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PAN2-PAN3 deadenylation complex subunit PAN3 (PAB1P-dependent poly(A)-specific ribonuclease) (Poly(A)-nuclease deadenylation complex subunit 3) (PAN deadenylation complex subunit 3)

 PAN3_YEAST              Reviewed;         679 AA.
P36102; D6VXQ9;
01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
01-JUN-1994, sequence version 1.
20-JUN-2018, entry version 159.
RecName: Full=PAN2-PAN3 deadenylation complex subunit PAN3 {ECO:0000255|HAMAP-Rule:MF_03181, ECO:0000305};
AltName: Full=PAB1P-dependent poly(A)-specific ribonuclease {ECO:0000255|HAMAP-Rule:MF_03181};
AltName: Full=Poly(A)-nuclease deadenylation complex subunit 3 {ECO:0000255|HAMAP-Rule:MF_03181};
Short=PAN deadenylation complex subunit 3 {ECO:0000255|HAMAP-Rule:MF_03181};
Name=PAN3 {ECO:0000255|HAMAP-Rule:MF_03181}; Synonyms=ECM35;
OrderedLocusNames=YKL025C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 443-453 AND
517-524, FUNCTION, AND INTERACTION WITH PAN2.
PubMed=8816488; DOI=10.1128/MCB.16.10.5744;
Brown C.E., Tarun S.Z. Jr., Boeck R., Sachs A.B.;
"PAN3 encodes a subunit of the Pab1p-dependent poly(A) nuclease in
Saccharomyces cerevisiae.";
Mol. Cell. Biol. 16:5744-5753(1996).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8196765; DOI=10.1038/369371a0;
Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V.,
Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M.,
Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L.,
Daignan-Fornier B., del Rey F., Dion C., Domdey H., Duesterhoeft A.,
Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H.,
Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L.,
Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M.,
Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H.,
Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J.,
Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H.,
Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J.,
Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S.,
Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F.,
Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R.,
Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W.,
Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M.,
Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C.,
Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H.,
Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L.,
van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C.,
Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G.,
Zimmermann J., Haasemann M., Becker I., Mewes H.-W.;
"Complete DNA sequence of yeast chromosome XI.";
Nature 369:371-378(1994).
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
FUNCTION.
PubMed=1358757; DOI=10.1101/gad.6.11.2088;
Lowell J.E., Rudner D.Z., Sachs A.B.;
"3'-UTR-dependent deadenylation by the yeast poly(A) nuclease.";
Genes Dev. 6:2088-2099(1992).
[5]
FUNCTION.
PubMed=9774670; DOI=10.1128/MCB.18.11.6548;
Brown C.E., Sachs A.B.;
"Poly(A) tail length control in Saccharomyces cerevisiae occurs by
message-specific deadenylation.";
Mol. Cell. Biol. 18:6548-6559(1998).
[6]
FUNCTION, AND INTERACTION WITH DUN1.
PubMed=11953437; DOI=10.1074/jbc.M202473200;
Hammet A., Pike B.L., Heierhorst J.;
"Posttranscriptional regulation of the RAD5 DNA repair gene by the
Dun1 kinase and the Pan2-Pan3 poly(A)-nuclease complex contributes to
survival of replication blocks.";
J. Biol. Chem. 277:22469-22474(2002).
[7]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[8]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[9]
INTERACTION WITH PAN2 AND PAB1.
PubMed=15169912; DOI=10.1128/MCB.24.12.5521-5533.2004;
Mangus D.A., Evans M.C., Agrin N.S., Smith M.M., Gongidi P.,
Jacobson A.;
"Positive and negative regulation of poly(A) nuclease.";
Mol. Cell. Biol. 24:5521-5533(2004).
[10]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=15894541; DOI=10.1074/jbc.M504720200;
Dheur S., Nykamp K.R., Viphakone N., Swanson M.S.,
Minvielle-Sebastia L.;
"Yeast mRNA poly(A) tail length control can be reconstituted in vitro
in the absence of Pab1p-dependent poly(A) nuclease activity.";
J. Biol. Chem. 280:24532-24538(2005).
[11]
PHOSPHORYLATION BY PCL1-PHO85.
PubMed=16330754; DOI=10.1073/pnas.0509080102;
Dephoure N., Howson R.W., Blethrow J.D., Shokat K.M., O'Shea E.K.;
"Combining chemical genetics and proteomics to identify protein kinase
substrates.";
Proc. Natl. Acad. Sci. U.S.A. 102:17940-17945(2005).
[12]
INTERACTION WITH PAB1, AND MUTAGENESIS OF PHE-156.
PubMed=17595167; DOI=10.1074/jbc.M701256200;
Siddiqui N., Mangus D.A., Chang T.C., Palermino J.M., Shyu A.B.,
Gehring K.;
"Poly(A) nuclease interacts with the C-terminal domain of
polyadenylate-binding protein domain from poly(A)-binding protein.";
J. Biol. Chem. 282:25067-25075(2007).
[13]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-57 AND SER-252, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[14]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
[15]
STRUCTURE BY NMR OF 1-41, FUNCTION, AND RNA-BINDING.
PubMed=24872509; DOI=10.15252/embj.201488373;
Wolf J., Valkov E., Allen M.D., Meineke B., Gordiyenko Y.,
McLaughlin S.H., Olsen T.M., Robinson C.V., Bycroft M., Stewart M.,
Passmore L.A.;
"Structural basis for Pan3 binding to Pan2 and its function in mRNA
recruitment and deadenylation.";
EMBO J. 33:1514-1526(2014).
[16]
X-RAY CRYSTALLOGRAPHY (3.80 ANGSTROMS) OF 226-679.
PubMed=24880344; DOI=10.1038/nsmb.2834;
Schaefer I.B., Rode M., Bonneau F., Schuessler S., Conti E.;
"The structure of the Pan2-Pan3 core complex reveals cross-talk
between deadenylase and pseudokinase.";
Nat. Struct. Mol. Biol. 21:591-598(2014).
-!- FUNCTION: Regulatory subunit of the poly(A)-nuclease (PAN)
deadenylation complex, one of two cytoplasmic mRNA deadenylases
involved in mRNA turnover. PAN specifically shortens poly(A) tails
of RNA and the activity is stimulated by poly(A)-binding protein
PAB1. PAN deadenylation is followed by rapid degradation of the
shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs
are then degraded by two alternative mechanisms, namely exosome-
mediated 3'-5' exonucleolytic degradation, or deadenlyation-
dependent mRNA decaping by DCP1-DCP2 and subsequent 5'-3'
exonucleolytic degradation by XRN1. May also be involved in post-
transcriptional maturation of mRNA poly(A) tails, trimming the
tails from their synthesized length to the slightly shorter,
apparently messenger-specific length found on newly exported
mRNAs. PAN3 acts as a positive regulator for PAN activity,
recruiting the catalytic subunit PAN2 to mRNA via its interaction
with RNA and with PAB1. PAN cooperates with protein kinase DUN1 in
the regulation of RAD5 mRNA levels and cell survival in response
to replicational stress. {ECO:0000255|HAMAP-Rule:MF_03181,
ECO:0000269|PubMed:11953437, ECO:0000269|PubMed:1358757,
ECO:0000269|PubMed:15894541, ECO:0000269|PubMed:24880344,
ECO:0000269|PubMed:8816488, ECO:0000269|PubMed:9774670}.
-!- SUBUNIT: Homodimer. Forms a heterotrimer with a catalytic subunit
PAN2 to form the poly(A)-nuclease (PAN) deadenylation complex.
Interacts (via PAM-2 motif) with poly(A)-binding protein PAB1 (via
PABC domain), conferring substrate specificity of the enzyme
complex. {ECO:0000255|HAMAP-Rule:MF_03181,
ECO:0000269|PubMed:11953437, ECO:0000269|PubMed:15169912,
ECO:0000269|PubMed:17595167, ECO:0000269|PubMed:8816488}.
-!- INTERACTION:
P04147:PAB1; NbExp=5; IntAct=EBI-12895, EBI-12823;
P53010:PAN2; NbExp=9; IntAct=EBI-12895, EBI-12887;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_03181,
ECO:0000269|PubMed:14562095, ECO:0000269|PubMed:15894541}.
-!- DOMAIN: The N-terminal zinc finger binds to poly(A) RNA.
{ECO:0000255|HAMAP-Rule:MF_03181, ECO:0000269|PubMed:24872509}.
-!- DOMAIN: Contains a pseudokinase domain. The protein kinase domain
is predicted to be catalytically inactive because some of the
residues important for catalytic activity are substituted and it
lacks the equivalent of the binding site for a peptide substrate
(PubMed:24880344). However, it has retained an ATP-binding site
and ATP-binding is required for mRNA degradation, stimulating the
activity of the PAN2 nuclease in vitro. The nucleotide-binding
site is juxtaposed to the RNase active site of PAN2 in the complex
and may actually bind nucleosides of a poly(A) RNA rather than
ATP, feeding the poly(A)-tail to the active site of the
deadenylase and thus increasing the efficiency with which this
distributive enzyme degrades oligo(A) RNAs (By similarity).
{ECO:0000250|UniProtKB:Q7SDP4, ECO:0000255|HAMAP-Rule:MF_03181,
ECO:0000269|PubMed:24880344}.
-!- DOMAIN: The pseudokinase domain, the coiled-coil (CC), and C-
terminal knob domain (CK) form a structural unit (PKC) that forms
an extensive high-affinity interaction surface for PAN2.
{ECO:0000255|HAMAP-Rule:MF_03181}.
-!- PTM: Phosphorylated by the cyclin-CDK complex PCL1-PHO85.
{ECO:0000269|PubMed:16330754}.
-!- MISCELLANEOUS: Present with 1600 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the protein kinase superfamily. PAN3
family. {ECO:0000255|HAMAP-Rule:MF_03181}.
-----------------------------------------------------------------------
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EMBL; Z28025; CAA81860.1; -; Genomic_DNA.
EMBL; BK006944; DAA09129.1; -; Genomic_DNA.
PIR; S37842; S37842.
RefSeq; NP_012900.1; NM_001179591.1.
PDB; 4CYK; NMR; -; A=1-41.
PDB; 4XR7; X-ray; 3.80 A; B/C/E/F/H/I/K/L=226-679.
PDBsum; 4CYK; -.
PDBsum; 4XR7; -.
ProteinModelPortal; P36102; -.
SMR; P36102; -.
BioGrid; 34106; 138.
ComplexPortal; CPX-3294; PAN complex.
DIP; DIP-3987N; -.
IntAct; P36102; 8.
MINT; P36102; -.
STRING; 4932.YKL025C; -.
iPTMnet; P36102; -.
MaxQB; P36102; -.
PaxDb; P36102; -.
PRIDE; P36102; -.
EnsemblFungi; YKL025C; YKL025C; YKL025C.
GeneID; 853843; -.
KEGG; sce:YKL025C; -.
EuPathDB; FungiDB:YKL025C; -.
SGD; S000001508; PAN3.
GeneTree; ENSGT00390000001504; -.
HOGENOM; HOG000007619; -.
InParanoid; P36102; -.
KO; K12572; -.
OMA; DSYFTKR; -.
OrthoDB; EOG092C1R5J; -.
BioCyc; YEAST:G3O-31832-MONOMER; -.
PRO; PR:P36102; -.
Proteomes; UP000002311; Chromosome XI.
GO; GO:0000932; C:P-body; IBA:GO_Central.
GO; GO:0031251; C:PAN complex; IDA:SGD.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0008143; F:poly(A) binding; IDA:SGD.
GO; GO:0004672; F:protein kinase activity; IEA:InterPro.
GO; GO:0003723; F:RNA binding; IDA:SGD.
GO; GO:0000290; P:deadenylation-dependent decapping of nuclear-transcribed mRNA; IBA:GO_Central.
GO; GO:0006281; P:DNA repair; IDA:SGD.
GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
GO; GO:0000289; P:nuclear-transcribed mRNA poly(A) tail shortening; IDA:SGD.
GO; GO:0010606; P:positive regulation of cytoplasmic mRNA processing body assembly; IBA:GO_Central.
GO; GO:0006301; P:postreplication repair; IGI:SGD.
GO; GO:0090503; P:RNA phosphodiester bond hydrolysis, exonucleolytic; IEA:GOC.
HAMAP; MF_03181; PAN3; 1.
InterPro; IPR011009; Kinase-like_dom_sf.
InterPro; IPR030844; PAN3.
InterPro; IPR000719; Prot_kinase_dom.
InterPro; IPR000571; Znf_CCCH.
SUPFAM; SSF56112; SSF56112; 1.
PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
PROSITE; PS50103; ZF_C3H1; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Coiled coil; Complete proteome; Cytoplasm;
Direct protein sequencing; Metal-binding; mRNA processing;
Nucleotide-binding; Phosphoprotein; Reference proteome; Zinc;
Zinc-finger.
CHAIN 1 679 PAN2-PAN3 deadenylation complex subunit
PAN3.
/FTId=PRO_0000058223.
ZN_FING 8 37 C3H1-type. {ECO:0000255|HAMAP-
Rule:MF_03181}.
NP_BIND 376 383 ATP. {ECO:0000255|HAMAP-Rule:MF_03181}.
NP_BIND 430 431 ATP. {ECO:0000255|HAMAP-Rule:MF_03181}.
REGION 275 548 Pseudokinase domain. {ECO:0000255|HAMAP-
Rule:MF_03181,
ECO:0000305|PubMed:24880344}.
REGION 588 679 Knob domain. {ECO:0000255|HAMAP-
Rule:MF_03181,
ECO:0000305|PubMed:24880344}.
COILED 549 587 {ECO:0000255|HAMAP-Rule:MF_03181,
ECO:0000305|PubMed:24880344}.
MOTIF 143 163 PABPC-interacting motif-2 (PAM-2).
{ECO:0000269|PubMed:17595167}.
BINDING 325 325 ATP. {ECO:0000255|HAMAP-Rule:MF_03181}.
MOD_RES 57 57 Phosphothreonine.
{ECO:0000244|PubMed:18407956}.
MOD_RES 252 252 Phosphoserine.
{ECO:0000244|PubMed:18407956}.
MUTAGEN 156 156 F->A: Significantly decreases interaction
with PAN1. {ECO:0000269|PubMed:17595167}.
HELIX 6 9 {ECO:0000244|PDB:4CYK}.
HELIX 15 19 {ECO:0000244|PDB:4CYK}.
HELIX 24 27 {ECO:0000244|PDB:4CYK}.
SEQUENCE 679 AA; 76455 MW; DE03E15BF4A5DA7C CRC64;
MDKINPDWAK DIPCRNITIY GYCKKEKEGC PFKHSDNTTA TTINDVPPPI DVGEATTPTM
TSVPKFNAKV SASFTPMTVG SDSLTTVTNT TSAATNATGN IAMAATSATA STVNPMINPI
VNSSLVNNNN NNSNISISIP TTASSSNYDP FNAPIFTPSS TSSIHTNANA HSFPFPSIAN
SGGININATD DNSNNMSMAN NVPPPMQPPP IESSNLKYPR IYPPPHSLLQ YHLYAPEQPS
SLKSLLKPNE RSADQLFIPN NIREDLTKKN LSILQVFPSS GKVIPSIVQD YFNLVPLNFN
NNDFLNKTTL FKVFSNYDGK AYVLKRLPNI DKSMNPNKIS KIYQIWSKIN CTNLIKFRDI
FQTTKFGDLS ICLVFDYYPN SLSLYDYHFV NFPKFPITNN YLWIYLVQLT NVINSIHSQN
LSIGNTLNWR KVLITGDPGR IKLSHCNFMD LLFNDDTDTV VSSGGSTIEG QQQLDYKYLG
ELLFNLSINI ENSNNNTAPK EYRLEEITPQ SIDDMRQIDD KFKDVLKYLI SDNGDSKKSI
HDLTSHFYDK MFMVLESSQT YTEYMESVLS RELENGRLFR LVNKLNCIFG RIESRIDINW
SESGTKFPII LFYDYVFHQV DSNGKPIMDL THVLRCLNKL DAGIQEKLML VTPDELNCII
ISYKELKDLI ESTFRSITQ


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