dehydration and reduction. {ECO:0000269|PubMed:11796113}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dTDP-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose
CC + H2O; Xref=Rhea:RHEA:17221, ChEBI:CHEBI:15377, ChEBI:CHEBI:57477,
CC ChEBI:CHEBI:57649; EC=4.2.1.46;
CC Evidence={ECO:0000269|PubMed:11796113};
CC -!- COFACTOR:
CC Name=NAD(+); Xref=ChEBI:CHEBI:57540;
CC Evidence={ECO:0000269|PubMed:11243820, ECO:0000269|PubMed:11796113};
CC Note=Binds 1 NAD(+) per subunit. {ECO:0000269|PubMed:11243820,
CC ECO:0000269|PubMed:11796113};
CC -!- PATHWAY: Carbohydrate biosynthesis; dTDP-L-rhamnose biosynthesis.
CC {ECO:0000250|UniProtKB:P37759}.
CC -!- PATHWAY: Bacterial outer membrane biogenesis; LPS O-antigen
CC biosynthesis. {ECO:0000250|UniProtKB:P37759}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11243820,
CC ECO:0000269|PubMed:11796113}.
CC -!- SIMILARITY: Belongs to the NAD(P)-dependent epimerase/dehydratase
CC family. dTDP-glucose dehydratase subfamily. {ECO:0000305}.
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DR EMBL; X56793; CAA40115.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL21001.1; -; Genomic_DNA.
DR PIR; S15299; S15299.
DR RefSeq; NP_461042.1; NC_003197.2.
DR RefSeq; WP_000697840.1; NC_003197.2.
DR PDB; 1G1A; X-ray; 2.47 A; A/B/C/D=1-361.
DR PDB; 1KEU; X-ray; 2.40 A; A/B=1-361.
DR PDB; 1KEW; X-ray; 1.80 A; A/B=1-361.
DR PDBsum; 1G1A; -.
DR PDBsum; 1KEU; -.
DR PDBsum; 1KEW; -.
DR AlphaFoldDB; P26391; -.
DR SMR; P26391; -.
DR STRING; 99287.STM2097; -.
DR DrugBank; DB03751; 2'deoxy-Thymidine-5'-Diphospho-Alpha-D-Glucose.
DR PaxDb; P26391; -.
DR EnsemblBacteria; AAL21001; AAL21001; STM2097.
DR GeneID; 1253618; -.
DR KEGG; stm:STM2097; -.
DR PATRIC; fig|99287.12.peg.2219; -.
DR HOGENOM; CLU_007383_1_14_6; -.
DR OMA; EWCQHVQ; -.
DR PhylomeDB; P26391; -.
DR BioCyc; SENT99287:STM2097-MON; -.
DR SABIO-RK; P26391; -.
DR UniPathway; UPA00124; -.
DR UniPathway; UPA00281; -.
DR EvolutionaryTrace; P26391; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0008460; F:dTDP-glucose 4,6-dehydratase activity; ISS:UniProtKB.
DR GO; GO:0070404; F:NADH binding; IDA:UniProtKB.
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 CDD; cd05246; dTDP_GD_SDR_e; 1.
DR InterPro; IPR005888; dTDP_Gluc_deHydtase.
DR InterPro; IPR016040; NAD(P)-bd_dom.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF16363; GDP_Man_Dehyd; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR01181; dTDP_gluc_dehyt; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lipopolysaccharide biosynthesis; Lyase; NAD;
KW Reference proteome.
FT CHAIN 1..361
FT /note="dTDP-glucose 4,6-dehydratase"
FT /id="PRO_0000183243"
FT ACT_SITE 134
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:11796113,
FT ECO:0007744|PDB:1KEU"
FT ACT_SITE 135
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P27830"
FT ACT_SITE 167
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:11796113,
FT ECO:0007744|PDB:1KEU"
FT BINDING 11..12
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:11243820,
FT ECO:0000269|PubMed:11796113, ECO:0007744|PDB:1G1A,
FT ECO:0007744|PDB:1KEU, ECO:0007744|PDB:1KEW"
FT BINDING 32..35
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:11243820,
FT ECO:0000269|PubMed:11796113, ECO:0007744|PDB:1G1A,
FT ECO:0007744|PDB:1KEU, ECO:0007744|PDB:1KEW"
FT BINDING 58..59
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:11243820,
FT ECO:0000269|PubMed:11796113, ECO:0007744|PDB:1G1A,
FT ECO:0007744|PDB:1KEU, ECO:0007744|PDB:1KEW"
FT BINDING 80..84
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:11796113,
FT ECO:0000305|PubMed:11243820, ECO:0007744|PDB:1G1A,
FT ECO:0007744|PDB:1KEU, ECO:0007744|PDB:1KEW"
FT BINDING 84
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11796113,
FT ECO:0007744|PDB:1KEU"
FT BINDING 99
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:11243820,
FT ECO:0000269|PubMed:11796113, ECO:0007744|PDB:1G1A"
FT BINDING 133
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11796113,
FT ECO:0007744|PDB:1KEU"
FT BINDING 167..171
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:11243820,
FT ECO:0000269|PubMed:11796113, ECO:0007744|PDB:1G1A,
FT ECO:0007744|PDB:1KEU, ECO:0007744|PDB:1KEW"
FT BINDING 196
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11796113,
FT ECO:0007744|PDB:1KEU"
FT BINDING 197
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:11243820,
FT ECO:0000269|PubMed:11796113, ECO:0007744|PDB:1G1A,
FT ECO:0007744|PDB:1KEU, ECO:0007744|PDB:1KEW"
FT BINDING 206..207
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11796113,
FT ECO:0007744|PDB:1KEU"
FT BINDING 222..224
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11796113,
FT ECO:0007744|PDB:1KEU"
FT BINDING 231
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11796113,
FT ECO:0007744|PDB:1KEU"
FT BINDING 266
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11796113,
FT ECO:0007744|PDB:1KEU"
FT BINDING 296..300
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11796113,
FT ECO:0007744|PDB:1KEU"
FT BINDING 357
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11796113,
FT ECO:0007744|PDB:1KEU"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 11..23
FT /evidence="ECO:0007829|PDB:1KEW"
FT STRAND 27..32
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 40..43
FT /evidence="ECO:0007829|PDB:1KEW"
FT TURN 44..48
FT /evidence="ECO:0007829|PDB:1KEW"
FT STRAND 52..56
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 62..72
FT /evidence="ECO:0007829|PDB:1KEW"
FT STRAND 75..79
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 86..91
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 94..100
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 102..116
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 120..125
FT /evidence="ECO:0007829|PDB:1KEW"
FT STRAND 127..133
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 134..137
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 143..145
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 166..185
FT /evidence="ECO:0007829|PDB:1KEW"
FT STRAND 189..194
FT /evidence="ECO:0007829|PDB:1KEW"
FT STRAND 196..199
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 207..217
FT /evidence="ECO:0007829|PDB:1KEW"
FT STRAND 221..224
FT /evidence="ECO:0007829|PDB:1KEW"
FT STRAND 230..235
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 236..249
FT /evidence="ECO:0007829|PDB:1KEW"
FT STRAND 255..258
FT /evidence="ECO:0007829|PDB:1KEW"
FT STRAND 263..265
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 266..280
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 287..290
FT /evidence="ECO:0007829|PDB:1KEW"
FT STRAND 291..294
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 309..315
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 323..336
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 338..343
FT /evidence="ECO:0007829|PDB:1KEW"
FT HELIX 347..357
FT /evidence="ECO:0007829|PDB:1KEW"
SQ SEQUENCE 361 AA; 40719 MW; 3A574B4D917EBC57 CRC64;
MKILITGGAG FIGSAVVRHI IKNTQDTVVN IDKLTYAGNL ESLSDISESN RYNFEHADIC
DSAEITRIFE QYQPDAVMHL AAESHVDRSI TGPAAFIETN IVGTYALLEV ARKYWSALGE
DKKNNFRFHH ISTDEVYGDL PHPDEVENSV TLPLFTETTA YAPSSPYSAS KASSDHLVRA
WRRTYGLPTI VTNCSNNYGP YHFPEKLIPL VILNALEGKP LPIYGKGDQI RDWLYVEDHA
RALHMVVTEG KAGETYNIGG HNEKKNLDVV FTICDLLDEI VPKATSYREQ ITYVADRPGH
DRRYAIDAGK ISRELGWKPL ETFESGIRKT VEWYLANTQW VNNVKSGAYQ SWIEQNYEGR
Q
