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Protein

Peptidyl-prolyl cis-trans isomerase CYP59

Gene

CYP59

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Influences somehow regulation of RNA pol II (CTD) phosphorylation. Binds RNA with preferences for GC-rich sequences. Probably involved in activities connecting transcription and pre-mRNA processing. Involved in brassinostroid response.2 Publications

Catalytic activityi

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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri341 – 35717CCHC-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. nucleotide binding Source: InterPro
  2. peptidyl-prolyl cis-trans isomerase activity Source: GO_Central
  3. RNA binding Source: TAIR
  4. zinc ion binding Source: InterPro

GO - Biological processi

  1. protein folding Source: InterPro
  2. protein peptidyl-prolyl isomerization Source: GO_Central
  3. regulation of phosphorylation of RNA polymerase II C-terminal domain Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Rotamase

Keywords - Ligandi

Metal-binding, RNA-binding, Zinc

Enzyme and pathway databases

BioCyciARA:AT1G53720-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptidyl-prolyl cis-trans isomerase CYP59 (EC:5.2.1.8)
Short name:
AtCYP59
Short name:
PPIase CYP59
Alternative name(s):
Cyclophilin-59
Gene namesi
Name:CYP59
Ordered Locus Names:At1g53720
ORF Names:F22G10.24
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G53720.

Subcellular locationi

Nucleus 1 Publication
Note: Shows a punctuate localization pattern distinct from the nuclear speckles.

GO - Cellular componenti

  1. cytosol Source: TAIR
  2. nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 506506Peptidyl-prolyl cis-trans isomerase CYP59PRO_0000429607Add
BLAST

Proteomic databases

PRIDEiQ6Q151.

Expressioni

Tissue specificityi

Ubiquitous.3 Publications

Gene expression databases

ExpressionAtlasiQ6Q151. baseline and differential.
GenevestigatoriQ6Q151.

Interactioni

Subunit structurei

Component of the BZR1 complex. Interacts with NRPB1 (via CTD domain), SCL28, SCL30, SCL30A, SCL33, SC35, SR30, SR34, RSZ21, RS2Z33, RS31 and RS40.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
NRPB1P186163EBI-1625989,EBI-1540537
SCL33Q9SEU43EBI-1625989,EBI-927103

Protein-protein interaction databases

IntActiQ6Q151. 14 interactions.
STRINGi3702.AT1G53720.1-P.

Structurei

3D structure databases

SMRiQ6Q151. Positions 2-156, 245-316.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 161161PPIase cyclophilin-typePROSITE-ProRule annotationAdd
BLAST
Domaini243 – 32179RRMPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi397 – 506110Arg-richAdd
BLAST

Sequence similaritiesi

Belongs to the cyclophilin-type PPIase family.Curated
Contains 1 CCHC-type zinc finger.PROSITE-ProRule annotation
Contains 1 PPIase cyclophilin-type domain.PROSITE-ProRule annotation
Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri341 – 35717CCHC-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0652.
HOGENOMiHOG000186284.
InParanoidiQ6Q151.
KOiK12735.
OMAiKLWSQFR.
PhylomeDBiQ6Q151.

Family and domain databases

Gene3Di2.40.100.10. 1 hit.
3.30.70.330. 1 hit.
InterProiIPR029000. Cyclophilin-like_dom.
IPR024936. Cyclophilin-type_PPIase.
IPR002130. Cyclophilin-type_PPIase_dom.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
IPR001878. Znf_CCHC.
[Graphical view]
PANTHERiPTHR11071. PTHR11071. 1 hit.
PfamiPF00160. Pro_isomerase. 1 hit.
PF00076. RRM_1. 1 hit.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
PRINTSiPR00153. CSAPPISMRASE.
SMARTiSM00360. RRM. 1 hit.
SM00343. ZnF_C2HC. 1 hit.
[Graphical view]
SUPFAMiSSF50891. SSF50891. 1 hit.
PROSITEiPS50072. CSA_PPIASE_2. 1 hit.
PS50102. RRM. 1 hit.
PS50158. ZF_CCHC. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q6Q151-1) [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
MSVLIVTSLG DIVIDLHSDK CPLTCKNFLK LCKIKYYNGC LFHTVQKDFT
60 70 80 90 100
AQTGDPTGTG AGGDSIYKFL YGEQARFYKD EIHLDLKHSK TGTVAMASGG
110 120 130 140 150
ENLNASQFYF TLRDDLDYLD GKHTVFGQIA EGFDTLTRIN EAYVDPKNRP
160 170 180 190 200
YKNIRIKHTH ILDDPFDDPP QLAEMMPDAS PEGKPKEEVK DDVRLEDDWV
210 220 230 240 250
PMDEELGAQE LEEVIREKAA HSSAVVLESI GDIPEAEVKP PDNVLFVCKL
260 270 280 290 300
NPVTEDEDLH TIFSRFGTVV SADVIRDFKT GDSLCYAFIE FENKESCEQA
310 320 330 340 350
YFKMDNALID DRRIHVDFSQ SVSKLWSQFR QKDSQKGKGN GCFKCGSTDH
360 370 380 390 400
IAKDCVGGPS SKFIVKDQNR QHGGGEGYEM VFEGDVHETP KHNSHERERS
410 420 430 440 450
EKIQRRSPHG NGEGKRQHRD ERDDGRRQHD REDARELERK HRERKERESR
460 470 480 490 500
EDEDRRRRRR REESRDKESR RERDEDDHRS HRDYKERRRE RDDRHGREAR

HERRDR
Length:506
Mass (Da):58,829
Last modified:July 4, 2004 - v1
Checksum:iEB33E6544794283E
GO
Isoform 2 (identifier: Q6Q151-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     441-506: HRERKERESREDEDRRRRRRREESRDKESRRERDEDDHRSHRDYKERRRERDDRHGREARHERRDR → L

Show »
Length:441
Mass (Da):50,057
Checksum:i6ECB854A92F03990
GO

Sequence cautioni

The sequence AAG51976.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei441 – 50666HRERK…ERRDR → L in isoform 2. 1 PublicationVSP_055001Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY568526 mRNA. Translation: AAS75309.1.
AC024260 Genomic DNA. Translation: AAG51976.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE32989.1.
AY059824 mRNA. Translation: AAL24306.1.
PIRiE96577.
RefSeqiNP_175776.2. NM_104250.4. [Q6Q151-1]
UniGeneiAt.37348.

Genome annotation databases

EnsemblPlantsiAT1G53720.1; AT1G53720.1; AT1G53720. [Q6Q151-1]
GeneIDi841810.
KEGGiath:AT1G53720.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY568526 mRNA. Translation: AAS75309.1.
AC024260 Genomic DNA. Translation: AAG51976.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE32989.1.
AY059824 mRNA. Translation: AAL24306.1.
PIRiE96577.
RefSeqiNP_175776.2. NM_104250.4. [Q6Q151-1]
UniGeneiAt.37348.

3D structure databases

SMRiQ6Q151. Positions 2-156, 245-316.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ6Q151. 14 interactions.
STRINGi3702.AT1G53720.1-P.

Proteomic databases

PRIDEiQ6Q151.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G53720.1; AT1G53720.1; AT1G53720. [Q6Q151-1]
GeneIDi841810.
KEGGiath:AT1G53720.

Organism-specific databases

TAIRiAT1G53720.

Phylogenomic databases

eggNOGiCOG0652.
HOGENOMiHOG000186284.
InParanoidiQ6Q151.
KOiK12735.
OMAiKLWSQFR.
PhylomeDBiQ6Q151.

Enzyme and pathway databases

BioCyciARA:AT1G53720-MONOMER.

Miscellaneous databases

PROiQ6Q151.

Gene expression databases

ExpressionAtlasiQ6Q151. baseline and differential.
GenevestigatoriQ6Q151.

Family and domain databases

Gene3Di2.40.100.10. 1 hit.
3.30.70.330. 1 hit.
InterProiIPR029000. Cyclophilin-like_dom.
IPR024936. Cyclophilin-type_PPIase.
IPR002130. Cyclophilin-type_PPIase_dom.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
IPR001878. Znf_CCHC.
[Graphical view]
PANTHERiPTHR11071. PTHR11071. 1 hit.
PfamiPF00160. Pro_isomerase. 1 hit.
PF00076. RRM_1. 1 hit.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
PRINTSiPR00153. CSAPPISMRASE.
SMARTiSM00360. RRM. 1 hit.
SM00343. ZnF_C2HC. 1 hit.
[Graphical view]
SUPFAMiSSF50891. SSF50891. 1 hit.
PROSITEiPS50072. CSA_PPIASE_2. 1 hit.
PS50102. RRM. 1 hit.
PS50158. ZF_CCHC. 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 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (MAR-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(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Strain: cv. Columbia.
  5. "Immunophilins and parvulins. Superfamily of peptidyl prolyl isomerases in Arabidopsis."
    He Z., Li L., Luan S.
    Plant Physiol. 134:1248-1267(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE, TISSUE SPECIFICITY.
    Strain: cv. Columbia.
  6. "AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II."
    Gullerova M., Barta A., Lorkovic Z.J.
    RNA 12:631-643(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, INTERACTION WITH NRPB1; SCL28; SCL30; SCL30A; SCL33; SC35; SR30; SR34; RSZ21; RS2Z33; RS31 AND RS40, SUBCELLULAR LOCATION, RNA-BINDING.
  7. "Identification of BZR1-interacting proteins as potential components of the brassinosteroid signaling pathway in Arabidopsis through tandem affinity purification."
    Wang C., Shang J.X., Chen Q.X., Oses-Prieto J.A., Bai M.Y., Yang Y., Yuan M., Zhang Y.L., Mu C.C., Deng Z., Wei C.Q., Burlingame A.L., Wang Z.Y., Sun Y.
    Mol. Cell. Proteomics 12:3653-3665(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE BZR1 COMPLEX.
  8. "Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity."
    Bannikova O., Zywicki M., Marquez Y., Skrahina T., Kalyna M., Barta A.
    Nucleic Acids Res. 41:1783-1796(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiCYP59_ARATH
AccessioniPrimary (citable) accession number: Q6Q151
Secondary accession number(s): Q93YQ8, Q9C8M7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 8, 2014
Last sequence update: July 4, 2004
Last modified: March 31, 2015
This is version 91 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

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. 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.