FKBP4_YEAST
ID FKBP4_YEAST Reviewed; 392 AA.
AC Q06205; D6VZ83;
DT 15-JUL-1999, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 190.
DE RecName: Full=FK506-binding protein 4 {ECO:0000305|PubMed:9371805};
DE EC=5.2.1.8 {ECO:0000269|PubMed:16959570, ECO:0000269|PubMed:23888048};
DE AltName: Full=Histone proline isomerase {ECO:0000303|PubMed:16959570};
DE AltName: Full=Peptidyl-prolyl cis-trans isomerase;
DE Short=PPIase;
DE AltName: Full=Rotamase;
GN Name=FPR4 {ECO:0000303|PubMed:9371805};
GN OrderedLocusNames=YLR449W {ECO:0000312|SGD:S000004441}; ORFNames=L9324.3;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP SUBCELLULAR LOCATION.
RX PubMed=9371805; DOI=10.1073/pnas.94.24.13093;
RA Dolinski K., Muir S., Cardenas M., Heitman J.;
RT "All cyclophilins and FK506 binding proteins are, individually and
RT collectively, dispensable for viability in Saccharomyces cerevisiae.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:13093-13098(1997).
RN [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [5]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=14981505; DOI=10.1038/nsmb733;
RA Kuzuhara T., Horikoshi M.;
RT "A nuclear FK506-binding protein is a histone chaperone regulating rDNA
RT silencing.";
RL Nat. Struct. Mol. Biol. 11:275-283(2004).
RN [6]
RP INTERACTION WITH NOP53, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=15686447; DOI=10.1042/bj20041297;
RA Sydorskyy Y., Dilworth D.J., Halloran B., Yi E.C., Makhnevych T.,
RA Wozniak R.W., Aitchison J.D.;
RT "Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein.";
RL Biochem. J. 388:819-826(2005).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND INTERACTION WITH HISTONE H3 AND H4.
RX PubMed=16959570; DOI=10.1016/j.cell.2006.07.026;
RA Nelson C.J., Santos-Rosa H., Kouzarides T.;
RT "Proline isomerization of histone H3 regulates lysine methylation and gene
RT expression.";
RL Cell 126:905-916(2006).
RN [8]
RP FUNCTION.
RX PubMed=16846601; DOI=10.1016/j.febslet.2006.06.093;
RA Xiao H., Jackson V., Lei M.;
RT "The FK506-binding protein, Fpr4, is an acidic histone chaperone.";
RL FEBS Lett. 580:4357-4364(2006).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-80 AND SER-82, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-80 AND SER-82, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-80 AND SER-82, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [12]
RP STRUCTURE BY NMR OF 280-392, FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=23888048; DOI=10.1074/jbc.m113.479964;
RA Monneau Y.R., Soufari H., Nelson C.J., Mackereth C.D.;
RT "Structure and activity of the peptidyl-prolyl isomerase domain from the
RT histone chaperone Fpr4 toward histone H3 proline isomerization.";
RL J. Biol. Chem. 288:25826-25837(2013).
CC -!- FUNCTION: PPIase that acts as a histone chaperone (PubMed:14981505,
CC PubMed:16846601). Histone proline isomerase that increases the rate of
CC cis-trans isomerization at 'Pro-17' (H3P16), 'Pro-31' (H3P30) and 'Pro-
CC 39 (H3P38) on the histone H3 N-terminal tail (PubMed:16959570,
CC PubMed:23888048). H3P16 and H3P30 are the major proline targets with
CC little activity shown against H3P38 (PubMed:23888048). H3P38
CC isomerization influences SET2-mediated H3K36 methylation thereby
CC regulating gene expression (PubMed:16959570).
CC {ECO:0000269|PubMed:14981505, ECO:0000269|PubMed:16846601,
CC ECO:0000269|PubMed:16959570, ECO:0000269|PubMed:23888048}.
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; Evidence={ECO:0000269|PubMed:16959570,
CC ECO:0000269|PubMed:23888048};
CC -!- SUBUNIT: Binds to histones H3 and H4 (PubMed:16959570). Interacts with
CC NOP53. {ECO:0000269|PubMed:15686447, ECO:0000269|PubMed:16959570}.
CC -!- INTERACTION:
CC Q06205; P38911: FPR3; NbExp=4; IntAct=EBI-6956, EBI-6951;
CC Q06205; P02309: HHF2; NbExp=5; IntAct=EBI-6956, EBI-8113;
CC Q06205; P61830: HHT2; NbExp=6; IntAct=EBI-6956, EBI-8098;
CC Q06205; P43586: LOC1; NbExp=3; IntAct=EBI-6956, EBI-22906;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14981505,
CC ECO:0000269|PubMed:9371805}.
CC -!- MISCELLANEOUS: Present with 14100 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the FKBP-type PPIase family. FKBP3/4 subfamily.
CC {ECO:0000305}.
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DR EMBL; U22382; AAB67528.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09749.1; -; Genomic_DNA.
DR PIR; S55971; S55971.
DR RefSeq; NP_013554.3; NM_001182337.3.
DR PDB; 4BF8; NMR; -; A=280-392.
DR PDBsum; 4BF8; -.
DR AlphaFoldDB; Q06205; -.
DR BMRB; Q06205; -.
DR SMR; Q06205; -.
DR BioGRID; 31707; 154.
DR DIP; DIP-909N; -.
DR IntAct; Q06205; 77.
DR MINT; Q06205; -.
DR STRING; 4932.YLR449W; -.
DR iPTMnet; Q06205; -.
DR MaxQB; Q06205; -.
DR PaxDb; Q06205; -.
DR PRIDE; Q06205; -.
DR EnsemblFungi; YLR449W_mRNA; YLR449W; YLR449W.
DR GeneID; 851170; -.
DR KEGG; sce:YLR449W; -.
DR SGD; S000004441; FPR4.
DR VEuPathDB; FungiDB:YLR449W; -.
DR eggNOG; KOG0552; Eukaryota.
DR GeneTree; ENSGT00940000176659; -.
DR HOGENOM; CLU_022297_3_1_1; -.
DR InParanoid; Q06205; -.
DR OMA; CQEELIG; -.
DR BioCyc; YEAST:YLR449W-MON; -.
DR PRO; PR:Q06205; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; Q06205; protein.
DR GO; GO:0005730; C:nucleolus; HDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0005527; F:macrolide binding; IDA:SGD.
DR GO; GO:0003755; F:peptidyl-prolyl cis-trans isomerase activity; IDA:SGD.
DR GO; GO:0000412; P:histone peptidyl-prolyl isomerization; IDA:SGD.
DR GO; GO:0000415; P:negative regulation of histone H3-K36 methylation; IMP:SGD.
DR GO; GO:0006334; P:nucleosome assembly; IDA:SGD.
DR Gene3D; 3.10.50.40; -; 1.
DR InterPro; IPR041232; NPL.
DR InterPro; IPR046357; PPIase_dom_sf.
DR InterPro; IPR001179; PPIase_FKBP_dom.
DR InterPro; IPR023566; PPIase_Fpr3/Fpr4-like.
DR Pfam; PF00254; FKBP_C; 1.
DR Pfam; PF17800; NPL; 1.
DR PIRSF; PIRSF001473; FK506-bp_FPR3; 1.
DR PROSITE; PS50059; FKBP_PPIASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chaperone; Isomerase; Nucleus; Phosphoprotein;
KW Reference proteome; Rotamase.
FT CHAIN 1..392
FT /note="FK506-binding protein 4"
FT /id="PRO_0000075314"
FT DOMAIN 306..392
FT /note="PPIase FKBP-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00277"
FT REGION 58..116
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 161..284
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 84..104
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 173..216
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 217..284
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 80
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MOD_RES 82
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT STRAND 282..285
FT /evidence="ECO:0007829|PDB:4BF8"
FT STRAND 291..296
FT /evidence="ECO:0007829|PDB:4BF8"
FT STRAND 308..317
FT /evidence="ECO:0007829|PDB:4BF8"
FT STRAND 322..326
FT /evidence="ECO:0007829|PDB:4BF8"
FT STRAND 332..336
FT /evidence="ECO:0007829|PDB:4BF8"
FT STRAND 339..341
FT /evidence="ECO:0007829|PDB:4BF8"
FT HELIX 343..348
FT /evidence="ECO:0007829|PDB:4BF8"
FT STRAND 357..362
FT /evidence="ECO:0007829|PDB:4BF8"
FT HELIX 364..366
FT /evidence="ECO:0007829|PDB:4BF8"
FT TURN 367..370
FT /evidence="ECO:0007829|PDB:4BF8"
FT STRAND 382..392
FT /evidence="ECO:0007829|PDB:4BF8"
SQ SEQUENCE 392 AA; 43903 MW; CF90C6714F04572E CRC64;
MSDMLPLATY SLNVEPYSPT PALNFKIPVT IRITMAAIDP EPFDDDKKPS TLRIIKRNPE
LTRGEYYNQD NNDGLEEDES ESEQEADVPK RSVKSKKGKA VEQSESEDSE DENEIDDEFE
ECVLLTLSPK GQYQQALDIT IAPEEDVQFV VTGSYTISLT GNYVKHPFDN SSDSDEDEED
YYSDEESSNG EEEEEEEEED DEELSSGDDD LDDLVDASDI ESRLDELVKK DEKKKNNKKD
SKRKHEEDEE ESAKPAEKKQ TTKKDKKAEK VKDSEESKPK PKTKLLEGGI IIEDRVTGKG
PHAKKGTRVG MRYVGKLKNG KVFDKNTKGK PFVFKLGQGE VIKGWDIGVA GMAVGGERRI
VIPAPYAYGK QALPGIPANS ELTFDVKLVS MK
