CERK_ORYSJ
ID CERK_ORYSJ Reviewed; 607 AA.
AC C0LT23; Q0DZ01; Q6H6H1;
DT 01-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 05-MAY-2009, sequence version 1.
DT 03-AUG-2022, entry version 70.
DE RecName: Full=Ceramide kinase;
DE Short=OsCERK;
DE EC=2.7.1.138;
GN Name=CERK; OrderedLocusNames=Os02g0656200, LOC_Os02g43906/LOC_Os02g43912;
GN ORFNames=OJ1003_B06.39, P0519E06.23;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, TISSUE SPECIFICITY, AND MUTAGENESIS OF
RP CYS-454; CYS-458 AND CYS-461.
RC STRAIN=cv. Nipponbare;
RX PubMed=21483860; DOI=10.1371/journal.pone.0018079;
RA Bi F.C., Zhang Q.F., Liu Z., Fang C., Li J., Su J.B., Greenberg J.T.,
RA Wang H.B., Yao N.;
RT "A conserved cysteine motif is critical for rice ceramide kinase activity
RT and function.";
RL PLoS ONE 6:E18079-E18079(2011).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
CC -!- FUNCTION: Catalyzes specifically the phosphorylation of ceramide to
CC form ceramide 1-phosphate. Possesses activity on ceramide analog (C6
CC synthetic ceramide) in vitro. Ceramide is a critical sphingolipid
CC metabolite that induces programmed cell death (PCD) in plants and
CC ceramide-1-phosphate has a PCD suppressive effect. Thus, ceramide
CC phosphorylation plays a role in the modulation of PCD and CERK activity
CC is crucial for the maintenance of cell viability.
CC {ECO:0000269|PubMed:21483860}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an N-acylsphing-4-enine + ATP = ADP + an N-acylsphing-4-enine
CC 1-phosphate + H(+); Xref=Rhea:RHEA:17929, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:52639, ChEBI:CHEBI:57674,
CC ChEBI:CHEBI:456216; EC=2.7.1.138;
CC Evidence={ECO:0000269|PubMed:21483860};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000269|PubMed:21483860};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:21483860};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.1 uM for C6 ceramide {ECO:0000269|PubMed:21483860};
CC KM=36.4 uM for ATP {ECO:0000269|PubMed:21483860};
CC Vmax=4.7 nmol/min/mg enzyme toward C6 ceramide
CC {ECO:0000269|PubMed:21483860};
CC Vmax=2.6 nmol/min/mg enzyme toward ATP {ECO:0000269|PubMed:21483860};
CC pH dependence:
CC Optimum pH is 7.0 (at 40 degrees Celsius).
CC {ECO:0000269|PubMed:21483860};
CC Temperature dependence:
CC Optimum temperature is 40 degrees Celsius.
CC {ECO:0000269|PubMed:21483860};
CC -!- TISSUE SPECIFICITY: Highly expressed in leaves and at lower levels in
CC stems. {ECO:0000269|PubMed:21483860}.
CC -!- MISCELLANEOUS: Overexpression of CERK in the Arabidopsis mutant acd5
CC restores wild-type phenotype. {ECO:0000305|PubMed:21483860}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAD25337.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAD25678.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAF09537.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; FJ765452; ACN66286.1; -; mRNA.
DR EMBL; AP004676; BAD25337.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP005006; BAD25678.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008208; BAF09537.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014958; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; XP_015627473.1; XM_015771987.1.
DR AlphaFoldDB; C0LT23; -.
DR SMR; C0LT23; -.
DR STRING; 4530.OS02T0656200-01; -.
DR PaxDb; C0LT23; -.
DR PRIDE; C0LT23; -.
DR GeneID; 4330198; -.
DR KEGG; osa:4330198; -.
DR eggNOG; KOG1115; Eukaryota.
DR HOGENOM; CLU_013399_2_2_1; -.
DR PlantReactome; R-OSA-1119325; Sphingolipid metabolism.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR Genevisible; C0LT23; OS.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0001729; F:ceramide kinase activity; IDA:UniProtKB.
DR GO; GO:0102773; F:dihydroceramide kinase activity; IEA:UniProtKB-EC.
DR GO; GO:0001727; F:lipid kinase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003951; F:NAD+ kinase activity; IEA:InterPro.
DR GO; GO:0006672; P:ceramide metabolic process; IDA:UniProtKB.
DR GO; GO:0043069; P:negative regulation of programmed cell death; IDA:UniProtKB.
DR GO; GO:0016310; P:phosphorylation; IBA:GO_Central.
DR GO; GO:0006665; P:sphingolipid metabolic process; IBA:GO_Central.
DR Gene3D; 3.40.50.10330; -; 1.
DR InterPro; IPR017438; ATP-NAD_kinase_N.
DR InterPro; IPR045363; CERK_C.
DR InterPro; IPR001206; Diacylglycerol_kinase_cat_dom.
DR InterPro; IPR016064; NAD/diacylglycerol_kinase_sf.
DR Pfam; PF19280; CERK_C; 1.
DR Pfam; PF00781; DAGK_cat; 1.
DR SUPFAM; SSF111331; SSF111331; 2.
DR PROSITE; PS50146; DAGK; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Calcium; Kinase; Magnesium; Metal-binding; Nucleotide-binding;
KW Reference proteome; Transferase.
FT CHAIN 1..607
FT /note="Ceramide kinase"
FT /id="PRO_0000430309"
FT DOMAIN 135..358
FT /note="DAGKc"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT REGION 246..297
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 454..461
FT /note="CXXXCXXC"
FT COMPBIAS 252..297
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 206
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT BINDING 145..149
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 176
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 204..207
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 205..211
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 320
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT MUTAGEN 454
FT /note="C->A: 26% reduction of activity."
FT /evidence="ECO:0000269|PubMed:21483860"
FT MUTAGEN 458
FT /note="C->A: 36% reduction of activity."
FT /evidence="ECO:0000269|PubMed:21483860"
FT MUTAGEN 461
FT /note="C->A: 75% reduction of activity."
FT /evidence="ECO:0000269|PubMed:21483860"
SQ SEQUENCE 607 AA; 67295 MW; D4014C87792F50A5 CRC64;
MEGGGEALFL DGVGEVTVAV GDDGLSFQPL HQEVSSSCWS SIIMQPKLES KLKFSDVYAV
ELLEVGPVCE PWNARATVQG KINTEMNRFV IHTVTRPRKR PSPWVPCEYI FGHKDQQTCK
TWVEHIKTCI NKEQDRPKSL MVFVHPLCGK GRGCKNWETV APLFERAKVK TKVIVTQRAG
HAYDTLASLS DKDLKKFDGV IAVGGDGLFN EILNGLLSTR HTNSYPPTPE GFGYFRNNMK
CQEHRNNDLS NSELTGDDAN AISGSSNTPD DHEPLLSTTR STGLDISSSD SSDEPCNGDQ
VPLVSFPNNW FRLGIIPSGS TDAIVLSTTG ERDPVTSALL IILGRRISLD IAQVVRWKSS
PSAEVSPTVR YAASFAGYGF YGEVIRESEK YRWMGPARYD FSGTMVFLKH RSYEAKVAFL
ENGNTHSLTA SAENNANGVQ TLQYHQNRHR KTICRTNCLI CKGTSTSEQN SEDENPDSSR
TACETPKWVW SKGRFLSVGA AVISCRNERA PDGLVADAHL SDGFLHLLLI RDCPLPFYLW
HLTQFTKKGS DPLSFKFVEH HKTQAFTFIS SHDESVWNLD GELLQACEVS VQAFRGLVNL
FASGPEV
