PPIL3_HUMAN
ID PPIL3_HUMAN Reviewed; 161 AA.
AC Q9H2H8; Q86WF9; Q96IA9; Q9BXZ1;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 169.
DE RecName: Full=Peptidyl-prolyl cis-trans isomerase-like 3;
DE Short=PPIase;
DE EC=5.2.1.8;
DE AltName: Full=Cyclophilin J;
DE Short=CyPJ;
DE AltName: Full=Cyclophilin-like protein PPIL3;
DE AltName: Full=Rotamase PPIL3;
GN Name=PPIL3;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), AND TISSUE SPECIFICITY.
RC TISSUE=Fetal brain;
RX PubMed=11435694; DOI=10.1159/000056909;
RA Zhou Z., Ying K., Dai J., Tang R., Wang W., Huang Y., Zhao W., Xie Y.,
RA Mao Y.;
RT "Molecular cloning and characterization of a novel peptidylprolyl isomerase
RT (cyclophilin)-like gene (PPIL3) from human fetal brain.";
RL Cytogenet. Cell Genet. 92:231-236(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RA Ding J.B., Yu L., Zhao S.Y.;
RL Submitted (APR-1999) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Embryo;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15815621; DOI=10.1038/nature03466;
RA Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P.,
RA Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C.,
RA Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L.,
RA Du H., Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A.,
RA Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J.,
RA Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M.,
RA Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T.,
RA Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S.,
RA Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K.,
RA McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C.,
RA Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S.,
RA Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C.,
RA Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M.,
RA Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C.,
RA Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J.,
RA Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E.,
RA Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X.,
RA Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M.,
RA Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C.,
RA Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S.,
RA Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H.,
RA Wilson R.K.;
RT "Generation and annotation of the DNA sequences of human chromosomes 2 and
RT 4.";
RL Nature 434:724-731(2005).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND VARIANT GLU-146.
RC TISSUE=Placenta;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND IDENTIFICATION IN THE SPLICEOSOMAL
RP C COMPLEX.
RX PubMed=11991638; DOI=10.1017/s1355838202021088;
RA Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J.;
RT "Purification and characterization of native spliceosomes suitable for
RT three-dimensional structural analysis.";
RL RNA 8:426-439(2002).
RN [7]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in a
RT refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [9]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L.,
RA Ye M., Zou H.;
RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver
RT phosphoproteome.";
RL J. Proteomics 96:253-262(2014).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
RX PubMed=15735342; DOI=10.1107/s0907444904033189;
RA Huang L.-L., Zhao X.-M., Huang C.-Q., Yu L., Xia Z.-X.;
RT "Structure of recombinant human cyclophilin J, a novel member of the
RT cyclophilin family.";
RL Acta Crystallogr. D 61:316-321(2005).
CC -!- FUNCTION: PPIases accelerate the folding of proteins. It catalyzes the
CC cis-trans isomerization of proline imidic peptide bonds in
CC oligopeptides. May be involved in pre-mRNA splicing.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[protein]-peptidylproline (omega=180) = [protein]-
CC peptidylproline (omega=0); Xref=Rhea:RHEA:16237, Rhea:RHEA-
CC COMP:10747, Rhea:RHEA-COMP:10748, ChEBI:CHEBI:83833,
CC ChEBI:CHEBI:83834; EC=5.2.1.8;
CC -!- SUBUNIT: Identified in the spliceosome C complex.
CC {ECO:0000269|PubMed:11991638}.
CC -!- INTERACTION:
CC Q9H2H8; Q86UT8: CENATAC; NbExp=3; IntAct=EBI-751051, EBI-11028020;
CC Q9H2H8; O95391: SLU7; NbExp=5; IntAct=EBI-751051, EBI-750559;
CC Q9H2H8; Q99152: VP3; Xeno; NbExp=3; IntAct=EBI-751051, EBI-1776808;
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1; Synonyms=PPIL3b;
CC IsoId=Q9H2H8-1; Sequence=Displayed;
CC Name=2; Synonyms=PPIL3a;
CC IsoId=Q9H2H8-2; Sequence=VSP_015468;
CC -!- TISSUE SPECIFICITY: Ubiquitous. Detected at low levels.
CC {ECO:0000269|PubMed:11435694}.
CC -!- SIMILARITY: Belongs to the cyclophilin-type PPIase family. PPIL3
CC subfamily. {ECO:0000305}.
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DR EMBL; AF251049; AAK34939.1; -; mRNA.
DR EMBL; AF271652; AAG44766.1; -; mRNA.
DR EMBL; AF146799; AAO64723.1; -; mRNA.
DR EMBL; AK027315; BAB55036.1; -; mRNA.
DR EMBL; AC005037; AAY14723.1; -; Genomic_DNA.
DR EMBL; BC007693; AAH07693.1; -; mRNA.
DR CCDS; CCDS2332.1; -. [Q9H2H8-2]
DR CCDS; CCDS2333.1; -. [Q9H2H8-1]
DR RefSeq; NP_115861.1; NM_032472.3. [Q9H2H8-2]
DR RefSeq; NP_570981.1; NM_130906.2. [Q9H2H8-1]
DR RefSeq; XP_005246708.1; XM_005246651.3. [Q9H2H8-2]
DR RefSeq; XP_005246709.1; XM_005246652.4. [Q9H2H8-1]
DR RefSeq; XP_011509660.1; XM_011511358.2. [Q9H2H8-1]
DR RefSeq; XP_016859841.1; XM_017004352.1. [Q9H2H8-2]
DR RefSeq; XP_016859842.1; XM_017004353.1. [Q9H2H8-2]
DR RefSeq; XP_016859843.1; XM_017004354.1. [Q9H2H8-2]
DR RefSeq; XP_016859844.1; XM_017004355.1. [Q9H2H8-1]
DR RefSeq; XP_016859845.1; XM_017004356.1. [Q9H2H8-1]
DR PDB; 1XYH; X-ray; 2.60 A; A=1-161.
DR PDB; 2OJU; X-ray; 2.40 A; A/B=1-161.
DR PDB; 2OK3; X-ray; 2.00 A; A=1-161.
DR PDBsum; 1XYH; -.
DR PDBsum; 2OJU; -.
DR PDBsum; 2OK3; -.
DR AlphaFoldDB; Q9H2H8; -.
DR SMR; Q9H2H8; -.
DR BioGRID; 119820; 76.
DR CORUM; Q9H2H8; -.
DR IntAct; Q9H2H8; 22.
DR MINT; Q9H2H8; -.
DR iPTMnet; Q9H2H8; -.
DR MetOSite; Q9H2H8; -.
DR PhosphoSitePlus; Q9H2H8; -.
DR BioMuta; PPIL3; -.
DR DMDM; 73921766; -.
DR EPD; Q9H2H8; -.
DR jPOST; Q9H2H8; -.
DR MassIVE; Q9H2H8; -.
DR MaxQB; Q9H2H8; -.
DR PeptideAtlas; Q9H2H8; -.
DR PRIDE; Q9H2H8; -.
DR ProteomicsDB; 80550; -. [Q9H2H8-1]
DR ProteomicsDB; 80551; -. [Q9H2H8-2]
DR TopDownProteomics; Q9H2H8-1; -. [Q9H2H8-1]
DR Antibodypedia; 34922; 238 antibodies from 24 providers.
DR DNASU; 53938; -.
DR Ensembl; ENST00000286175.12; ENSP00000286175.8; ENSG00000240344.9. [Q9H2H8-2]
DR Ensembl; ENST00000392283.9; ENSP00000376107.4; ENSG00000240344.9. [Q9H2H8-1]
DR Ensembl; ENST00000409449.5; ENSP00000387012.1; ENSG00000240344.9. [Q9H2H8-2]
DR GeneID; 53938; -.
DR KEGG; hsa:53938; -.
DR MANE-Select; ENST00000392283.9; ENSP00000376107.4; NM_130906.3; NP_570981.1.
DR UCSC; uc002uwh.4; human. [Q9H2H8-1]
DR CTD; 53938; -.
DR DisGeNET; 53938; -.
DR GeneCards; PPIL3; -.
DR HGNC; HGNC:9262; PPIL3.
DR HPA; ENSG00000240344; Low tissue specificity.
DR MIM; 615811; gene.
DR neXtProt; NX_Q9H2H8; -.
DR OpenTargets; ENSG00000240344; -.
DR PharmGKB; PA33589; -.
DR VEuPathDB; HostDB:ENSG00000240344; -.
DR GeneTree; ENSGT00940000153189; -.
DR HOGENOM; CLU_012062_16_3_1; -.
DR InParanoid; Q9H2H8; -.
DR OMA; VPFHRVM; -.
DR PhylomeDB; Q9H2H8; -.
DR TreeFam; TF352224; -.
DR BRENDA; 5.2.1.8; 2681.
DR PathwayCommons; Q9H2H8; -.
DR Reactome; R-HSA-72163; mRNA Splicing - Major Pathway.
DR SignaLink; Q9H2H8; -.
DR BioGRID-ORCS; 53938; 12 hits in 1082 CRISPR screens.
DR ChiTaRS; PPIL3; human.
DR EvolutionaryTrace; Q9H2H8; -.
DR GeneWiki; PPIL3; -.
DR GenomeRNAi; 53938; -.
DR Pharos; Q9H2H8; Tbio.
DR PRO; PR:Q9H2H8; -.
DR Proteomes; UP000005640; Chromosome 2.
DR RNAct; Q9H2H8; protein.
DR Bgee; ENSG00000240344; Expressed in ileal mucosa and 178 other tissues.
DR ExpressionAtlas; Q9H2H8; baseline and differential.
DR Genevisible; Q9H2H8; HS.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IDA:UniProtKB.
DR GO; GO:0003755; F:peptidyl-prolyl cis-trans isomerase activity; IBA:GO_Central.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IC:UniProtKB.
DR GO; GO:0006457; P:protein folding; IEA:InterPro.
DR GO; GO:0000413; P:protein peptidyl-prolyl isomerization; IBA:GO_Central.
DR Gene3D; 2.40.100.10; -; 1.
DR InterPro; IPR029000; Cyclophilin-like_dom_sf.
DR InterPro; IPR024936; Cyclophilin-type_PPIase.
DR InterPro; IPR020892; Cyclophilin-type_PPIase_CS.
DR InterPro; IPR002130; Cyclophilin-type_PPIase_dom.
DR InterPro; IPR044666; Cyclophilin_A-like.
DR PANTHER; PTHR45625; PTHR45625; 1.
DR Pfam; PF00160; Pro_isomerase; 1.
DR PIRSF; PIRSF001467; Peptidylpro_ismrse; 1.
DR PRINTS; PR00153; CSAPPISMRASE.
DR SUPFAM; SSF50891; SSF50891; 1.
DR PROSITE; PS00170; CSA_PPIASE_1; 1.
DR PROSITE; PS50072; CSA_PPIASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative splicing; Isomerase; Methylation;
KW mRNA processing; mRNA splicing; Reference proteome; Rotamase; Spliceosome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:19413330,
FT ECO:0007744|PubMed:22223895"
FT CHAIN 2..161
FT /note="Peptidyl-prolyl cis-trans isomerase-like 3"
FT /id="PRO_0000064166"
FT DOMAIN 2..154
FT /note="PPIase cyclophilin-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00156"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:19413330,
FT ECO:0007744|PubMed:22223895"
FT MOD_RES 61
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0000250|UniProtKB:Q9D6L8"
FT VAR_SEQ 27..58
FT /note="NFLALCASNYYNGCIFHRNIKGFMVQTGDPTG -> MESRCVPQAGVQWRDL
FT GSLQPPPPGFKQVFCLSLPR (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:11435694,
FT ECO:0000303|PubMed:14702039"
FT /id="VSP_015468"
FT VARIANT 146
FT /note="D -> E (in dbSNP:rs7562391)"
FT /evidence="ECO:0000269|PubMed:15489334"
FT /id="VAR_023417"
FT CONFLICT 61..62
FT /note="RG -> KR (in Ref. 2; AAO64723)"
FT /evidence="ECO:0000305"
FT CONFLICT 65
FT /note="S -> V (in Ref. 2; AAO64723)"
FT /evidence="ECO:0000305"
FT CONFLICT 78
FT /note="Y -> I (in Ref. 2; AAO64723)"
FT /evidence="ECO:0000305"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:2OK3"
FT STRAND 10..16
FT /evidence="ECO:0007829|PDB:2OK3"
FT TURN 18..20
FT /evidence="ECO:0007829|PDB:2OK3"
FT HELIX 22..33
FT /evidence="ECO:0007829|PDB:2OK3"
FT TURN 34..39
FT /evidence="ECO:0007829|PDB:2OK3"
FT STRAND 44..46
FT /evidence="ECO:0007829|PDB:2OK3"
FT TURN 47..49
FT /evidence="ECO:0007829|PDB:2OK3"
FT STRAND 50..53
FT /evidence="ECO:0007829|PDB:2OK3"
FT STRAND 58..61
FT /evidence="ECO:0007829|PDB:2OK3"
FT STRAND 86..89
FT /evidence="ECO:0007829|PDB:2OK3"
FT STRAND 92..95
FT /evidence="ECO:0007829|PDB:2OJU"
FT STRAND 101..106
FT /evidence="ECO:0007829|PDB:2OK3"
FT HELIX 109..111
FT /evidence="ECO:0007829|PDB:2OK3"
FT TURN 112..114
FT /evidence="ECO:0007829|PDB:2OK3"
FT STRAND 117..123
FT /evidence="ECO:0007829|PDB:2OK3"
FT HELIX 125..132
FT /evidence="ECO:0007829|PDB:2OK3"
FT TURN 138..140
FT /evidence="ECO:0007829|PDB:2OK3"
FT STRAND 143..145
FT /evidence="ECO:0007829|PDB:2OK3"
FT STRAND 148..155
FT /evidence="ECO:0007829|PDB:2OK3"
SQ SEQUENCE 161 AA; 18155 MW; 5FE190D7858B07D4 CRC64;
MSVTLHTDVG DIKIEVFCER TPKTCENFLA LCASNYYNGC IFHRNIKGFM VQTGDPTGTG
RGGNSIWGKK FEDEYSEYLK HNVRGVVSMA NNGPNTNGSQ FFITYGKQPH LDMKYTVFGK
VIDGLETLDE LEKLPVNEKT YRPLNDVHIK DITIHANPFA Q
