YBEY_ARATH
ID YBEY_ARATH Reviewed; 584 AA.
AC Q8L5Z4; O82311; Q67Y53;
DT 25-OCT-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=Endoribonuclease YBEY, chloroplastic {ECO:0000305};
DE EC=3.1.-.- {ECO:0000269|PubMed:25810095};
DE Flags: Precursor;
GN Name=YBEY {ECO:0000303|PubMed:25810095};
GN OrderedLocusNames=At2g25870 {ECO:0000312|Araport:AT2G25870};
GN ORFNames=F17H15.10 {ECO:0000312|EMBL:AEC07765.1};
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
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].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Bautista V.R., Kim C.J., Chen H., Wu S.Y., De Los Reyes C., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION.
RX PubMed=21365755; DOI=10.1002/pmic.201000495;
RA Bayer R.G., Stael S., Csaszar E., Teige M.;
RT "Mining the soluble chloroplast proteome by affinity chromatography.";
RL Proteomics 11:1287-1299(2011).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=25810095; DOI=10.1104/pp.114.255000;
RA Liu J., Zhou W., Liu G., Yang C., Sun Y., Wu W., Cao S., Wang C., Hai G.,
RA Wang Z., Bock R., Huang J., Cheng Y.;
RT "The conserved endoribonuclease YbeY is required for chloroplast ribosomal
RT RNA processing in Arabidopsis.";
RL Plant Physiol. 168:205-221(2015).
CC -!- FUNCTION: Endoribonuclease required for chloroplast ribosomal RNA
CC (rRNA) processing and essential for normal growth and development. May
CC be involved in maturation of both the 5' and 3' ends of 16S, 23S, and
CC 4.5S rRNAs. Cleaves chloroplast rRNAs, mRNAs and tRNAs in vitro.
CC {ECO:0000269|PubMed:25810095}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:P71335};
CC Note=Binds 1 zinc ion. {ECO:0000250|UniProtKB:P71335};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:21365755}.
CC -!- DISRUPTION PHENOTYPE: Seedling lethality.
CC {ECO:0000269|PubMed:25810095}.
CC -!- SIMILARITY: Belongs to the endoribonuclease YbeY family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC42244.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAD44378.1; Type=Miscellaneous discrepancy; Note=Sequencing errors.; Evidence={ECO:0000305};
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DR EMBL; AC005395; AAC42244.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC07765.1; -; Genomic_DNA.
DR EMBL; AK118762; BAC43355.1; -; mRNA.
DR EMBL; AY099804; AAM20655.1; -; mRNA.
DR EMBL; AK176615; BAD44378.1; ALT_SEQ; mRNA.
DR EMBL; BT030369; ABO38782.1; -; mRNA.
DR PIR; F84653; F84653.
DR RefSeq; NP_850072.1; NM_179741.2.
DR AlphaFoldDB; Q8L5Z4; -.
DR SMR; Q8L5Z4; -.
DR STRING; 3702.AT2G25870.1; -.
DR PaxDb; Q8L5Z4; -.
DR PRIDE; Q8L5Z4; -.
DR ProteomicsDB; 228571; -.
DR EnsemblPlants; AT2G25870.1; AT2G25870.1; AT2G25870.
DR GeneID; 817128; -.
DR Gramene; AT2G25870.1; AT2G25870.1; AT2G25870.
DR KEGG; ath:AT2G25870; -.
DR Araport; AT2G25870; -.
DR TAIR; locus:2043535; AT2G25870.
DR eggNOG; ENOG502S1YA; Eukaryota.
DR HOGENOM; CLU_024900_1_0_1; -.
DR InParanoid; Q8L5Z4; -.
DR OMA; HYVYHEP; -.
DR OrthoDB; 1288281at2759; -.
DR PhylomeDB; Q8L5Z4; -.
DR PRO; PR:Q8L5Z4; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q8L5Z4; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
DR GO; GO:0004521; F:endoribonuclease activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro.
DR GO; GO:0009658; P:chloroplast organization; IMP:TAIR.
DR GO; GO:1901259; P:chloroplast rRNA processing; IMP:TAIR.
DR Gene3D; 3.40.390.30; -; 1.
DR Gene3D; 3.40.50.1000; -; 1.
DR HAMAP; MF_00009; Endoribonucl_YbeY; 1.
DR InterPro; IPR000150; Cof.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006379; HAD-SF_hydro_IIB.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR023091; MetalPrtase_cat_dom_sf_prd.
DR InterPro; IPR002036; YbeY.
DR InterPro; IPR020549; YbeY_CS.
DR PANTHER; PTHR46986; PTHR46986; 1.
DR Pfam; PF02130; YbeY; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR00099; Cof-subfamily; 1.
DR TIGRFAMs; TIGR01484; HAD-SF-IIB; 1.
DR TIGRFAMs; TIGR00043; TIGR00043; 1.
DR PROSITE; PS01306; UPF0054; 1.
PE 1: Evidence at protein level;
KW Chloroplast; Endonuclease; Hydrolase; Metal-binding; Nuclease; Plastid;
KW Reference proteome; Ribosome biogenesis; rRNA processing; Transit peptide;
KW Zinc.
FT TRANSIT 1..50
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 51..584
FT /note="Endoribonuclease YBEY, chloroplastic"
FT /id="PRO_0000441901"
FT BINDING 240
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P71335"
FT BINDING 244
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P71335"
FT BINDING 250
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P71335"
SQ SEQUENCE 584 AA; 65306 MW; 0693218D9F2474BB CRC64;
MLSRVCPTLR YNRIWSAHAR EMPRATLLLL QPNFFHSSPK TALVNRLDVT SSEFSSMFRR
SFHALRSTVG DWRKLPKPPG QVFAERREYR KIRRRAPKKK QELELSVSIC IEEQLPDDLE
IQNIAEMLRL NVPMAMTLAF NGLKDSKYKT RETDIEDLGG YETVELSVML CNDDFICKLN
KEWRGEDHAT DVLSMSQHVP ELKLPVLMMG DLVISVETAA RQAAERGHTL LDEIRILVIH
GLLHLLGFDH EISDEAEQEM EEEEELLLKN LGWKGKGLIQ SAYDIQKTTT VQPEKSDDRK
EGDGLRLYKP KFSYIFCDMD GTLLNSKSQI SEANAKALKE ALLRGLKVVI ATGKSRPGAI
RILKTADLTG SDGIISESSP GVFVQGLLVY GRQGKEVYRG NLDRDVCRET CLYSLEHRIP
LIAFSQDRCL TLFDHPLVDS LHTIYNEPKA EIISSVDQLI AEADIQKVIF MDTTEGVSSV
IRPYWSEATG DRANVVQAQS DMLEIVPPGT SKGNGVKMLL NHLGVSPDEI MAIGDGENDI
EMLQLASLGV ALSNGAEKTK AVADVIGVSN DQDGVADAIY RYAF
