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Q9SSA5

- CYP38_ARATH

UniProt

Q9SSA5 - CYP38_ARATH

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Protein
Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic
Gene
CYP38, At3g01480, F4P13.3
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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
Complete GO annotation...

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
Complete GO annotation...

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 – 3636Chloroplast Reviewed prediction
Add
BLAST
Transit peptidei37 – 9256Thylakoid2 Publications
Add
BLAST
Chaini93 – 437345Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic
PRO_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

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.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini245 – 437193PPIase cyclophilin-type
Add
BLAST

Domaini

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

Sequence similaritiesi

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.
VSP_055391Add
BLAST
Alternative sequencei356 – 43782Missing in isoform 2.
VSP_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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 101 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

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