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Q9SSA5

- CYP38_ARATH

UniProt

Q9SSA5 - CYP38_ARATH

Protein

Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic

Gene

CYP38

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 102 (01 Oct 2014)
      Sequence version 1 (01 May 2000)
      Previous versions | rss
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    Functioni

    Required for the assembly and stabilization of PSII, but has no PPIases activity.2 Publications

    Catalytic activityi

    Peptidylproline (omega=180) = peptidylproline (omega=0).

    GO - Molecular functioni

    1. peptidyl-prolyl cis-trans isomerase activity Source: UniProtKB-KW

    GO - Biological processi

    1. defense response to bacterium Source: TAIR
    2. protein folding Source: UniProtKB-KW

    Keywords - Molecular functioni

    Isomerase, Rotamase

    Enzyme and pathway databases

    BioCyciARA:AT3G01480-MONOMER.
    ARA:GQT-36-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic (EC:5.2.1.8)
    Short name:
    PPIase CYP38
    Alternative name(s):
    Rotamase CYP38
    Thylakoid lumen PPIase
    Gene namesi
    Name:CYP38
    Ordered Locus Names:At3g01480
    ORF Names:F4P13.3
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 3

    Organism-specific databases

    TAIRiAT3G01480.

    Subcellular locationi

    Plastidchloroplast thylakoid lumen 2 Publications

    GO - Cellular componenti

    1. chloroplast Source: TAIR
    2. chloroplast stroma Source: TAIR
    3. chloroplast thylakoid Source: TAIR
    4. chloroplast thylakoid lumen Source: UniProtKB-SubCell
    5. chloroplast thylakoid membrane Source: TAIR
    6. thylakoid Source: TAIR
    7. thylakoid lumen Source: TAIR

    Keywords - Cellular componenti

    Chloroplast, Plastid, Thylakoid

    Pathology & Biotechi

    Disruption phenotypei

    Stunted growth and hypersensitivity to high light.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 3636ChloroplastSequence AnalysisAdd
    BLAST
    Transit peptidei37 – 9256Thylakoid2 PublicationsAdd
    BLAST
    Chaini93 – 437345Peptidyl-prolyl cis-trans isomerase CYP38, chloroplasticPRO_0000342095Add
    BLAST

    Proteomic databases

    PaxDbiQ9SSA5.
    PRIDEiQ9SSA5.

    Expressioni

    Tissue specificityi

    Ubiquitous. Lower levels of expression in roots.2 Publications

    Inductioni

    Up-regulated by light. Down-regulated by dark.1 Publication

    Gene expression databases

    ArrayExpressiQ9SSA5.
    GenevestigatoriQ9SSA5.

    Interactioni

    Protein-protein interaction databases

    IntActiQ9SSA5. 1 interaction.

    Structurei

    Secondary structure

    1
    437
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi93 – 975
    Helixi103 – 1108
    Helixi116 – 12611
    Helixi128 – 1314
    Turni137 – 1393
    Helixi140 – 15415
    Helixi157 – 1615
    Turni162 – 1643
    Helixi167 – 1693
    Helixi170 – 18819
    Beta strandi197 – 1993
    Helixi200 – 2023
    Helixi203 – 21614
    Beta strandi237 – 24610
    Beta strandi254 – 26310
    Turni264 – 2663
    Helixi268 – 27912
    Turni280 – 2856
    Beta strandi289 – 2968
    Beta strandi318 – 3236
    Beta strandi325 – 3284
    Helixi338 – 3403
    Beta strandi342 – 3498
    Beta strandi378 – 3825
    Beta strandi388 – 3903
    Beta strandi394 – 40310
    Helixi406 – 4094
    Beta strandi415 – 4239
    Helixi425 – 4273
    Beta strandi428 – 4303

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3RFYX-ray2.39A83-437[»]
    ProteinModelPortaliQ9SSA5.
    SMRiQ9SSA5. Positions 83-433.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini245 – 437193PPIase cyclophilin-typePROSITE-ProRule annotationAdd
    BLAST

    Domaini

    The N-teminal helical domain blocks the interaction with the potential target PSII subunit chlorophyll protein 47 (CP47).1 Publication

    Sequence similaritiesi

    Contains 1 PPIase cyclophilin-type domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0652.
    HOGENOMiHOG000065979.
    InParanoidiQ9SSA5.
    OMAiGFYDGLP.
    PhylomeDBiQ9SSA5.

    Family and domain databases

    Gene3Di1.20.120.290. 1 hit.
    2.40.100.10. 1 hit.
    InterProiIPR029000. Cyclophilin-like_dom.
    IPR002130. Cyclophilin-type_PPIase_dom.
    IPR023222. PsbQ-like_domain.
    [Graphical view]
    PfamiPF00160. Pro_isomerase. 1 hit.
    [Graphical view]
    SUPFAMiSSF101112. SSF101112. 1 hit.
    SSF50891. SSF50891. 2 hits.
    PROSITEiPS50072. CSA_PPIASE_2. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9SSA5-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MAAAFASLPT FSVVNSSRFP RRRIGFSCSK KPLEVRCSSG NTRYTKQRGA    50
    FTSLKECAIS LALSVGLMVS VPSIALPPNA HAVANPVIPD VSVLISGPPI 100
    KDPEALLRYA LPIDNKAIRE VQKPLEDITD SLKIAGVKAL DSVERNVRQA 150
    SRTLQQGKSI IVAGFAESKK DHGNEMIEKL EAGMQDMLKI VEDRKRDAVA 200
    PKQKEILKYV GGIEEDMVDG FPYEVPEEYR NMPLLKGRAS VDMKVKIKDN 250
    PNIEDCVFRI VLDGYNAPVT AGNFVDLVER HFYDGMEIQR SDGFVVQTGD 300
    PEGPAEGFID PSTEKTRTVP LEIMVTGEKT PFYGSTLEEL GLYKAQVVIP 350
    FNAFGTMAMA REEFENDSGS SQVFWLLKES ELTPSNSNIL DGRYAVFGYV 400
    TDNEDFLADL KVGDVIESIQ VVSGLENLAN PSYKIAG 437
    Length:437
    Mass (Da):47,982
    Last modified:May 1, 2000 - v1
    Checksum:i7239C7ADE83953E0
    GO
    Isoform 2 (identifier: Q9SSA5-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         338-355: EELGLYKAQVVIPFNAFG → EVSLSKSLLVRDLYYIVF
         356-437: Missing.

    Note: No experimental confirmation available. Derived from EST data.

    Show »
    Length:355
    Mass (Da):39,141
    Checksum:i460A33063125B06E
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei338 – 35518EELGL…FNAFG → EVSLSKSLLVRDLYYIVF in isoform 2. CuratedVSP_055391Add
    BLAST
    Alternative sequencei356 – 43782Missing in isoform 2. CuratedVSP_055392Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY568524 mRNA. Translation: AAS75307.1.
    AC009325 Genomic DNA. Translation: AAF01533.1.
    CP002686 Genomic DNA. Translation: AEE73672.1.
    CP002686 Genomic DNA. Translation: AEE73673.1.
    AY039843 mRNA. Translation: AAK63947.1.
    AY113168 mRNA. Translation: AAM47471.1.
    AY087781 mRNA. Translation: AAM65317.1.
    AK317631 mRNA. Translation: BAH20293.1.
    RefSeqiNP_001118550.1. NM_001125078.1.
    NP_186797.1. NM_111014.3. [Q9SSA5-1]
    UniGeneiAt.20535.

    Genome annotation databases

    EnsemblPlantsiAT3G01480.1; AT3G01480.1; AT3G01480. [Q9SSA5-1]
    AT3G01480.2; AT3G01480.2; AT3G01480. [Q9SSA5-2]
    GeneIDi821137.
    KEGGiath:AT3G01480.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY568524 mRNA. Translation: AAS75307.1 .
    AC009325 Genomic DNA. Translation: AAF01533.1 .
    CP002686 Genomic DNA. Translation: AEE73672.1 .
    CP002686 Genomic DNA. Translation: AEE73673.1 .
    AY039843 mRNA. Translation: AAK63947.1 .
    AY113168 mRNA. Translation: AAM47471.1 .
    AY087781 mRNA. Translation: AAM65317.1 .
    AK317631 mRNA. Translation: BAH20293.1 .
    RefSeqi NP_001118550.1. NM_001125078.1.
    NP_186797.1. NM_111014.3. [Q9SSA5-1 ]
    UniGenei At.20535.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3RFY X-ray 2.39 A 83-437 [» ]
    ProteinModelPortali Q9SSA5.
    SMRi Q9SSA5. Positions 83-433.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q9SSA5. 1 interaction.

    Proteomic databases

    PaxDbi Q9SSA5.
    PRIDEi Q9SSA5.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT3G01480.1 ; AT3G01480.1 ; AT3G01480 . [Q9SSA5-1 ]
    AT3G01480.2 ; AT3G01480.2 ; AT3G01480 . [Q9SSA5-2 ]
    GeneIDi 821137.
    KEGGi ath:AT3G01480.

    Organism-specific databases

    TAIRi AT3G01480.

    Phylogenomic databases

    eggNOGi COG0652.
    HOGENOMi HOG000065979.
    InParanoidi Q9SSA5.
    OMAi GFYDGLP.
    PhylomeDBi Q9SSA5.

    Enzyme and pathway databases

    BioCyci ARA:AT3G01480-MONOMER.
    ARA:GQT-36-MONOMER.

    Gene expression databases

    ArrayExpressi Q9SSA5.
    Genevestigatori Q9SSA5.

    Family and domain databases

    Gene3Di 1.20.120.290. 1 hit.
    2.40.100.10. 1 hit.
    InterProi IPR029000. Cyclophilin-like_dom.
    IPR002130. Cyclophilin-type_PPIase_dom.
    IPR023222. PsbQ-like_domain.
    [Graphical view ]
    Pfami PF00160. Pro_isomerase. 1 hit.
    [Graphical view ]
    SUPFAMi SSF101112. SSF101112. 1 hit.
    SSF50891. SSF50891. 2 hits.
    PROSITEi PS50072. CSA_PPIASE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, GENE FAMILY, NOMENCLATURE.
    2. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
      Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
      , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
      Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Strain: cv. Columbia.
    5. "Full-length cDNA from Arabidopsis thaliana."
      Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
      Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    6. Cited for: PROTEIN SEQUENCE OF 93-114, SUBCELLULAR LOCATION.
    7. "Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs."
      Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K.
      DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 63-437 (ISOFORM 1).
      Strain: cv. Columbia.
    8. "Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction."
      Peltier J.-B., Emanuelsson O., Kalume D.E., Ytterberg J., Friso G., Rudella A., Liberles D.A., Soederberg L., Roepstorff P., von Heijne G., van Wijk K.J.
      Plant Cell 14:211-236(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF N-TERMINUS, SUBCELLULAR LOCATION, IDENTIFICATION BY MASS SPECTROMETRY.
    9. "Immunophilins and parvulins. Superfamily of peptidyl prolyl isomerases in Arabidopsis."
      He Z., Li L., Luan S.
      Plant Physiol. 134:1248-1267(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY, GENE FAMILY, NOMENCLATURE, INDUCTION.
    10. "A chloroplast cyclophilin functions in the assembly and maintenance of photosystem II in Arabidopsis thaliana."
      Fu A., He Z., Cho H.S., Lima A., Buchanan B.B., Luan S.
      Proc. Natl. Acad. Sci. U.S.A. 104:15947-15952(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
    11. "Sorting signals, N-terminal modifications and abundance of the chloroplast proteome."
      Zybailov B., Rutschow H., Friso G., Rudella A., Emanuelsson O., Sun Q., van Wijk K.J.
      PLoS ONE 3:E1994-E1994(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY.
    12. "Crystal structure of Arabidopsis cyclophilin38 reveals a previously uncharacterized immunophilin fold and a possible autoinhibitory mechanism."
      Vasudevan D., Fu A., Luan S., Swaminathan K.
      Plant Cell 24:2666-2674(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.39 ANGSTROMS) OF 83-437, FUNCTION, DOMAIN.

    Entry informationi

    Entry nameiCYP38_ARATH
    AccessioniPrimary (citable) accession number: Q9SSA5
    Secondary accession number(s): B3H5B8, B9DHS6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 1, 2008
    Last sequence update: May 1, 2000
    Last modified: October 1, 2014
    This is version 102 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3