CK5P1_ORYSJ
ID CK5P1_ORYSJ Reviewed; 600 AA.
AC Q2R1U4; Q0IRV6;
DT 25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT 24-JAN-2006, sequence version 1.
DT 03-AUG-2022, entry version 98.
DE RecName: Full=CDK5RAP1-like protein;
GN OrderedLocusNames=Os11g0592800, LOC_Os11g38030;
GN ORFNames=OsJ_34478 {ECO:0000312|EMBL:EEE52386.1}, OSJNBa0074L11;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG The rice chromosomes 11 and 12 sequencing consortia;
RT "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT genes and recent gene duplications.";
RL BMC Biol. 3:20-20(2005).
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).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
CC -!- FUNCTION: Potential regulator of CDK5 activity. {ECO:0000250}.
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00780};
CC Note=Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000255|PROSITE-ProRule:PRU00780};
CC -!- SIMILARITY: Belongs to the methylthiotransferase family. MiaB
CC subfamily. {ECO:0000305}.
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DR EMBL; AC137744; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; DP000010; ABA94563.1; -; Genomic_DNA.
DR EMBL; AP008217; BAF28559.1; -; Genomic_DNA.
DR EMBL; AP014967; BAT14692.1; -; Genomic_DNA.
DR EMBL; CM000148; EEE52386.1; -; Genomic_DNA.
DR EMBL; AK066319; BAG89909.1; -; mRNA.
DR RefSeq; XP_015615154.1; XM_015759668.1.
DR AlphaFoldDB; Q2R1U4; -.
DR SMR; Q2R1U4; -.
DR BioGRID; 819866; 1.
DR STRING; 4530.OS11T0592800-01; -.
DR PaxDb; Q2R1U4; -.
DR PRIDE; Q2R1U4; -.
DR EnsemblPlants; Os11t0592800-01; Os11t0592800-01; Os11g0592800.
DR GeneID; 4350829; -.
DR Gramene; Os11t0592800-01; Os11t0592800-01; Os11g0592800.
DR KEGG; osa:4350829; -.
DR eggNOG; KOG2492; Eukaryota.
DR HOGENOM; CLU_018697_2_1_1; -.
DR InParanoid; Q2R1U4; -.
DR OMA; CEHFHIP; -.
DR OrthoDB; 835984at2759; -.
DR Proteomes; UP000000763; Chromosome 11.
DR Proteomes; UP000007752; Chromosome 11.
DR Proteomes; UP000059680; Chromosome 11.
DR Genevisible; Q2R1U4; OS.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0035597; F:N6-isopentenyladenosine methylthiotransferase activity; IBA:GO_Central.
DR GO; GO:0045736; P:negative regulation of cyclin-dependent protein serine/threonine kinase activity; IBA:GO_Central.
DR Gene3D; 3.40.50.12160; -; 1.
DR Gene3D; 3.80.30.20; -; 1.
DR InterPro; IPR006638; Elp3/MiaB/NifB.
DR InterPro; IPR005839; Methylthiotransferase.
DR InterPro; IPR020612; Methylthiotransferase_CS.
DR InterPro; IPR013848; Methylthiotransferase_N.
DR InterPro; IPR038135; Methylthiotransferase_N_sf.
DR InterPro; IPR006463; MiaB_methiolase.
DR InterPro; IPR007197; rSAM.
DR InterPro; IPR023404; rSAM_horseshoe.
DR InterPro; IPR002792; TRAM_dom.
DR Pfam; PF04055; Radical_SAM; 1.
DR Pfam; PF01938; TRAM; 1.
DR Pfam; PF00919; UPF0004; 1.
DR SFLD; SFLDF00273; (dimethylallyl)adenosine_tRNA; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SMART; SM00729; Elp3; 1.
DR TIGRFAMs; TIGR00089; TIGR00089; 1.
DR PROSITE; PS51449; MTTASE_N; 1.
DR PROSITE; PS01278; MTTASE_RADICAL; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
DR PROSITE; PS50926; TRAM; 1.
PE 2: Evidence at transcript level;
KW 4Fe-4S; Iron; Iron-sulfur; Metal-binding; Reference proteome;
KW S-adenosyl-L-methionine.
FT CHAIN 1..600
FT /note="CDK5RAP1-like protein"
FT /id="PRO_0000247313"
FT DOMAIN 93..222
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00780"
FT DOMAIN 246..501
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 504..580
FT /note="TRAM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00208"
FT REGION 45..66
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 47..61
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 102
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00780"
FT BINDING 139
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00780"
FT BINDING 185
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00780"
FT BINDING 260
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00780"
FT BINDING 264
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00780"
FT BINDING 267
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00780"
SQ SEQUENCE 600 AA; 67106 MW; 2699DA80A91975EB CRC64;
MAAPLTAAAA LRLGRGLSHR RAFLLRRRYS PAPLAPSPCA APRCLSSAAH PPPPPPRRLA
RSGPSRPLAA SAATAVSEAQ TDLESGPVTA SKGRIYHETY GCQMNVNDME IVLSIMKNEG
YDEIVPDPES AEIIFINTCA IRDNAEQKVW QRLNYFWFLK RQWKANVAAG RSRSLRPPKI
AVLGCMAERL KEKILDSDKM VDVVCGPDAY RDLPRLLQEV DYGQKGINTL LSLEETYADI
TPVRISDNSV TAFVSIMRGC NNMCSFCIVP FTRGRERSRP VSSIVREVGE LWKAGVKEVM
LLGQNVNSYN DTSEVEELEP GKNWELSEGF SSMCKVKNMG LRFADLLDQL SLEYPEMRFR
FTSPHPKDYP DELLYLMRDR HNVCKLIHMP AQSGSSAVLE RMRRGYTREA YLELVQKIRS
IIPDVGLSSD FISGFCGETE EEHAETLTLV RAVGYDMAYM FAYSMREKTH AHRNYVDDVP
DDVKQRRLAE LISTFRETTA KIYDSQVGTV QLVLVEGPNK RAPETEMIGK TDRGHRVSFA
SVPVPHTFEG DELRKPVVGD FIEVKITKSS TASLSGDVIA RTSLSKFYKN HSSEAHAVAA
