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Protein

PAN2-PAN3 deadenylation complex catalytic subunit PAN2

Gene

PAN2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic 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. PAN cooperates with protein kinase DUN1 in the regulation of RAD5 mRNA levels and cell survival in response to replicational stress.UniRule annotation9 Publications

Miscellaneous

Present with 1510 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

Exonucleolytic cleavage of poly(A) to 5'-AMP.UniRule annotation2 Publications

Cofactori

a divalent metal cationUniRule annotation1 PublicationNote: Binds 2 metal cations per subunit in the catalytic exonuclease domain.UniRule annotation1 Publication

Enzyme regulationi

Positively regulated by the regulatory subunit PAN3. Negatively regulated by PAB1-binding protein PBP1. Inhibited under stress conditions. Inhibition of deadenylation under stress increases mRNA stability, which may be a mechanism to retain the majority of the cytoplasmic pool of mRNAs for later reuse and recovery from stress.UniRule annotation3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi660ZincCombined sources1 Publication1
Metal bindingi662Zinc; via pros nitrogenCombined sources1 Publication1
Metal bindingi713ZincCombined sources1 Publication1
Metal bindingi716ZincCombined sources1 Publication1
Metal bindingi910Divalent metal cation; catalyticUniRule annotationBy similarity1 Publication1
Metal bindingi912Divalent metal cation; catalyticUniRule annotationBy similarity1 Publication1
Metal bindingi1020Divalent metal cation; catalyticUniRule annotationBy similarity1
Metal bindingi1071Divalent metal cation; catalyticUniRule annotationBy similarity1 Publication1

GO - Molecular functioni

GO - Biological processi

  • mRNA processing Source: UniProtKB-KW
  • nuclear-transcribed mRNA poly(A) tail shortening Source: SGD
  • postreplication repair Source: SGD

Keywordsi

Molecular functionExonuclease, Hydrolase, Nuclease
Biological processmRNA processing
LigandMetal-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-30594-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
PAN2-PAN3 deadenylation complex catalytic subunit PAN2UniRule annotationCurated (EC:3.1.13.4UniRule annotation)
Alternative name(s):
PAB1P-dependent poly(A)-specific ribonucleaseUniRule annotation
Poly(A)-nuclease deadenylation complex subunit 2UniRule annotation
Short name:
PAN deadenylation complex subunit 2UniRule annotation
Gene namesi
Name:PAN2UniRule annotation
Ordered Locus Names:YGL094C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VII

Organism-specific databases

EuPathDBiFungiDB:YGL094C.
SGDiS000003062. PAN2.

Subcellular locationi

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi912E → A: Abolishes nuclease activity. 1 Publication1
Mutagenesisi1020D → A: Abolishes nuclease activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000582221 – 1115PAN2-PAN3 deadenylation complex catalytic subunit PAN2Add BLAST1115

Proteomic databases

MaxQBiP53010.
PRIDEiP53010.

PTM databases

iPTMnetiP53010.

Interactioni

Subunit structurei

Forms a heterotrimer with an asymmetric homodimer of the regulatory subunit PAN3 to form the poly(A)-nuclease (PAN) deadenylation complex.UniRule annotation4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PAN3P361029EBI-12887,EBI-12895

Protein-protein interaction databases

BioGridi33157. 119 interactors.
DIPiDIP-2466N.
IntActiP53010. 6 interactors.
MINTiMINT-637100.
STRINGi4932.YGL094C.

Structurei

Secondary structure

11115
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni460 – 465Combined sources6
Helixi477 – 479Combined sources3
Helixi488 – 490Combined sources3
Helixi497 – 499Combined sources3
Beta strandi502 – 504Combined sources3
Turni512 – 515Combined sources4
Helixi516 – 524Combined sources9
Helixi527 – 536Combined sources10
Helixi546 – 559Combined sources14
Beta strandi560 – 562Combined sources3
Helixi568 – 576Combined sources9
Helixi595 – 600Combined sources6
Turni603 – 605Combined sources3
Beta strandi610 – 613Combined sources4
Helixi618 – 636Combined sources19
Beta strandi637 – 639Combined sources3
Helixi643 – 648Combined sources6
Beta strandi650 – 657Combined sources8
Beta strandi659 – 661Combined sources3
Beta strandi666 – 675Combined sources10
Helixi696 – 703Combined sources8
Beta strandi704 – 712Combined sources9
Turni714 – 716Combined sources3
Beta strandi719 – 728Combined sources10
Beta strandi733 – 739Combined sources7
Helixi743 – 751Combined sources9
Beta strandi752 – 754Combined sources3
Beta strandi758 – 765Combined sources8
Beta strandi768 – 774Combined sources7
Helixi775 – 777Combined sources3
Beta strandi782 – 797Combined sources16
Beta strandi803 – 813Combined sources11
Turni814 – 817Combined sources4
Beta strandi818 – 825Combined sources8
Beta strandi828 – 832Combined sources5
Helixi834 – 838Combined sources5
Beta strandi845 – 854Combined sources10
Helixi857 – 859Combined sources3
Helixi865 – 867Combined sources3
Helixi873 – 876Combined sources4
Helixi897 – 899Combined sources3
Beta strandi906 – 915Combined sources10
Beta strandi937 – 946Combined sources10
Beta strandi948 – 950Combined sources3
Turni951 – 954Combined sources4
Beta strandi956 – 962Combined sources7
Helixi973 – 976Combined sources4
Beta strandi983 – 986Combined sources4
Turni988 – 990Combined sources3
Turni994 – 996Combined sources3
Helixi997 – 1008Combined sources12
Beta strandi1011 – 1013Combined sources3
Helixi1017 – 1024Combined sources8
Helixi1030 – 1032Combined sources3
Helixi1036 – 1039Combined sources4
Helixi1049 – 1056Combined sources8
Helixi1068 – 1087Combined sources20
Helixi1091 – 1105Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4Q8GX-ray2.10A/B416-870[»]
4Q8HX-ray3.10A460-1115[»]
4XR7X-ray3.80A/D/G/J340-1115[»]
ProteinModelPortaliP53010.
SMRiP53010.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati27 – 66WD 1UniRule annotationAdd BLAST40
Repeati112 – 153WD 2UniRule annotationAdd BLAST42
Repeati155 – 194WD 3UniRule annotationAdd BLAST40
Repeati197 – 236WD 4UniRule annotationAdd BLAST40
Repeati295 – 334WD 5UniRule annotationAdd BLAST40
Domaini474 – 855USPUniRule annotation1 PublicationAdd BLAST382
Domaini907 – 1079ExonucleaseUniRule annotationAdd BLAST173

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni337 – 473LinkerUniRule annotation1 PublicationAdd BLAST137

Domaini

Contains a pseudo-UCH domain. This ubiquitin C-terminal hydrolase (UCH)-like or ubiquitin specific protease (USP)-like domain is predicted to be catalytically inactive because it lacks the active site catalytic triad characteristic of thiol proteases, with residues at the equivalent structural positions that are incompatible with catalysis, and it cannot bind ubiquitin. It functions as a structural scaffold for intra- and intermolecular interactions in the complex.UniRule annotation1 Publication
The linker, or PAN3 interaction domain (PID), between the WD40 repeats and the pseudo-UCH domain mediates interaction with PAN3.UniRule annotation1 Publication

Sequence similaritiesi

Belongs to the peptidase C19 family. PAN2 subfamily.UniRule annotation

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

GeneTreeiENSGT00390000013978.
HOGENOMiHOG000230585.
InParanoidiP53010.
KOiK12571.
OMAiMVYDLRM.
OrthoDBiEOG092C0KHR.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
3.30.420.10. 1 hit.
HAMAPiMF_03182. PAN2. 1 hit.
InterProiView protein in InterPro
IPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR030843. PAN2.
IPR028881. PAN2_dom.
IPR011047. Quinoprotein_ADH-like_supfam.
IPR012337. RNaseH-like_sf.
IPR036397. RNaseH_sf.
IPR028889. USP_dom.
IPR015943. WD40/YVTN_repeat-like_dom.
PfamiView protein in Pfam
PF00929. RNase_T. 1 hit.
PF13423. UCH_1. 1 hit.
SMARTiView protein in SMART
SM00479. EXOIII. 1 hit.
SUPFAMiSSF50998. SSF50998. 2 hits.
SSF53098. SSF53098. 1 hit.
PROSITEiView protein in PROSITE
PS50235. USP_3. 1 hit.

Sequencei

Sequence statusi: Complete.

P53010-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNNWQHFFNN PVDLSEHLKK PYFRFDNRDK EITAISFDEK ANLIWSGDSY
60 70 80 90 100
GCISSYDPTF QLYTRYRGHI GGNSVKDILS HRDGILSISE DSLHFANRRG
110 120 130 140 150
VTKLNLTSID IAAFSELNTM CYSPHSLKNN IYCGGDNTNW GIASIDLNRG
160 170 180 190 200
CLDSLLNYSS KVKLMCSNNK VLSIGRQTGT VDLLDPTSNR TIKSFNAHSA
210 220 230 240 250
SISAMDLRDN TLVTVGKSKR FYNLYADPFV NVYDLRTMRQ LPPVSFSKGT
260 270 280 290 300
TMGSGGADFV QLHPLLPTVM IVASSSGSFD FIDLSNPTLR TQYVHPCQSI
310 320 330 340 350
KKLCLSPNGD VLGILEADNH LDTWRRSSNN MGMFTNTPEM LAYPDYFNDI
360 370 380 390 400
TSDGPISVDD ETYPLSSVGM PYYLDKLLSA WPPVVFKSEG TIPQLTGKSP
410 420 430 440 450
LPSSGKLKSN LAVISSQNEK LSTQEFPLLR YDRTKYGMRN AIPDYVCLRD
460 470 480 490 500
IRKQITSGLE TSDIQTYTSI NKYEVPPAYS RLPLTSGRFG TDNFDFTPFN
510 520 530 540 550
NTEYSGLDPD VDNHYTNAII QLYRFIPEMF NFVVGCLKDE NFETTLLTDL
560 570 580 590 600
GYLFDMMERS HGKICSSSNF QASLKSLTDK RQLENGEPQE HLEEYLESLC
610 620 630 640 650
IRESIEDFNS SESIKRNMPQ KFNRFLLSQL IKEEAQTVNH NITLNQCFGL
660 670 680 690 700
ETEIRTECSC DHYDTTVKLL PSLSISGINK TVIKQLNKKS NGQNILPYIE
710 720 730 740 750
YAMKNVTQKN SICPTCGKTE TITQECTVKN LPSVLSLELS LLDTEFSNIR
760 770 780 790 800
SSKNWLTSEF YGSIIKNKAV LRSTASELKG TSHIFKYELN GYVAKITDNN
810 820 830 840 850
NETRLVTYVK KYNPKENCFK WLMFNDYLVV EITEEEALKM TYPWKTPEII
860 870 880 890 900
IYCDAEELRK PFFSVDTYSI NYDILFRDYF ANGIRDTARR EYKLLTHDEA
910 920 930 940 950
PKSGTLVAID AEFVSLQSEL CEIDHQGIRS IIRPKRTALA RISIIRGEEG
960 970 980 990 1000
ELYGVPFVDD YVVNTNHIED YLTRYSGILP GDLDPEKSTK RLVRRNVVYR
1010 1020 1030 1040 1050
KVWLLMQLGC VFVGHGLNND FKHININVPR NQIRDTAIYF LQGKRYLSLR
1060 1070 1080 1090 1100
YLAYVLLGMN IQEGNHDSIE DAHTALILYK KYLHLKEKAI FEKVLNSVYE
1110
EGRAHNFKVP ETSKG
Length:1,115
Mass (Da):127,039
Last modified:October 1, 1996 - v1
Checksum:i4F91B737F761AE5A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U39204 Genomic DNA. Translation: AAC49152.1.
Z72616 Genomic DNA. Translation: CAA96800.1.
BK006941 Genomic DNA. Translation: DAA08012.1.
PIRiS64101.
RefSeqiNP_011421.1. NM_001180959.1.

Genome annotation databases

EnsemblFungiiYGL094C; YGL094C; YGL094C.
GeneIDi852786.
KEGGisce:YGL094C.

Similar proteinsi

Entry informationi

Entry nameiPAN2_YEAST
AccessioniPrimary (citable) accession number: P53010
Secondary accession number(s): D6VU51
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: October 25, 2017
This is version 161 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names