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Q9SSA5 (CYP38_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 100. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic

Short name=PPIase CYP38
EC=5.2.1.8
Alternative name(s):
Rotamase CYP38
Thylakoid lumen PPIase
Gene names
Name:CYP38
Ordered Locus Names:At3g01480
ORF Names:F4P13.3
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length437 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Required for the assembly and stabilization of PSII, but has no PPIases activity. Ref.10 Ref.12

Catalytic activity

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

Subcellular location

Plastidchloroplast thylakoid lumen Ref.6 Ref.8.

Tissue specificity

Ubiquitous. Lower levels of expression in roots. Ref.1 Ref.9

Induction

Up-regulated by light. Down-regulated by dark. Ref.9

Domain

The N-teminal helical domain blocks the interaction with the potential target PSII subunit chlorophyll protein 47 (CP47). Ref.12

Disruption phenotype

Stunted growth and hypersensitivity to high light. Ref.10

Sequence similarities

Contains 1 PPIase cyclophilin-type domain.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9SSA5-1)

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.
Isoform 2 (identifier: Q9SSA5-2)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 3636Chloroplast Potential
Transit peptide37 – 9256Thylakoid Ref.6 Ref.8
Chain93 – 437345Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic
PRO_0000342095

Regions

Domain245 – 437193PPIase cyclophilin-type

Natural variations

Alternative sequence338 – 35518EELGL…FNAFG → EVSLSKSLLVRDLYYIVF in isoform 2.
VSP_055391
Alternative sequence356 – 43782Missing in isoform 2.
VSP_055392

Secondary structure

..................................................... 437
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 1, 2000. Version 1.
Checksum: 7239C7ADE83953E0

FASTA43747,982
        10         20         30         40         50         60 
MAAAFASLPT FSVVNSSRFP RRRIGFSCSK KPLEVRCSSG NTRYTKQRGA FTSLKECAIS 

        70         80         90        100        110        120 
LALSVGLMVS VPSIALPPNA HAVANPVIPD VSVLISGPPI KDPEALLRYA LPIDNKAIRE 

       130        140        150        160        170        180 
VQKPLEDITD SLKIAGVKAL DSVERNVRQA SRTLQQGKSI IVAGFAESKK DHGNEMIEKL 

       190        200        210        220        230        240 
EAGMQDMLKI VEDRKRDAVA PKQKEILKYV GGIEEDMVDG FPYEVPEEYR NMPLLKGRAS 

       250        260        270        280        290        300 
VDMKVKIKDN PNIEDCVFRI VLDGYNAPVT AGNFVDLVER HFYDGMEIQR SDGFVVQTGD 

       310        320        330        340        350        360 
PEGPAEGFID PSTEKTRTVP LEIMVTGEKT PFYGSTLEEL GLYKAQVVIP FNAFGTMAMA 

       370        380        390        400        410        420 
REEFENDSGS SQVFWLLKES ELTPSNSNIL DGRYAVFGYV TDNEDFLADL KVGDVIESIQ 

       430 
VVSGLENLAN PSYKIAG 

« Hide

Isoform 2 [UniParc].

Checksum: 460A33063125B06E
Show »

FASTA35539,141

References

« Hide 'large scale' references
[1]"The Arabidopsis cyclophilin gene family."
Romano P.G.N., Horton P., Gray J.E.
Plant Physiol. 134:1268-1282(2004) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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. expand/collapse author list , 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]"Proteome map of the chloroplast lumen of Arabidopsis thaliana."
Schubert M., Petersson U.A., Haas B.J., Funk C., Schroeder W.P., Kieselbach T.
J. Biol. Chem. 277:8354-8365(2002) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_186797.1. NM_111014.3. [Q9SSA5-1]
UniGeneAt.20535.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3RFYX-ray2.39A83-437[»]
ProteinModelPortalQ9SSA5.
SMRQ9SSA5. Positions 83-433.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActQ9SSA5. 1 interaction.

Proteomic databases

PaxDbQ9SSA5.
PRIDEQ9SSA5.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT3G01480.1; AT3G01480.1; AT3G01480. [Q9SSA5-1]
GeneID821137.
KEGGath:AT3G01480.

Organism-specific databases

TAIRAT3G01480.

Phylogenomic databases

eggNOGCOG0652.
HOGENOMHOG000065979.
InParanoidQ9SSA5.
OMAGFYDGLP.
PhylomeDBQ9SSA5.

Enzyme and pathway databases

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

Gene expression databases

ArrayExpressQ9SSA5.
GenevestigatorQ9SSA5.

Family and domain databases

Gene3D1.20.120.290. 1 hit.
2.40.100.10. 1 hit.
InterProIPR029000. Cyclophilin-like_dom.
IPR002130. Cyclophilin-type_PPIase_dom.
IPR023222. PsbQ-like_domain.
[Graphical view]
PfamPF00160. Pro_isomerase. 1 hit.
[Graphical view]
SUPFAMSSF101112. SSF101112. 1 hit.
SSF50891. SSF50891. 2 hits.
PROSITEPS50072. CSA_PPIASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameCYP38_ARATH
AccessionPrimary (citable) accession number: Q9SSA5
Secondary accession number(s): B3H5B8, B9DHS6
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: May 1, 2000
Last modified: July 9, 2014
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names