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Protein

Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic

Gene

CYP38

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: 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

GO - Biological processi

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 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G01480.

Subcellular locationi

GO - Cellular componenti

  • chloroplast Source: TAIR
  • chloroplast stroma Source: TAIR
  • chloroplast thylakoid Source: TAIR
  • chloroplast thylakoid lumen Source: UniProtKB-SubCell
  • chloroplast thylakoid membrane Source: TAIR
  • thylakoid Source: TAIR
  • 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 – 3636ChloroplastSequence AnalysisAdd
BLAST
Transit peptidei37 – 9256Thylakoid2 PublicationsAdd
BLAST
Chaini93 – 437345Peptidyl-prolyl cis-trans isomerase CYP38, chloroplasticPRO_0000342095Add
BLAST

Proteomic databases

PaxDbiQ9SSA5.
PRIDEiQ9SSA5.
ProMEXiQ9SSA5.

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

ExpressionAtlasiQ9SSA5. baseline and differential.

Interactioni

Protein-protein interaction databases

IntActiQ9SSA5. 1 interaction.
STRINGi3702.AT3G01480.1.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
OMAiRNAAFGY.
PhylomeDBiQ9SSA5.

Family and domain databases

Gene3Di1.20.120.290. 1 hit.
2.40.100.10. 1 hit.
InterProiIPR029000. Cyclophilin-like_dom.
IPR024936. Cyclophilin-type_PPIase.
IPR002130. Cyclophilin-type_PPIase_dom.
IPR023222. PsbQ-like_domain.
[Graphical view]
PANTHERiPTHR11071. PTHR11071. 1 hit.
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. AlignAdd to basket

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

        10         20         30         40         50
MAAAFASLPT FSVVNSSRFP RRRIGFSCSK KPLEVRCSSG NTRYTKQRGA
60 70 80 90 100
FTSLKECAIS LALSVGLMVS VPSIALPPNA HAVANPVIPD VSVLISGPPI
110 120 130 140 150
KDPEALLRYA LPIDNKAIRE VQKPLEDITD SLKIAGVKAL DSVERNVRQA
160 170 180 190 200
SRTLQQGKSI IVAGFAESKK DHGNEMIEKL EAGMQDMLKI VEDRKRDAVA
210 220 230 240 250
PKQKEILKYV GGIEEDMVDG FPYEVPEEYR NMPLLKGRAS VDMKVKIKDN
260 270 280 290 300
PNIEDCVFRI VLDGYNAPVT AGNFVDLVER HFYDGMEIQR SDGFVVQTGD
310 320 330 340 350
PEGPAEGFID PSTEKTRTVP LEIMVTGEKT PFYGSTLEEL GLYKAQVVIP
360 370 380 390 400
FNAFGTMAMA REEFENDSGS SQVFWLLKES ELTPSNSNIL DGRYAVFGYV
410 420 430
TDNEDFLADL KVGDVIESIQ VVSGLENLAN PSYKIAG
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:
EMBLi
GenBanki
DDBJi
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. [Q9SSA5-2]
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:
EMBLi
GenBanki
DDBJi
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. [Q9SSA5-2]
NP_186797.1. NM_111014.3. [Q9SSA5-1]
UniGeneiAt.20535.

3D structure databases

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

Protein-protein interaction databases

IntActiQ9SSA5. 1 interaction.
STRINGi3702.AT3G01480.1.

Proteomic databases

PaxDbiQ9SSA5.
PRIDEiQ9SSA5.
ProMEXiQ9SSA5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

TAIRiAT3G01480.

Phylogenomic databases

eggNOGiCOG0652.
HOGENOMiHOG000065979.
InParanoidiQ9SSA5.
OMAiRNAAFGY.
PhylomeDBiQ9SSA5.

Enzyme and pathway databases

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

Miscellaneous databases

PROiQ9SSA5.

Gene expression databases

ExpressionAtlasiQ9SSA5. baseline and differential.

Family and domain databases

Gene3Di1.20.120.290. 1 hit.
2.40.100.10. 1 hit.
InterProiIPR029000. Cyclophilin-like_dom.
IPR024936. Cyclophilin-type_PPIase.
IPR002130. Cyclophilin-type_PPIase_dom.
IPR023222. PsbQ-like_domain.
[Graphical view]
PANTHERiPTHR11071. PTHR11071. 1 hit.
PfamiPF00160. Pro_isomerase. 1 hit.
[Graphical view]
SUPFAMiSSF101112. SSF101112. 1 hit.
SSF50891. SSF50891. 2 hits.
PROSITEiPS50072. CSA_PPIASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: June 24, 2015
This is version 109 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.