KDSB_ARATH
ID KDSB_ARATH Reviewed; 290 AA.
AC Q9C920;
DT 06-MAR-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 25-MAY-2022, entry version 123.
DE RecName: Full=3-deoxy-manno-octulosonate cytidylyltransferase, mitochondrial {ECO:0000303|PubMed:21893514};
DE EC=2.7.7.38 {ECO:0000269|PubMed:19914588};
DE AltName: Full=CMP-2-keto-3-deoxyoctulosonic acid synthase {ECO:0000303|Ref.1};
DE Short=AtCKS {ECO:0000303|PubMed:21893514};
DE Short=CMP-KDO synthase {ECO:0000303|Ref.1};
DE Flags: Precursor;
GN Name=KDSB {ECO:0000305};
GN Synonyms=CKS {ECO:0000303|PubMed:21893514}, KDO1 {ECO:0000303|Ref.1};
GN OrderedLocusNames=At1g53000 {ECO:0000312|Araport:AT1G53000};
GN ORFNames=F14G24.28 {ECO:0000312|EMBL:AAG52266.1};
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].
RC STRAIN=cv. Columbia;
RA Wilson I.B.H.;
RT "Cloning of Arabidopsis CMP-KDO synthetase.";
RL Submitted (AUG-2002) to the EMBL/GenBank/DDBJ databases.
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=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, TISSUE SPECIFICITY, AND COFACTOR.
RX PubMed=19914588; DOI=10.1016/j.jbiosc.2009.05.022;
RA Misaki R., Kajiura H., Fujii K., Fujiyama K., Seki T.;
RT "Cloning and characterization of cytidine monophosphate-3-deoxy-d-manno-
RT octulosonate synthetase from Arabidopsis thaliana.";
RL J. Biosci. Bioeng. 108:527-529(2009).
RN [6]
RP SUBCELLULAR LOCATION.
RX PubMed=21896887; DOI=10.1104/pp.111.183160;
RA Duncan O., Taylor N.L., Carrie C., Eubel H., Kubiszewski-Jakubiak S.,
RA Zhang B., Narsai R., Millar A.H., Whelan J.;
RT "Multiple lines of evidence localize signaling, morphology, and lipid
RT biosynthesis machinery to the mitochondrial outer membrane of
RT Arabidopsis.";
RL Plant Physiol. 157:1093-1113(2011).
RN [7]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBCELLULAR LOCATION.
RX PubMed=21893514; DOI=10.1093/pcp/pcr120;
RA Kobayashi M., Kouzu N., Inami A., Toyooka K., Konishi Y., Matsuoka K.,
RA Matoh T.;
RT "Characterization of Arabidopsis CTP:3-deoxy-D-manno-2-octulosonate
RT cytidylyltransferase (CMP-KDO synthetase), the enzyme that activates KDO
RT during rhamnogalacturonan II biosynthesis.";
RL Plant Cell Physiol. 52:1832-1843(2011).
RN [8]
RP ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND 3D-STRUCTURE
RP MODELING.
RX PubMed=23335734; DOI=10.1093/mp/sst011;
RA Smyth K.M., Mikolajek H., Werner J.M., Marchant A.;
RT "2beta-deoxy-Kdo is an inhibitor of the Arabidopsis thaliana CMP-2-Keto-3-
RT deoxymanno-octulosonic acid synthetase, the enzyme required for activation
RT of Kdo prior to incorporation into rhamnogalacturonan II.";
RL Mol. Plant 6:981-984(2013).
CC -!- FUNCTION: Catalyzes the production of the sugar nucleotide CMP-3-deoxy-
CC D-manno-octulosonate (CMP-KDO). CTP is the preferred nucleotide donor,
CC but it can partially be replaced with UTP. Activates KDO during the
CC biosynthesis of rhamnogalacturonan II (RG-II), a structurally complex
CC pectic polysaccharide of the primary cell wall. RG-II is essential for
CC the cell wall integrity of rapidly growing tissues and pollen tube
CC growth and elongation. {ECO:0000269|PubMed:19914588,
CC ECO:0000269|PubMed:21893514}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-deoxy-alpha-D-manno-oct-2-ulosonate + CTP = CMP-3-deoxy-
CC beta-D-manno-octulosonate + diphosphate; Xref=Rhea:RHEA:23448,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:37563, ChEBI:CHEBI:85986,
CC ChEBI:CHEBI:85987; EC=2.7.7.38;
CC Evidence={ECO:0000269|PubMed:19914588};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:19914588};
CC -!- ACTIVITY REGULATION: Inhibited by 2beta-deoxy-Kdo.
CC {ECO:0000269|PubMed:23335734}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=88.59 uM for 3-deoxy-D-manno-octulosonate
CC {ECO:0000269|PubMed:23335734};
CC Vmax=14.62 umol/min/ug enzyme {ECO:0000269|PubMed:23335734};
CC Note=kcat is 8.77 sec(-1) for 3-deoxy-D-manno-octulosonate.
CC {ECO:0000269|PubMed:23335734};
CC pH dependence:
CC Optimum pH is 9.5. {ECO:0000269|PubMed:21893514};
CC -!- PATHWAY: Nucleotide-sugar biosynthesis; CMP-3-deoxy-D-manno-
CC octulosonate biosynthesis; CMP-3-deoxy-D-manno-octulosonate from 3-
CC deoxy-D-manno-octulosonate and CTP: step 1/1. {ECO:0000305}.
CC -!- INTERACTION:
CC Q9C920; Q38845: PP2AA1; NbExp=3; IntAct=EBI-25521209, EBI-1645478;
CC -!- SUBCELLULAR LOCATION: Mitochondrion outer membrane
CC {ECO:0000305|PubMed:21893514, ECO:0000305|PubMed:21896887}; Peripheral
CC membrane protein {ECO:0000305|PubMed:21893514,
CC ECO:0000305|PubMed:21896887}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems and siliques.
CC {ECO:0000269|PubMed:19914588}.
CC -!- MISCELLANEOUS: Rhamnogalacturonan II (RG-II) RG-II is a structurally
CC complex pectic polysaccharide present in the primary cell wall. RG-II
CC consists of a linear 1,4-linked a-Dgalacturonic acid backbone with four
CC distinct side chains, two of which contain apiosyl residues. Boric acid
CC forms a diester with two apiosyl residues from separate RG-II
CC molecules, thereby covalently cross-linking two RG-II molecules as a
CC dimer.
CC -!- SIMILARITY: Belongs to the KdsB family. {ECO:0000305}.
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DR EMBL; AJ505021; CAD43603.1; -; mRNA.
DR EMBL; AC019018; AAG52266.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE32875.1; -; Genomic_DNA.
DR EMBL; AK317553; BAH20217.1; -; mRNA.
DR RefSeq; NP_175708.2; NM_104178.5.
DR AlphaFoldDB; Q9C920; -.
DR SMR; Q9C920; -.
DR BioGRID; 26958; 5.
DR IntAct; Q9C920; 1.
DR STRING; 3702.AT1G53000.1; -.
DR SwissPalm; Q9C920; -.
DR PaxDb; Q9C920; -.
DR PRIDE; Q9C920; -.
DR ProteomicsDB; 237136; -.
DR EnsemblPlants; AT1G53000.1; AT1G53000.1; AT1G53000.
DR GeneID; 841733; -.
DR Gramene; AT1G53000.1; AT1G53000.1; AT1G53000.
DR KEGG; ath:AT1G53000; -.
DR Araport; AT1G53000; -.
DR TAIR; locus:2037015; AT1G53000.
DR eggNOG; ENOG502QPIP; Eukaryota.
DR HOGENOM; CLU_065038_2_0_1; -.
DR InParanoid; Q9C920; -.
DR PhylomeDB; Q9C920; -.
DR BRENDA; 2.7.7.38; 399.
DR UniPathway; UPA00358; UER00476.
DR PRO; PR:Q9C920; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9C920; baseline and differential.
DR Genevisible; Q9C920; AT.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0031307; C:integral component of mitochondrial outer membrane; IDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
DR GO; GO:0008690; F:3-deoxy-manno-octulosonate cytidylyltransferase activity; IDA:TAIR.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0033468; P:CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process; IDA:TAIR.
DR GO; GO:0009555; P:pollen development; IMP:TAIR.
DR GO; GO:0009860; P:pollen tube growth; IMP:TAIR.
DR CDD; cd02517; CMP-KDO-Synthetase; 1.
DR Gene3D; 3.90.550.10; -; 1.
DR HAMAP; MF_00057; KdsB; 1.
DR InterPro; IPR003329; Cytidylyl_trans.
DR InterPro; IPR004528; KdsB.
DR InterPro; IPR029044; Nucleotide-diphossugar_trans.
DR Pfam; PF02348; CTP_transf_3; 1.
DR SUPFAM; SSF53448; SSF53448; 1.
DR TIGRFAMs; TIGR00466; kdsB; 1.
PE 1: Evidence at protein level;
KW Cell wall biogenesis/degradation; Magnesium; Membrane; Mitochondrion;
KW Mitochondrion outer membrane; Nucleotidyltransferase; Reference proteome;
KW Transferase; Transit peptide.
FT TRANSIT 1..50
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 51..290
FT /note="3-deoxy-manno-octulosonate cytidylyltransferase,
FT mitochondrial"
FT /id="PRO_0000421464"
SQ SEQUENCE 290 AA; 32245 MW; 7A6AE112A3D51E62 CRC64;
MSVCSSSSSS QKTWIVNGIL AGTAIAAAIG ARAYLGRSKK FRSRVVGIIP ARYASSRFEG
KPLVQILGKP MIQRTWERSK LATTLDHIVV ATDDERIAEC CRGFGADVIM TSESCRNGTE
RCNEALEKLE KKYDVVVNIQ GDEPLIEPEI IDGVVKALQV TPDAVFSTAV TSLKPEDGLD
PNRVKCVVDN RGYAIYFSRG LIPYNKSGKV NPDFPYMLHL GIQSFDSKFL KVYSELQPTP
LQQEEDLEQL KVLENGYKMK VIKVDHEAHG VDTPDDVEKI ESLMRERNMS
