RMLC_PSEAE
ID RMLC_PSEAE Reviewed; 181 AA.
AC Q9HU21; Q7AYQ8;
DT 13-JUL-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=dTDP-4-dehydrorhamnose 3,5-epimerase {ECO:0000305|PubMed:17046787};
DE EC=5.1.3.13 {ECO:0000305|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};
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=rmlC; OrderedLocusNames=PA5164;
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RA Maeki M.;
RT "Cloning and characterization of the rmlC gene of Pseudomonas aeruginosa.";
RL Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT pathogen.";
RL Nature 406:959-964(2000).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG,
RP AND SUBUNIT.
RA Dong C.J., Naismith J.H.;
RT "RmlC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) crystal structure from
RT Pseudomonas aeruginosa, apo structure.";
RL Submitted (DEC-2003) to the PDB data bank.
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.79 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS,
RP FUNCTION IN DTDP-RHAMNOSE BIOSYNTHESIS, CATALYTIC ACTIVITY, REACTION
RP MECHANISM, ACTIVE SITE, AND SUBUNIT.
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).
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:0000305|PubMed:17046787};
CC -!- PATHWAY: Carbohydrate biosynthesis; dTDP-L-rhamnose biosynthesis.
CC {ECO:0000250|UniProtKB:P26394}.
CC -!- PATHWAY: Bacterial outer membrane biogenesis; lipopolysaccharide
CC biosynthesis. {ECO:0000250|UniProtKB:P26394}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:17046787, ECO:0000305|Ref.3}.
CC -!- SIMILARITY: Belongs to the dTDP-4-dehydrorhamnose 3,5-epimerase family.
CC {ECO:0000305}.
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DR EMBL; AJ298594; CAC82199.1; -; Genomic_DNA.
DR EMBL; AE004091; AAG08549.1; -; Genomic_DNA.
DR PIR; E83000; E83000.
DR RefSeq; NP_253851.1; NC_002516.2.
DR RefSeq; WP_003096184.1; NZ_QZGE01000002.1.
DR PDB; 1RTV; X-ray; 2.50 A; A=1-181.
DR PDB; 2IXH; X-ray; 2.00 A; A/B=1-181.
DR PDB; 2IXI; X-ray; 1.80 A; A/B=1-181.
DR PDB; 2IXJ; X-ray; 2.54 A; A=1-181.
DR PDB; 2IXK; X-ray; 1.70 A; A/B=1-181.
DR PDBsum; 1RTV; -.
DR PDBsum; 2IXH; -.
DR PDBsum; 2IXI; -.
DR PDBsum; 2IXJ; -.
DR PDBsum; 2IXK; -.
DR AlphaFoldDB; Q9HU21; -.
DR SMR; Q9HU21; -.
DR STRING; 287.DR97_2532; -.
DR DrugBank; DB01694; D-tartaric acid.
DR PaxDb; Q9HU21; -.
DR PRIDE; Q9HU21; -.
DR DNASU; 879991; -.
DR EnsemblBacteria; AAG08549; AAG08549; PA5164.
DR GeneID; 879991; -.
DR KEGG; pae:PA5164; -.
DR PATRIC; fig|208964.12.peg.5412; -.
DR PseudoCAP; PA5164; -.
DR HOGENOM; CLU_090940_1_1_6; -.
DR InParanoid; Q9HU21; -.
DR OMA; RGVFLEW; -.
DR PhylomeDB; Q9HU21; -.
DR BioCyc; PAER208964:G1FZ6-5281-MON; -.
DR UniPathway; UPA00030; -.
DR UniPathway; UPA00124; -.
DR EvolutionaryTrace; Q9HU21; -.
DR Proteomes; UP000002438; 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; IDA:PseudoCAP.
DR GO; GO:0045226; P:extracellular polysaccharide biosynthetic process; IDA:UniProtKB.
DR GO; GO:0009103; P:lipopolysaccharide biosynthetic process; IDA:UniProtKB.
DR GO; GO:0009244; P:lipopolysaccharide core region biosynthetic process; IDA:PseudoCAP.
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..181
FT /note="dTDP-4-dehydrorhamnose 3,5-epimerase"
FT /id="PRO_0000395350"
FT ACT_SITE 62
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:17046787"
FT ACT_SITE 131
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:17046787"
FT BINDING 23
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17046787,
FT ECO:0007744|PDB:2IXI, ECO:0007744|PDB:2IXK"
FT BINDING 28
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17046787,
FT ECO:0007744|PDB:2IXI, ECO:0007744|PDB:2IXK"
FT BINDING 47..49
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:17046787,
FT ECO:0007744|PDB:2IXH"
FT BINDING 59
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17046787, ECO:0000269|Ref.3,
FT ECO:0007744|PDB:1RTV, ECO:0007744|PDB:2IXH,
FT ECO:0007744|PDB:2IXJ, ECO:0007744|PDB:2IXK"
FT BINDING 71
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17046787, ECO:0000269|Ref.3,
FT ECO:0007744|PDB:1RTV, ECO:0007744|PDB:2IXH,
FT ECO:0007744|PDB:2IXI, ECO:0007744|PDB:2IXJ,
FT ECO:0007744|PDB:2IXK"
FT BINDING 118
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17046787, ECO:0000269|Ref.3,
FT ECO:0007744|PDB:1RTV, ECO:0007744|PDB:2IXH,
FT ECO:0007744|PDB:2IXI, ECO:0007744|PDB:2IXJ,
FT ECO:0007744|PDB:2IXK"
FT BINDING 142
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17046787, ECO:0000269|Ref.3,
FT ECO:0007744|PDB:1RTV, ECO:0007744|PDB:2IXJ"
FT BINDING 167
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17046787,
FT ECO:0007744|PDB:2IXH, ECO:0007744|PDB:2IXK"
FT SITE 137
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 STRAND 2..5
FT /evidence="ECO:0007829|PDB:2IXK"
FT STRAND 11..15
FT /evidence="ECO:0007829|PDB:2IXK"
FT STRAND 18..21
FT /evidence="ECO:0007829|PDB:2IXK"
FT STRAND 24..31
FT /evidence="ECO:0007829|PDB:2IXK"
FT HELIX 32..39
FT /evidence="ECO:0007829|PDB:2IXK"
FT STRAND 47..54
FT /evidence="ECO:0007829|PDB:2IXK"
FT STRAND 57..67
FT /evidence="ECO:0007829|PDB:2IXK"
FT STRAND 71..86
FT /evidence="ECO:0007829|PDB:2IXK"
FT TURN 92..95
FT /evidence="ECO:0007829|PDB:2IXK"
FT STRAND 97..103
FT /evidence="ECO:0007829|PDB:2IXK"
FT TURN 104..106
FT /evidence="ECO:0007829|PDB:2IXK"
FT STRAND 109..112
FT /evidence="ECO:0007829|PDB:2IXK"
FT STRAND 116..122
FT /evidence="ECO:0007829|PDB:2IXK"
FT STRAND 124..135
FT /evidence="ECO:0007829|PDB:2IXK"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:2IXK"
FT STRAND 142..145
FT /evidence="ECO:0007829|PDB:2IXK"
FT TURN 150..152
FT /evidence="ECO:0007829|PDB:2IXK"
FT HELIX 166..169
FT /evidence="ECO:0007829|PDB:2IXK"
FT HELIX 174..176
FT /evidence="ECO:0007829|PDB:2IXK"
SQ SEQUENCE 181 AA; 20766 MW; F44AA1D59C1772C2 CRC64;
MKATRLAIPD VILFEPRVFG DDRGFFFESY NQRAFEEACG HPVSFVQDNH SRSARGVLRG
LHYQIRQAQG KLVRATLGEV FDVAVDLRRG SPTFGQWVGE RLSAENKRQM WIPAGFAHGF
VVLSEYAEFL YKTTDFWAPE HERCIVWNDP ELKIDWPLQD APLLSEKDRQ GKAFADADCF
P
