Q9SSA5 (CYP38_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	437 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Required for the assembly and stabilization of PSII. Ref.8
Catalytic activity	Peptidylproline (omega=180) = peptidylproline (omega=0).
Subcellular location	Plastid › chloroplast thylakoid lumen Ref.6 Ref.7.
Tissue specificity	Expressed in leaves, flower buds and stems. Ref.1
Sequence similarities	Contains 1 PPIase cyclophilin-type domain.

Ontologies

Keywords
Cellular component	Chloroplast Plastid Thylakoid
Coding sequence diversity	Alternative splicing
Domain	Transit peptide
Molecular function	Isomerase Rotamase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	defense response to bacterium Inferred from expression pattern PubMed 17028151. Source: TAIR protein folding Inferred from electronic annotation. Source: UniProtKB-KW protein peptidyl-prolyl isomerization Inferred from electronic annotation. Source: GOC
Cellular_component	chloroplast stroma Inferred from direct assay PubMed 16207701. Source: TAIR chloroplast thylakoid lumen Inferred from electronic annotation. Source: UniProtKB-SubCell chloroplast thylakoid membrane Inferred from direct assay PubMed 15322131. Source: TAIR thylakoid lumen Inferred from direct assay Ref.7. Source: TAIR
Molecular_function	peptidyl-prolyl cis-trans isomerase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.

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.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 36

36

Chloroplast Potential

Transit peptide

37 – 92

56

Thylakoid Ref.6

Chain

93 – 437

345

Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic

PRO_0000342095

Regions

Domain

245 – 437

193

PPIase cyclophilin-type

Secondary structure

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437

Helix Strand Turn

Details...

Beta strand

93 – 97

5

Helix

103 – 110

8

Helix

116 – 126

11

Helix

128 – 131

4

Turn

137 – 139

3

Helix

140 – 154

15

Helix

157 – 161

5

Turn

162 – 164

3

Helix

167 – 169

3

Helix

170 – 188

19

Beta strand

197 – 199

3

Helix

200 – 202

3

Helix

203 – 216

14

Beta strand

237 – 246

10

Beta strand

254 – 263

10

Turn

264 – 266

3

Helix

268 – 279

12

Turn

280 – 285

6

Beta strand

289 – 296

8

Beta strand

318 – 323

6

Beta strand

325 – 328

4

Helix

338 – 340

3

Beta strand

342 – 349

8

Beta strand

378 – 382

5

Beta strand

388 – 390

3

Beta strand

394 – 403

10

Helix

406 – 409

4

Beta strand

415 – 423

9

Helix

425 – 427

3

Beta strand

428 – 430

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: 7239C7ADE83953E0	FASTA	437	47,982
	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

References

	« Hide 'large scale' referencesShow '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], 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]. 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].
[6]	"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.
[7]	"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: SUBCELLULAR LOCATION, IDENTIFICATION BY MASS SPECTROMETRY.
[8]	"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.
[9]	"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.
+	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.
AY039843 mRNA. Translation: AAK63947.1.
AY113168 mRNA. Translation: AAM47471.1.
AY087781 mRNA. Translation: AAM65317.1.

IPI

IPI00535764.

RefSeq

NP_186797.1. NM_111014.3.

UniGene

At.20535.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3RFY	X-ray	2.39	A	83-437	[»]

ProteinModelPortal

Q9SSA5.

SMR

Q9SSA5. Positions 83-433.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9SSA5. 1 interaction.

Proteomic databases

PaxDb

Q9SSA5.

PRIDE

Q9SSA5.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT3G01480.1; AT3G01480.1; AT3G01480.

GeneID

821137.

KEGG

ath:AT3G01480.

Organism-specific databases

TAIR

At3g01480.

Phylogenomic databases

eggNOG

COG0652.

HOGENOM

HOG000065979.

InParanoid

Q9SSA5.

OMA

RNAAFGY.

PhylomeDB

Q9SSA5.

ProtClustDB

CLSN2915594.

Gene expression databases

ArrayExpress

Q9SSA5.

Genevestigator

Q9SSA5.

Family and domain databases

Gene3D

1.20.120.290. 1 hit.

InterPro

IPR002130. Cyclophilin-like_PPIase_dom.
IPR023222. PsbQ-like_domain.
[Graphical view]

Pfam

PF00160. Pro_isomerase. 1 hit.
[Graphical view]

SUPFAM

SSF50891. CSA_PPIase. 1 hit.
SSF101112. PsbQ-like_domain. 1 hit.

PROSITE

PS00170. CSA_PPIASE_1. False negative.
PS50072. CSA_PPIASE_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

CYP38_ARATH

Accession

Primary (citable) accession number: Q9SSA5

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 2008
Last sequence update:	May 1, 2000
Last modified:	May 1, 2013
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program