ID   CYP59_ARATH             Reviewed;         506 AA.
AC   Q6Q151; Q93YQ8; Q9C8M7;
DT   09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2004, sequence version 1.
DT   24-JAN-2024, entry version 141.
DE   RecName: Full=Peptidyl-prolyl cis-trans isomerase CYP59;
DE            Short=AtCYP59;
DE            Short=PPIase CYP59;
DE            EC=5.2.1.8;
DE   AltName: Full=Cyclophilin-59;
GN   Name=CYP59; OrderedLocusNames=At1g53720; ORFNames=F22G10.24;
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] (ISOFORM 1), TISSUE SPECIFICITY, GENE FAMILY,
RP   AND NOMENCLATURE.
RX   PubMed=15051864; DOI=10.1104/pp.103.022160;
RA   Romano P.G.N., Horton P., Gray J.E.;
RT   "The Arabidopsis cyclophilin gene family.";
RL   Plant Physiol. 134:1268-1282(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] (ISOFORM 2).
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   GENE FAMILY, NOMENCLATURE, AND TISSUE SPECIFICITY.
RC   STRAIN=cv. Columbia;
RX   PubMed=15047905; DOI=10.1104/pp.103.031005;
RA   He Z., Li L., Luan S.;
RT   "Immunophilins and parvulins. Superfamily of peptidyl prolyl isomerases in
RT   Arabidopsis.";
RL   Plant Physiol. 134:1248-1267(2004).
RN   [6]
RP   FUNCTION, TISSUE SPECIFICITY, INTERACTION WITH NRPB1; SCL28; SCL30; SCL30A;
RP   SCL33; SC35; SR30; SR34; RSZ21; RS2Z33; RS31 AND RS40, SUBCELLULAR
RP   LOCATION, AND RNA-BINDING.
RX   PubMed=16497658; DOI=10.1261/rna.2226106;
RA   Gullerova M., Barta A., Lorkovic Z.J.;
RT   "AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that
RT   interacts with SR proteins and the C-terminal domain of the RNA polymerase
RT   II.";
RL   RNA 12:631-643(2006).
RN   [7]
RP   IDENTIFICATION IN THE BZR1 COMPLEX.
RX   PubMed=24019147; DOI=10.1074/mcp.m113.029256;
RA   Wang C., Shang J.X., Chen Q.X., Oses-Prieto J.A., Bai M.Y., Yang Y.,
RA   Yuan M., Zhang Y.L., Mu C.C., Deng Z., Wei C.Q., Burlingame A.L.,
RA   Wang Z.Y., Sun Y.;
RT   "Identification of BZR1-interacting proteins as potential components of the
RT   brassinosteroid signaling pathway in Arabidopsis through tandem affinity
RT   purification.";
RL   Mol. Cell. Proteomics 12:3653-3665(2013).
RN   [8]
RP   FUNCTION.
RX   PubMed=23248006; DOI=10.1093/nar/gks1252;
RA   Bannikova O., Zywicki M., Marquez Y., Skrahina T., Kalyna M., Barta A.;
RT   "Identification of RNA targets for the nuclear multidomain cyclophilin
RT   atCyp59 and their effect on PPIase activity.";
RL   Nucleic Acids Res. 41:1783-1796(2013).
CC   -!- FUNCTION: PPIases accelerate the folding of proteins. It catalyzes the
CC       cis-trans isomerization of proline imidic peptide bonds in
CC       oligopeptides. Influences somehow regulation of RNA pol II (CTD)
CC       phosphorylation. Binds RNA with preferences for GC-rich sequences.
CC       Probably involved in activities connecting transcription and pre-mRNA
CC       processing. Involved in brassinostroid response.
CC       {ECO:0000269|PubMed:16497658, ECO:0000269|PubMed:23248006}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=[protein]-peptidylproline (omega=180) = [protein]-
CC         peptidylproline (omega=0); Xref=Rhea:RHEA:16237, Rhea:RHEA-
CC         COMP:10747, Rhea:RHEA-COMP:10748, ChEBI:CHEBI:83833,
CC         ChEBI:CHEBI:83834; EC=5.2.1.8;
CC   -!- SUBUNIT: Component of the BZR1 complex. Interacts with NRPB1 (via CTD
CC       domain), SCL28, SCL30, SCL30A, SCL33, SC35, SR30, SR34, RSZ21, RS2Z33,
CC       RS31 and RS40. {ECO:0000269|PubMed:16497658,
CC       ECO:0000269|PubMed:24019147}.
CC   -!- INTERACTION:
CC       Q6Q151; P18616: NRPB1; NbExp=3; IntAct=EBI-1625989, EBI-1540537;
CC       Q6Q151; Q9SEU4: SCL33; NbExp=3; IntAct=EBI-1625989, EBI-927103;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16497658}. Note=Shows
CC       a punctuate localization pattern distinct from the nuclear speckles.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q6Q151-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q6Q151-2; Sequence=VSP_055001;
CC   -!- TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:15047905,
CC       ECO:0000269|PubMed:15051864, ECO:0000269|PubMed:16497658}.
CC   -!- SIMILARITY: Belongs to the cyclophilin-type PPIase family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAG51976.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AY568526; AAS75309.1; -; mRNA.
DR   EMBL; AC024260; AAG51976.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002684; AEE32989.1; -; Genomic_DNA.
DR   EMBL; AY059824; AAL24306.1; -; mRNA.
DR   PIR; E96577; E96577.
DR   RefSeq; NP_175776.2; NM_104250.5. [Q6Q151-1]
DR   AlphaFoldDB; Q6Q151; -.
DR   SMR; Q6Q151; -.
DR   BioGRID; 27035; 13.
DR   IntAct; Q6Q151; 14.
DR   STRING; 3702.Q6Q151; -.
DR   iPTMnet; Q6Q151; -.
DR   PaxDb; 3702-AT1G53720-1; -.
DR   ProteomicsDB; 222749; -. [Q6Q151-1]
DR   EnsemblPlants; AT1G53720.1; AT1G53720.1; AT1G53720. [Q6Q151-1]
DR   GeneID; 841810; -.
DR   Gramene; AT1G53720.1; AT1G53720.1; AT1G53720. [Q6Q151-1]
DR   KEGG; ath:AT1G53720; -.
DR   Araport; AT1G53720; -.
DR   TAIR; AT1G53720; CYP59.
DR   eggNOG; KOG0415; Eukaryota.
DR   HOGENOM; CLU_018791_3_0_1; -.
DR   InParanoid; Q6Q151; -.
DR   OMA; KMRHTRM; -.
DR   OrthoDB; 169228at2759; -.
DR   PhylomeDB; Q6Q151; -.
DR   PRO; PR:Q6Q151; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   ExpressionAtlas; Q6Q151; baseline and differential.
DR   GO; GO:0005634; C:nucleus; IDA:TAIR.
DR   GO; GO:0003755; F:peptidyl-prolyl cis-trans isomerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IDA:TAIR.
DR   GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR   CDD; cd01921; cyclophilin_RRM; 1.
DR   CDD; cd12235; RRM_PPIL4; 1.
DR   Gene3D; 3.30.70.330; -; 1.
DR   Gene3D; 2.40.100.10; Cyclophilin-like; 1.
DR   Gene3D; 4.10.60.10; Zinc finger, CCHC-type; 1.
DR   InterPro; IPR035542; CRIP.
DR   InterPro; IPR029000; Cyclophilin-like_dom_sf.
DR   InterPro; IPR002130; Cyclophilin-type_PPIase_dom.
DR   InterPro; IPR035538; Cyclophilin_PPIL4.
DR   InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR   InterPro; IPR035979; RBD_domain_sf.
DR   InterPro; IPR000504; RRM_dom.
DR   InterPro; IPR001878; Znf_CCHC.
DR   PANTHER; PTHR45843; PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 4; 1.
DR   PANTHER; PTHR45843:SF1; PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 4; 1.
DR   Pfam; PF00160; Pro_isomerase; 1.
DR   Pfam; PF00076; RRM_1; 1.
DR   Pfam; PF00098; zf-CCHC; 1.
DR   PRINTS; PR00153; CSAPPISMRASE.
DR   SMART; SM00360; RRM; 1.
DR   SMART; SM00343; ZnF_C2HC; 1.
DR   SUPFAM; SSF50891; Cyclophilin-like; 1.
DR   SUPFAM; SSF54928; RNA-binding domain, RBD; 1.
DR   PROSITE; PS50072; CSA_PPIASE_2; 1.
DR   PROSITE; PS50102; RRM; 1.
DR   PROSITE; PS50158; ZF_CCHC; 1.
DR   Genevisible; Q6Q151; AT.
PE   1: Evidence at protein level;
KW   Alternative splicing; Isomerase; Metal-binding; Nucleus;
KW   Reference proteome; RNA-binding; Rotamase; Zinc; Zinc-finger.
FT   CHAIN           1..506
FT                   /note="Peptidyl-prolyl cis-trans isomerase CYP59"
FT                   /id="PRO_0000429607"
FT   DOMAIN          1..161
FT                   /note="PPIase cyclophilin-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00156"
FT   DOMAIN          243..321
FT                   /note="RRM"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT   ZN_FING         341..357
FT                   /note="CCHC-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT   REGION          388..506
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   VAR_SEQ         441..506
FT                   /note="HRERKERESREDEDRRRRRRREESRDKESRRERDEDDHRSHRDYKERRRERD
FT                   DRHGREARHERRDR -> L (in isoform 2)"
FT                   /evidence="ECO:0000303|PubMed:14593172"
FT                   /id="VSP_055001"
SQ   SEQUENCE   506 AA;  58829 MW;  EB33E6544794283E CRC64;
     MSVLIVTSLG DIVIDLHSDK CPLTCKNFLK LCKIKYYNGC LFHTVQKDFT AQTGDPTGTG
     AGGDSIYKFL YGEQARFYKD EIHLDLKHSK TGTVAMASGG ENLNASQFYF TLRDDLDYLD
     GKHTVFGQIA EGFDTLTRIN EAYVDPKNRP YKNIRIKHTH ILDDPFDDPP QLAEMMPDAS
     PEGKPKEEVK DDVRLEDDWV PMDEELGAQE LEEVIREKAA HSSAVVLESI GDIPEAEVKP
     PDNVLFVCKL NPVTEDEDLH TIFSRFGTVV SADVIRDFKT GDSLCYAFIE FENKESCEQA
     YFKMDNALID DRRIHVDFSQ SVSKLWSQFR QKDSQKGKGN GCFKCGSTDH IAKDCVGGPS
     SKFIVKDQNR QHGGGEGYEM VFEGDVHETP KHNSHERERS EKIQRRSPHG NGEGKRQHRD
     ERDDGRRQHD REDARELERK HRERKERESR EDEDRRRRRR REESRDKESR RERDEDDHRS
     HRDYKERRRE RDDRHGREAR HERRDR
//