CYP38_ARATH
ID CYP38_ARATH Reviewed; 437 AA.
AC Q9SSA5; B3H5B8; B9DHS6;
DT 01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic;
DE Short=PPIase CYP38;
DE EC=5.2.1.8;
DE AltName: Full=Rotamase CYP38;
DE AltName: Full=Thylakoid lumen PPIase;
DE Flags: Precursor;
GN Name=CYP38; OrderedLocusNames=At3g01480; ORFNames=F4P13.3;
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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 1).
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] (ISOFORM 1).
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP PROTEIN SEQUENCE OF 93-114, AND SUBCELLULAR LOCATION.
RX PubMed=11719511; DOI=10.1074/jbc.m108575200;
RA Schubert M., Petersson U.A., Haas B.J., Funk C., Schroeder W.P.,
RA Kieselbach T.;
RT "Proteome map of the chloroplast lumen of Arabidopsis thaliana.";
RL J. Biol. Chem. 277:8354-8365(2002).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 63-437 (ISOFORM 1).
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 [8]
RP PROTEIN SEQUENCE OF N-TERMINUS, SUBCELLULAR LOCATION, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RX PubMed=11826309; DOI=10.1105/tpc.010304;
RA Peltier J.-B., Emanuelsson O., Kalume D.E., Ytterberg J., Friso G.,
RA Rudella A., Liberles D.A., Soederberg L., Roepstorff P., von Heijne G.,
RA van Wijk K.J.;
RT "Central functions of the lumenal and peripheral thylakoid proteome of
RT Arabidopsis determined by experimentation and genome-wide prediction.";
RL Plant Cell 14:211-236(2002).
RN [9]
RP TISSUE SPECIFICITY, GENE FAMILY, NOMENCLATURE, AND INDUCTION.
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 [10]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=17909185; DOI=10.1073/pnas.0707851104;
RA Fu A., He Z., Cho H.S., Lima A., Buchanan B.B., Luan S.;
RT "A chloroplast cyclophilin functions in the assembly and maintenance of
RT photosystem II in Arabidopsis thaliana.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:15947-15952(2007).
RN [11]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=18431481; DOI=10.1371/journal.pone.0001994;
RA Zybailov B., Rutschow H., Friso G., Rudella A., Emanuelsson O., Sun Q.,
RA van Wijk K.J.;
RT "Sorting signals, N-terminal modifications and abundance of the chloroplast
RT proteome.";
RL PLoS ONE 3:E1994-E1994(2008).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.39 ANGSTROMS) OF 83-437, FUNCTION, AND DOMAIN.
RX PubMed=22706283; DOI=10.1105/tpc.111.093781;
RA Vasudevan D., Fu A., Luan S., Swaminathan K.;
RT "Crystal structure of Arabidopsis cyclophilin38 reveals a previously
RT uncharacterized immunophilin fold and a possible autoinhibitory
RT mechanism.";
RL Plant Cell 24:2666-2674(2012).
CC -!- FUNCTION: Required for the assembly and stabilization of PSII, but has
CC no PPIases activity. {ECO:0000269|PubMed:17909185,
CC ECO:0000269|PubMed:22706283}.
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 -!- SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid lumen
CC {ECO:0000269|PubMed:11719511, ECO:0000269|PubMed:11826309,
CC ECO:0000269|PubMed:18431481}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9SSA5-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9SSA5-2; Sequence=VSP_055391, VSP_055392;
CC -!- TISSUE SPECIFICITY: Ubiquitous. Lower levels of expression in roots.
CC {ECO:0000269|PubMed:15047905, ECO:0000269|PubMed:15051864}.
CC -!- INDUCTION: Up-regulated by light. Down-regulated by dark.
CC {ECO:0000269|PubMed:15047905}.
CC -!- DOMAIN: The N-terminal helical domain blocks the interaction with the
CC potential target PSII subunit chlorophyll protein 47 (CP47).
CC {ECO:0000269|PubMed:22706283}.
CC -!- DISRUPTION PHENOTYPE: Stunted growth and hypersensitivity to high
CC light. {ECO:0000269|PubMed:17909185}.
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DR EMBL; AY568524; AAS75307.1; -; mRNA.
DR EMBL; AC009325; AAF01533.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE73672.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE73673.1; -; Genomic_DNA.
DR EMBL; AY039843; AAK63947.1; -; mRNA.
DR EMBL; AY113168; AAM47471.1; -; mRNA.
DR EMBL; AY087781; AAM65317.1; -; mRNA.
DR EMBL; AK317631; BAH20293.1; -; mRNA.
DR RefSeq; NP_001118550.1; NM_001125078.1. [Q9SSA5-2]
DR RefSeq; NP_186797.1; NM_111014.4. [Q9SSA5-1]
DR PDB; 3RFY; X-ray; 2.39 A; A=83-437.
DR PDBsum; 3RFY; -.
DR AlphaFoldDB; Q9SSA5; -.
DR SMR; Q9SSA5; -.
DR IntAct; Q9SSA5; 1.
DR STRING; 3702.AT3G01480.1; -.
DR iPTMnet; Q9SSA5; -.
DR MetOSite; Q9SSA5; -.
DR PaxDb; Q9SSA5; -.
DR PRIDE; Q9SSA5; -.
DR ProMEX; Q9SSA5; -.
DR ProteomicsDB; 222740; -. [Q9SSA5-1]
DR EnsemblPlants; AT3G01480.1; AT3G01480.1; AT3G01480. [Q9SSA5-1]
DR EnsemblPlants; AT3G01480.2; AT3G01480.2; AT3G01480. [Q9SSA5-2]
DR GeneID; 821137; -.
DR Gramene; AT3G01480.1; AT3G01480.1; AT3G01480. [Q9SSA5-1]
DR Gramene; AT3G01480.2; AT3G01480.2; AT3G01480. [Q9SSA5-2]
DR KEGG; ath:AT3G01480; -.
DR Araport; AT3G01480; -.
DR TAIR; locus:2084138; AT3G01480.
DR eggNOG; ENOG502QSSP; Eukaryota.
DR HOGENOM; CLU_012062_19_2_1; -.
DR InParanoid; Q9SSA5; -.
DR OMA; QFFFFLY; -.
DR PhylomeDB; Q9SSA5; -.
DR PRO; PR:Q9SSA5; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SSA5; baseline and differential.
DR Genevisible; Q9SSA5; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0009534; C:chloroplast thylakoid; HDA:TAIR.
DR GO; GO:0009543; C:chloroplast thylakoid lumen; IEA:UniProtKB-SubCell.
DR GO; GO:0009535; C:chloroplast thylakoid membrane; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0009579; C:thylakoid; HDA:TAIR.
DR GO; GO:0031977; C:thylakoid lumen; HDA:TAIR.
DR GO; GO:0003755; F:peptidyl-prolyl cis-trans isomerase activity; IEA:UniProtKB-KW.
DR GO; GO:0010102; P:lateral root morphogenesis; IMP:TAIR.
DR GO; GO:0010207; P:photosystem II assembly; IMP:TAIR.
DR GO; GO:0042549; P:photosystem II stabilization; IMP:TAIR.
DR GO; GO:0000413; P:protein peptidyl-prolyl isomerization; IEA:InterPro.
DR Gene3D; 1.20.120.290; -; 1.
DR Gene3D; 2.40.100.10; -; 1.
DR InterPro; IPR029000; Cyclophilin-like_dom_sf.
DR InterPro; IPR002130; Cyclophilin-type_PPIase_dom.
DR InterPro; IPR044665; E_coli_cyclophilin_A-like.
DR InterPro; IPR023222; PsbQ-like_dom_sf.
DR PANTHER; PTHR43246; PTHR43246; 1.
DR Pfam; PF00160; Pro_isomerase; 1.
DR SUPFAM; SSF101112; SSF101112; 1.
DR SUPFAM; SSF50891; SSF50891; 1.
DR PROSITE; PS50072; CSA_PPIASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Chloroplast; Direct protein sequencing;
KW Isomerase; Plastid; Reference proteome; Rotamase; Thylakoid;
KW Transit peptide.
FT TRANSIT 1..36
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT TRANSIT 37..92
FT /note="Thylakoid"
FT /evidence="ECO:0000269|PubMed:11719511,
FT ECO:0000269|PubMed:11826309"
FT CHAIN 93..437
FT /note="Peptidyl-prolyl cis-trans isomerase CYP38,
FT chloroplastic"
FT /id="PRO_0000342095"
FT DOMAIN 245..437
FT /note="PPIase cyclophilin-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00156"
FT VAR_SEQ 338..355
FT /note="EELGLYKAQVVIPFNAFG -> EVSLSKSLLVRDLYYIVF (in isoform
FT 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_055391"
FT VAR_SEQ 356..437
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_055392"
FT STRAND 93..97
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 103..110
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 116..126
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 128..131
FT /evidence="ECO:0007829|PDB:3RFY"
FT TURN 137..139
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 140..154
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 157..161
FT /evidence="ECO:0007829|PDB:3RFY"
FT TURN 162..164
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 167..169
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 170..188
FT /evidence="ECO:0007829|PDB:3RFY"
FT STRAND 197..199
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 200..202
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 203..216
FT /evidence="ECO:0007829|PDB:3RFY"
FT STRAND 237..246
FT /evidence="ECO:0007829|PDB:3RFY"
FT STRAND 254..263
FT /evidence="ECO:0007829|PDB:3RFY"
FT TURN 264..266
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 268..279
FT /evidence="ECO:0007829|PDB:3RFY"
FT TURN 280..285
FT /evidence="ECO:0007829|PDB:3RFY"
FT STRAND 289..296
FT /evidence="ECO:0007829|PDB:3RFY"
FT STRAND 318..323
FT /evidence="ECO:0007829|PDB:3RFY"
FT STRAND 325..328
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 338..340
FT /evidence="ECO:0007829|PDB:3RFY"
FT STRAND 342..349
FT /evidence="ECO:0007829|PDB:3RFY"
FT STRAND 378..382
FT /evidence="ECO:0007829|PDB:3RFY"
FT STRAND 388..390
FT /evidence="ECO:0007829|PDB:3RFY"
FT STRAND 394..403
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 406..409
FT /evidence="ECO:0007829|PDB:3RFY"
FT STRAND 415..423
FT /evidence="ECO:0007829|PDB:3RFY"
FT HELIX 425..427
FT /evidence="ECO:0007829|PDB:3RFY"
FT STRAND 428..430
FT /evidence="ECO:0007829|PDB:3RFY"
SQ SEQUENCE 437 AA; 47982 MW; 7239C7ADE83953E0 CRC64;
MAAAFASLPT FSVVNSSRFP RRRIGFSCSK KPLEVRCSSG NTRYTKQRGA FTSLKECAIS
LALSVGLMVS VPSIALPPNA HAVANPVIPD VSVLISGPPI KDPEALLRYA LPIDNKAIRE
VQKPLEDITD SLKIAGVKAL DSVERNVRQA SRTLQQGKSI IVAGFAESKK DHGNEMIEKL
EAGMQDMLKI VEDRKRDAVA PKQKEILKYV GGIEEDMVDG FPYEVPEEYR NMPLLKGRAS
VDMKVKIKDN PNIEDCVFRI VLDGYNAPVT AGNFVDLVER HFYDGMEIQR SDGFVVQTGD
PEGPAEGFID PSTEKTRTVP LEIMVTGEKT PFYGSTLEEL GLYKAQVVIP FNAFGTMAMA
REEFENDSGS SQVFWLLKES ELTPSNSNIL DGRYAVFGYV TDNEDFLADL KVGDVIESIQ
VVSGLENLAN PSYKIAG
