RMLCD_ARATH
ID RMLCD_ARATH Reviewed; 301 AA.
AC Q9LQ04; Q8L9Z8; Q94EZ7;
DT 26-NOV-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=Bifunctional dTDP-4-dehydrorhamnose 3,5-epimerase/dTDP-4-dehydrorhamnose reductase {ECO:0000305};
DE EC=1.1.1.133 {ECO:0000269|PubMed:15020741};
DE EC=5.1.3.13 {ECO:0000269|PubMed:15020741};
DE AltName: Full=dTDP-L-rhamnose synthase;
GN Name=NRS/ER {ECO:0000303|PubMed:15020741};
GN OrderedLocusNames=At1g63000 {ECO:0000312|Araport:AT1G63000};
GN ORFNames=F16P17.17 {ECO:0000312|EMBL:AAF75813.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND TISSUE SPECIFICITY.
RX PubMed=15020741; DOI=10.1104/pp.103.037192;
RA Watt G., Leoff C., Harper A.D., Bar-Peled M.;
RT "A bifunctional 3,5-epimerase/4-keto reductase for nucleotide-rhamnose
RT synthesis in Arabidopsis.";
RL Plant Physiol. 134:1337-1346(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Bifunctional enzyme involved in dTDP-beta-L-rhamnose
CC biosynthesis. Catalyzes the epimerization of the C3' and C5'positions
CC of dTDP-6-deoxy-4-keto-alpha-D-glucose to form dTDP-4-keto-beta-L-
CC rhamnose and its reduction to yield dTDP-beta-L-rhamnose. Can form UDP-
CC beta-L-rhamnose from UDP-6-deoxy-4-keto-alpha-D-glucose, but cannot
CC convert GDP-4-dehydro-6-deoxy-D-mannose to GDP-fucose.
CC {ECO:0000269|PubMed:15020741}.
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:15020741};
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:0000269|PubMed:15020741};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=16.9 uM for dTDP-4-dehydro-6-deoxy-alpha-D-glucose
CC {ECO:0000269|PubMed:15020741};
CC KM=90 uM for NADPH {ECO:0000269|PubMed:15020741};
CC pH dependence:
CC Optimum pH is 5.5-7.5. {ECO:0000269|PubMed:15020741};
CC Temperature dependence:
CC Optimum temperature is 30 degrees Celsius.
CC {ECO:0000269|PubMed:15020741};
CC -!- PATHWAY: Carbohydrate biosynthesis; dTDP-L-rhamnose biosynthesis.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems and flowers.
CC {ECO:0000269|PubMed:15020741}.
CC -!- SIMILARITY: Belongs to the dTDP-4-dehydrorhamnose reductase family.
CC {ECO:0000305}.
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DR EMBL; AY513232; AAR99502.1; -; mRNA.
DR EMBL; AC011000; AAF75813.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE34035.1; -; Genomic_DNA.
DR EMBL; AF332445; AAG48808.1; -; mRNA.
DR EMBL; AF387005; AAK62450.1; -; mRNA.
DR EMBL; AY088123; AAM65668.1; -; mRNA.
DR PIR; B96655; B96655.
DR RefSeq; NP_564806.1; NM_104978.5.
DR PDB; 4QQR; X-ray; 2.70 A; A/B=1-301.
DR PDBsum; 4QQR; -.
DR AlphaFoldDB; Q9LQ04; -.
DR SMR; Q9LQ04; -.
DR BioGRID; 27824; 6.
DR IntAct; Q9LQ04; 1.
DR STRING; 3702.AT1G63000.1; -.
DR iPTMnet; Q9LQ04; -.
DR MetOSite; Q9LQ04; -.
DR PaxDb; Q9LQ04; -.
DR PRIDE; Q9LQ04; -.
DR ProMEX; Q9LQ04; -.
DR ProteomicsDB; 228122; -.
DR DNASU; 842603; -.
DR EnsemblPlants; AT1G63000.1; AT1G63000.1; AT1G63000.
DR GeneID; 842603; -.
DR Gramene; AT1G63000.1; AT1G63000.1; AT1G63000.
DR KEGG; ath:AT1G63000; -.
DR Araport; AT1G63000; -.
DR TAIR; locus:2015489; AT1G63000.
DR eggNOG; KOG0747; Eukaryota.
DR HOGENOM; CLU_055718_1_0_1; -.
DR InParanoid; Q9LQ04; -.
DR OMA; NADWCED; -.
DR OrthoDB; 848823at2759; -.
DR PhylomeDB; Q9LQ04; -.
DR BioCyc; ARA:AT1G63000-MON; -.
DR BioCyc; MetaCyc:AT1G63000-MON; -.
DR BRENDA; 1.1.1.133; 399.
DR UniPathway; UPA00124; -.
DR PRO; PR:Q9LQ04; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9LQ04; baseline and differential.
DR Genevisible; Q9LQ04; AT.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0008830; F:dTDP-4-dehydrorhamnose 3,5-epimerase activity; IDA:TAIR.
DR GO; GO:0008831; F:dTDP-4-dehydrorhamnose reductase activity; IDA:TAIR.
DR GO; GO:0016616; F:oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor; IBA:GO_Central.
DR GO; GO:0010489; F:UDP-4-keto-6-deoxy-glucose-3,5-epimerase activity; TAS:TAIR.
DR GO; GO:0010490; F:UDP-4-keto-rhamnose-4-keto-reductase activity; TAS:TAIR.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0019305; P:dTDP-rhamnose biosynthetic process; IDA:TAIR.
DR GO; GO:0010253; P:UDP-rhamnose biosynthetic process; IDA:TAIR.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR029903; RmlD-like-bd.
DR Pfam; PF04321; RmlD_sub_bind; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell wall biogenesis/degradation; Isomerase; NADP;
KW Oxidoreductase; Reference proteome.
FT CHAIN 1..301
FT /note="Bifunctional dTDP-4-dehydrorhamnose 3,5-
FT epimerase/dTDP-4-dehydrorhamnose reductase"
FT /id="PRO_0000431251"
FT BINDING 23..24
FT /ligand="NADPH"
FT /ligand_id="ChEBI:CHEBI:57783"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 69..71
FT /ligand="NADPH"
FT /ligand_id="ChEBI:CHEBI:57783"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT BINDING 111
FT /ligand="NADPH"
FT /ligand_id="ChEBI:CHEBI:57783"
FT /evidence="ECO:0000250|UniProtKB:P26392"
FT CONFLICT 8
FT /note="Missing (in Ref. 5; AAM65668)"
FT CONFLICT 34..38
FT /note="AQGIT -> SQGIS (in Ref. 5; AAM65668)"
FT CONFLICT 124
FT /note="P -> H (in Ref. 4; AAK62450)"
FT STRAND 14..18
FT /evidence="ECO:0007829|PDB:4QQR"
FT HELIX 23..34
FT /evidence="ECO:0007829|PDB:4QQR"
FT STRAND 38..41
FT /evidence="ECO:0007829|PDB:4QQR"
FT HELIX 49..59
FT /evidence="ECO:0007829|PDB:4QQR"
FT STRAND 62..66
FT /evidence="ECO:0007829|PDB:4QQR"
FT HELIX 80..90
FT /evidence="ECO:0007829|PDB:4QQR"
FT HELIX 92..103
FT /evidence="ECO:0007829|PDB:4QQR"
FT STRAND 107..114
FT /evidence="ECO:0007829|PDB:4QQR"
FT HELIX 143..155
FT /evidence="ECO:0007829|PDB:4QQR"
FT STRAND 161..166
FT /evidence="ECO:0007829|PDB:4QQR"
FT HELIX 180..186
FT /evidence="ECO:0007829|PDB:4QQR"
FT STRAND 187..190
FT /evidence="ECO:0007829|PDB:4QQR"
FT HELIX 200..212
FT /evidence="ECO:0007829|PDB:4QQR"
FT STRAND 217..220
FT /evidence="ECO:0007829|PDB:4QQR"
FT HELIX 229..239
FT /evidence="ECO:0007829|PDB:4QQR"
FT HELIX 270..275
FT /evidence="ECO:0007829|PDB:4QQR"
FT HELIX 282..289
FT /evidence="ECO:0007829|PDB:4QQR"
FT HELIX 292..294
FT /evidence="ECO:0007829|PDB:4QQR"
SQ SEQUENCE 301 AA; 33597 MW; 30A231E3CD351BA1 CRC64;
MVADANGSSS SSFNFLIYGK TGWIGGLLGK LCEAQGITYT YGSGRLQDRQ SIVADIESVK
PSHVFNAAGV TGRPNVDWCE SHKVETIRTN VAGTLTLADI CREKGLVLIN YATGCIFEYD
SGHPLGSGIG FKEEDTPNFT GSFYSKTKAM VEELLKNYEN VCTLRVRMPI SSDLTNPRNF
ITKIARYEKV VDIPNSMTIL DELLPISIEM AKRNLTGIYN FTNPGVVSHN EILEMYRDYI
DPSFTWKNFT LEEQAKVIVA PRSNNELDAT KLKTEFPELM SIKESLIKFV FEPNKKTEVK
A
