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Peptidyl-prolyl cis-trans isomerase F, mitochondrial (PPIase F) (EC 5.2.1.8) (Cyclophilin D) (CyP-D) (CypD) (Cyclophilin F) (Rotamase F)

 PPIF_RAT                Reviewed;         206 AA.
P29117;
01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
01-NOV-1997, sequence version 2.
27-SEP-2017, entry version 141.
RecName: Full=Peptidyl-prolyl cis-trans isomerase F, mitochondrial;
Short=PPIase F;
EC=5.2.1.8;
AltName: Full=Cyclophilin D;
Short=CyP-D;
Short=CypD;
AltName: Full=Cyclophilin F;
AltName: Full=Rotamase F;
Flags: Precursor;
Name=Ppif;
Rattus norvegicus (Rat).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Rattus.
NCBI_TaxID=10116;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
STRAIN=Wistar; TISSUE=Skeletal muscle;
Price N.T., Woodfield K.Y., Halestrap A.P.;
Submitted (SEP-1996) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Heart;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[3]
PROTEIN SEQUENCE OF 30-58.
TISSUE=Liver;
PubMed=1599421; DOI=10.1042/bj2840381;
Connern C.P., Halestrap A.P.;
"Purification and N-terminal sequencing of peptidyl-prolyl cis-trans-
isomerase from rat liver mitochondrial matrix reveals the existence of
a distinct mitochondrial cyclophilin.";
Biochem. J. 284:381-385(1992).
[4]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=8567677; DOI=10.1074/jbc.271.4.2185;
Nicolli A., Basso E., Petronilli V., Wenger R.M., Bernardi P.;
"Interactions of cyclophilin with the mitochondrial inner membrane and
regulation of the permeability transition pore, and cyclosporin A-
sensitive channel.";
J. Biol. Chem. 271:2185-2192(1996).
[5]
FUNCTION.
PubMed=9309684; DOI=10.1023/A:1006887921810;
Scorrano L., Nicolli A., Basso E., Petronilli V., Bernardi P.;
"Two modes of activation of the permeability transition pore: the role
of mitochondrial cyclophilin.";
Mol. Cell. Biochem. 174:181-184(1997).
[6]
FUNCTION.
PubMed=9820802; DOI=10.1042/bj3360287;
Woodfield K., Ruck A., Brdiczka D., Halestrap A.P.;
"Direct demonstration of a specific interaction between cyclophilin-D
and the adenine nucleotide translocase confirms their role in the
mitochondrial permeability transition.";
Biochem. J. 336:287-290(1998).
[7]
INTERACTION WITH VDAC1.
PubMed=9874241; DOI=10.1046/j.1432-1327.1998.2580729.x;
Crompton M., Virji S., Ward J.M.;
"Cyclophilin-D binds strongly to complexes of the voltage-dependent
anion channel and the adenine nucleotide translocase to form the
permeability transition pore.";
Eur. J. Biochem. 258:729-735(1998).
[8]
INTERACTION WITH SLC25A3.
PubMed=18667415; DOI=10.1074/jbc.M805235200;
Leung A.W., Varanyuwatana P., Halestrap A.P.;
"The mitochondrial phosphate carrier interacts with cyclophilin D and
may play a key role in the permeability transition.";
J. Biol. Chem. 283:26312-26323(2008).
[9]
SUBCELLULAR LOCATION, AND INTERACTION WITH BCL2.
PubMed=19228691; DOI=10.1074/jbc.M808750200;
Eliseev R.A., Malecki J., Lester T., Zhang Y., Humphrey J.,
Gunter T.E.;
"Cyclophilin D interacts with Bcl2 and exerts an anti-apoptotic
effect.";
J. Biol. Chem. 284:9692-9699(2009).
-!- FUNCTION: PPIases accelerate the folding of proteins. It catalyzes
the cis-trans isomerization of proline imidic peptide bonds in
oligopeptides. Involved in regulation of the mitochondrial
permeability transition pore (mPTP). It is proposed that its
association with the mPTP is masking a binding site for inhibiting
inorganic phosphate (Pi) and promotes the open probability of the
mPTP leading to apoptosis or necrosis; the requirement of the
PPIase activity for this function is debated. In cooperation with
mitochondrial TP53 is involved in activating oxidative stress-
induced necrosis. Involved in modulation of mitochondrial membrane
F(1)F(0) ATP synthase activity and regulation of mitochondrial
matrix adenine nucleotide levels. Has anti-apoptotic activity
independently of mPTP and in cooperation with BCL2 inhibits
cytochrome c-dependent apoptosis. {ECO:0000269|PubMed:8567677,
ECO:0000269|PubMed:9309684, ECO:0000269|PubMed:9820802}.
-!- CATALYTIC ACTIVITY: Peptidylproline (omega=180) = peptidylproline
(omega=0).
-!- ENZYME REGULATION: Binds cyclosporin A (CsA). Is displaced by CsA
from the mPTP leading to a lower open probability of the mPTP.
-!- SUBUNIT: Believed to associate with the mitochondrial permeability
transition pore complex (PTPC). Associates with the mitochondrial
membrane ATP synthase F(1)F(0) ATP synthase; the association is
increased by inorganic phosphate (Pi) and decreased by cyclosporin
A (CsA). Interacts with ATP5B; ATP5H and ATP5O. Interacts with
SLC25A3; the interaction is impaired by CsA. Interacts with BCL2;
the interaction is impaired by CsA. Interacts with TP53; the
association implicates preferentially tetrameric TP53, is induced
by oxidative stress and is impaired by CsA. Interacts with C1QBP.
Interacts with MCUR1 (By similarity).
{ECO:0000250|UniProtKB:P30405, ECO:0000269|PubMed:18667415,
ECO:0000269|PubMed:19228691, ECO:0000269|PubMed:9874241}.
-!- SUBCELLULAR LOCATION: Mitochondrion matrix
{ECO:0000269|PubMed:19228691, ECO:0000269|PubMed:8567677}.
-!- PTM: Deacteylated at Lys-166 by SIRT3 (By similarity). Interacts
with BCL2; the interaction is impaired by CsA. {ECO:0000250}.
-!- SIMILARITY: Belongs to the cyclophilin-type PPIase family.
{ECO:0000305}.
-!- CAUTION: The polyclonal antibody used in PubMed:9820802 and
PubMed:9874241 and initially thought to detect SLC25A4/ANT1 in
interactions with Ppif/CyP-D is rather detecting SLC25A3.
{ECO:0000305|PubMed:18667415}.
-----------------------------------------------------------------------
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EMBL; U68544; AAB08453.1; -; mRNA.
EMBL; BC086977; AAH86977.1; -; mRNA.
PIR; S23122; S23122.
RefSeq; NP_758443.1; NM_172243.1.
UniGene; Rn.2923; -.
PDB; 4TOT; X-ray; 2.39 A; A/B/C/D=43-206.
PDBsum; 4TOT; -.
ProteinModelPortal; P29117; -.
SMR; P29117; -.
IntAct; P29117; 7.
MINT; MINT-1542363; -.
STRING; 10116.ENSRNOP00000014382; -.
iPTMnet; P29117; -.
PhosphoSitePlus; P29117; -.
PaxDb; P29117; -.
PRIDE; P29117; -.
Ensembl; ENSRNOT00000014382; ENSRNOP00000014382; ENSRNOG00000010558.
GeneID; 282819; -.
KEGG; rno:282819; -.
UCSC; RGD:628670; rat.
CTD; 10105; -.
RGD; 628670; Ppif.
eggNOG; KOG0865; Eukaryota.
eggNOG; COG0652; LUCA.
GeneTree; ENSGT00760000119119; -.
HOGENOM; HOG000065981; -.
HOVERGEN; HBG001065; -.
InParanoid; P29117; -.
KO; K09565; -.
OMA; DIEWEGP; -.
OrthoDB; EOG091G0BGL; -.
PhylomeDB; P29117; -.
TreeFam; TF312801; -.
PRO; PR:P29117; -.
Proteomes; UP000002494; Chromosome 16.
Bgee; ENSRNOG00000010558; -.
Genevisible; P29117; RN.
GO; GO:0005743; C:mitochondrial inner membrane; IDA:RGD.
GO; GO:0005759; C:mitochondrial matrix; IDA:RGD.
GO; GO:0005739; C:mitochondrion; IDA:RGD.
GO; GO:0016018; F:cyclosporin A binding; IDA:RGD.
GO; GO:0042277; F:peptide binding; IDA:RGD.
GO; GO:0003755; F:peptidyl-prolyl cis-trans isomerase activity; IDA:RGD.
GO; GO:0008637; P:apoptotic mitochondrial changes; IBA:GO_Central.
GO; GO:0071243; P:cellular response to arsenic-containing substance; ISS:UniProtKB.
GO; GO:0071277; P:cellular response to calcium ion; ISS:UniProtKB.
GO; GO:0070301; P:cellular response to hydrogen peroxide; ISS:UniProtKB.
GO; GO:0070266; P:necroptotic process; IEA:Ensembl.
GO; GO:0043066; P:negative regulation of apoptotic process; ISS:UniProtKB.
GO; GO:0032780; P:negative regulation of ATPase activity; ISS:UniProtKB.
GO; GO:2001243; P:negative regulation of intrinsic apoptotic signaling pathway; ISS:UniProtKB.
GO; GO:0090324; P:negative regulation of oxidative phosphorylation; ISS:UniProtKB.
GO; GO:2000276; P:negative regulation of oxidative phosphorylation uncoupler activity; ISS:UniProtKB.
GO; GO:0090201; P:negative regulation of release of cytochrome c from mitochondria; ISS:UniProtKB.
GO; GO:0090200; P:positive regulation of release of cytochrome c from mitochondria; ISS:UniProtKB.
GO; GO:0006457; P:protein folding; IEA:InterPro.
GO; GO:0042981; P:regulation of apoptotic process; IDA:RGD.
GO; GO:0046902; P:regulation of mitochondrial membrane permeability; IDA:RGD.
GO; GO:1902445; P:regulation of mitochondrial membrane permeability involved in programmed necrotic cell death; ISS:UniProtKB.
GO; GO:0010939; P:regulation of necrotic cell death; IEA:Ensembl.
GO; GO:0010849; P:regulation of proton-transporting ATPase activity, rotational mechanism; ISS:UniProtKB.
GO; GO:0002931; P:response to ischemia; ISS:UniProtKB.
Gene3D; 2.40.100.10; -; 1.
InterPro; IPR029000; Cyclophilin-like_dom.
InterPro; IPR024936; Cyclophilin-type_PPIase.
InterPro; IPR020892; Cyclophilin-type_PPIase_CS.
InterPro; IPR002130; Cyclophilin-type_PPIase_dom.
PANTHER; PTHR11071; PTHR11071; 1.
Pfam; PF00160; Pro_isomerase; 1.
PIRSF; PIRSF001467; Peptidylpro_ismrse; 1.
PRINTS; PR00153; CSAPPISMRASE.
SUPFAM; SSF50891; SSF50891; 1.
PROSITE; PS00170; CSA_PPIASE_1; 1.
PROSITE; PS50072; CSA_PPIASE_2; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Apoptosis; Complete proteome;
Direct protein sequencing; Isomerase; Mitochondrion; Necrosis;
Reference proteome; Rotamase; S-nitrosylation; Transit peptide.
TRANSIT 1 29 Mitochondrion.
{ECO:0000269|PubMed:1599421}.
CHAIN 30 206 Peptidyl-prolyl cis-trans isomerase F,
mitochondrial.
/FTId=PRO_0000025491.
DOMAIN 48 204 PPIase cyclophilin-type.
{ECO:0000255|PROSITE-ProRule:PRU00156}.
MOD_RES 66 66 N6-acetyllysine; alternate.
{ECO:0000250|UniProtKB:Q99KR7}.
MOD_RES 66 66 N6-succinyllysine; alternate.
{ECO:0000250|UniProtKB:Q99KR7}.
MOD_RES 85 85 N6-succinyllysine.
{ECO:0000250|UniProtKB:Q99KR7}.
MOD_RES 166 166 N6-acetyllysine.
{ECO:0000250|UniProtKB:Q99KR7}.
MOD_RES 174 174 N6-succinyllysine.
{ECO:0000250|UniProtKB:Q99KR7}.
MOD_RES 189 189 N6-succinyllysine.
{ECO:0000250|UniProtKB:Q99KR7}.
MOD_RES 202 202 S-nitrosocysteine.
{ECO:0000250|UniProtKB:Q99KR7}.
VARIANT 30 39 Missing (in a minor form).
VARIANT 31 31 S -> R.
CONFLICT 30 30 C -> A (in Ref. 3; AA sequence).
{ECO:0000305}.
STRAND 46 53 {ECO:0000244|PDB:4TOT}.
STRAND 56 65 {ECO:0000244|PDB:4TOT}.
TURN 67 69 {ECO:0000244|PDB:4TOT}.
HELIX 71 82 {ECO:0000244|PDB:4TOT}.
TURN 83 85 {ECO:0000244|PDB:4TOT}.
STRAND 96 98 {ECO:0000244|PDB:4TOT}.
TURN 99 101 {ECO:0000244|PDB:4TOT}.
STRAND 102 105 {ECO:0000244|PDB:4TOT}.
STRAND 109 114 {ECO:0000244|PDB:4TOT}.
STRAND 119 122 {ECO:0000244|PDB:4TOT}.
STRAND 138 141 {ECO:0000244|PDB:4TOT}.
STRAND 143 145 {ECO:0000244|PDB:4TOT}.
STRAND 153 158 {ECO:0000244|PDB:4TOT}.
HELIX 161 163 {ECO:0000244|PDB:4TOT}.
TURN 164 166 {ECO:0000244|PDB:4TOT}.
STRAND 169 175 {ECO:0000244|PDB:4TOT}.
HELIX 177 185 {ECO:0000244|PDB:4TOT}.
STRAND 197 206 {ECO:0000244|PDB:4TOT}.
SEQUENCE 206 AA; 21810 MW; 69048482631B9FAD CRC64;
MLALRCGPRL LGLLSGPRSA PLLLSTTRTC SDGGARGANS SSQNPLVYLD VGADGQPLGR
VVLELKADVV PKTAENFRAL CTGEKGFGYK GSTFHRVIPA FMCQAGDFTN HNGTGGKSIY
GSRFPDENFT LKHVGPGVLS MANAGPNTNG SQFFICTIKT DWLDGKHVVF GHVKEGMDVV
KKIESFGSKS GKTSKKIVIT DCGQLS


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