CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-011630
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Peptidyl-prolyl cis-trans isomerase D 
Protein Synonyms/Alias
 PPIase D; 40 kDa peptidyl-prolyl cis-trans isomerase; Cyclophilin-40; CYP-40; Cyclophilin-related protein; Rotamase D 
Gene Name
 PPID 
Gene Synonyms/Alias
 CYP40; CYPD 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
9SHPSPQAKPSNPSNPubiquitination[1, 2]
168ILENVEVKGEKPAKLubiquitination[2]
218IDLKDVDKILLITEDubiquitination[3]
227LLITEDLKNIGNTFFubiquitination[2]
245NWEMAIKKYAEVLRYubiquitination[2]
257LRYVDSSKAVIETADacetylation[4]
257LRYVDSSKAVIETADubiquitination[1, 2, 5]
267IETADRAKLQPIALSubiquitination[2]
283VLNIGACKLKMSNWQubiquitination[1, 6, 7]
285NIGACKLKMSNWQGAubiquitination[2, 7]
308ELDPSNTKALYRRAQubiquitination[6]
331DQALADLKKAQGIAPubiquitination[2, 5]
341QGIAPEDKAIQAELLubiquitination[1, 2, 5, 7]
367KEKAVYAKMFA****ubiquitination[2]
Reference
 [1] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [2] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [3] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [4] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377]
 [5] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [6] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [7] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302] 
Functional Description
 PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Proposed to act as a co-chaperone in HSP90 complexes such as in unligated steroid receptors heterocomplexes. Different co-chaperones seem to compete for association with HSP90 thus establishing distinct HSP90-co-chaperone-receptor complexes with the potential to exert tissue-specific receptor activity control. May have a preference for estrogen receptor complexes and is not found in glucocorticoid receptor complexes. May be involved in cytoplasmic dynein-dependent movement of the receptor from the cytoplasm to the nucleus. May regulate MYB by inhibiting its DNA- binding activity. Involved in regulation of AHR signaling by promoting the formation of the AHR:ARNT dimer; the function is independent of HSP90 but requires the chaperone activity. Involved in regulation of UV radiation-induced apoptosis. Promotes cell viability in anaplastic lymphoma kinase-positive anaplastic large- cell lymphoma (ALK+ ALCL) cell lines. May be involved in hepatitis C virus (HCV) replication and release. 
Sequence Annotation
 DOMAIN 19 183 PPIase cyclophilin-type.
 REPEAT 223 256 TPR 1.
 REPEAT 273 306 TPR 2.
 REPEAT 307 340 TPR 3.
 REGION 185 215 Chaperone activity (By similarity).
 REGION 214 370 Interaction with HSP90AB1 (By
 MOD_RES 198 198 Phosphoserine.  
Keyword
 Apoptosis; Chaperone; Complete proteome; Cyclosporin; Cytoplasm; Direct protein sequencing; Isomerase; Nucleus; Phosphoprotein; Polymorphism; Protein transport; Reference proteome; Repeat; Rotamase; TPR repeat; Transport. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 370 AA 
Protein Sequence
MSHPSPQAKP SNPSNPRVFF DVDIGGERVG RIVLELFADI VPKTAENFRA LCTGEKGIGH 60
TTGKPLHFKG CPFHRIIKKF MIQGGDFSNQ NGTGGESIYG EKFEDENFHY KHDREGLLSM 120
ANAGRNTNGS QFFITTVPTP HLDGKHVVFG QVIKGIGVAR ILENVEVKGE KPAKLCVIAE 180
CGELKEGDDG GIFPKDGSGD SHPDFPEDAD IDLKDVDKIL LITEDLKNIG NTFFKSQNWE 240
MAIKKYAEVL RYVDSSKAVI ETADRAKLQP IALSCVLNIG ACKLKMSNWQ GAIDSCLEAL 300
ELDPSNTKAL YRRAQGWQGL KEYDQALADL KKAQGIAPED KAIQAELLKV KQKIKAQKDK 360
EKAVYAKMFA 370 
Gene Ontology
 GO:0005737; C:cytoplasm; IDA:UniProtKB.
 GO:0045111; C:intermediate filament cytoskeleton; IDA:HPA.
 GO:0005730; C:nucleolus; IDA:UniProtKB.
 GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
 GO:0016018; F:cyclosporin A binding; TAS:UniProtKB.
 GO:0030331; F:estrogen receptor binding; ISS:UniProtKB.
 GO:0030544; F:Hsp70 protein binding; ISS:UniProtKB.
 GO:0051879; F:Hsp90 protein binding; IDA:UniProtKB.
 GO:0003755; F:peptidyl-prolyl cis-trans isomerase activity; IDA:UniProtKB.
 GO:0008134; F:transcription factor binding; IDA:UniProtKB.
 GO:0006915; P:apoptotic process; IEA:UniProtKB-KW.
 GO:0071492; P:cellular response to UV-A; IMP:UniProtKB.
 GO:0061077; P:chaperone-mediated protein folding; IDA:UniProtKB.
 GO:0034389; P:lipid particle organization; IMP:UniProtKB.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IMP:UniProtKB.
 GO:0043065; P:positive regulation of apoptotic process; IMP:UniProtKB.
 GO:0050714; P:positive regulation of protein secretion; IMP:UniProtKB.
 GO:0045070; P:positive regulation of viral genome replication; IMP:UniProtKB.
 GO:0006461; P:protein complex assembly; IDA:UniProtKB.
 GO:0015031; P:protein transport; IEA:UniProtKB-KW.
 GO:0019076; P:viral release from host cell; TAS:UniProtKB. 
Interpro
 IPR002130; Cyclophilin-like_PPIase_dom.
 IPR020892; Cyclophilin-type_PPIase_CS.
 IPR013026; TPR-contain_dom.
 IPR011990; TPR-like_helical.
 IPR019734; TPR_repeat. 
Pfam
 PF00160; Pro_isomerase
 PF13176; TPR_7 
SMART
 SM00028; TPR 
PROSITE
 PS00170; CSA_PPIASE_1
 PS50072; CSA_PPIASE_2
 PS50005; TPR
 PS50293; TPR_REGION 
PRINTS
 PR00153; CSAPPISMRASE.