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Protein

PAB-dependent poly(A)-specific ribonuclease subunit PAN3

Gene

PAN3

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

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 when the poly(A) stretch is bound by poly(A)-binding protein PAB1, which 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 PAB1. PAN cooperates with protein kinase DUN1 in the regulation of RAD5 mRNA levels and cell survival in response to replicational stress.UniRule annotation5 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei325ATPUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri8 – 37C3H1-typeUniRule annotationAdd BLAST30
Nucleotide bindingi305 – 313ATPUniRule annotation9
Nucleotide bindingi376 – 381ATPUniRule annotation6

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • metal ion binding Source: UniProtKB-HAMAP
  • poly(A) RNA binding Source: SGD
  • protein kinase activity Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-31832-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
PAB-dependent poly(A)-specific ribonuclease subunit PAN3UniRule annotation
Alternative name(s):
PAB1P-dependent poly(A)-nucleaseUniRule annotation
PAN deadenylation complex subunit 3UniRule annotation
Gene namesi
Name:PAN3UniRule annotation
Synonyms:ECM35
Ordered Locus Names:YKL025C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XI

Organism-specific databases

EuPathDBiFungiDB:YKL025C.
SGDiS000001508. PAN3.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic mRNA processing body Source: GO_Central
  • PAN complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi156F → A: Significantly decreases interaction with PAN1. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000582231 – 679PAB-dependent poly(A)-specific ribonuclease subunit PAN3Add BLAST679

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei57PhosphothreonineCombined sources1
Modified residuei252PhosphoserineCombined sources1

Post-translational modificationi

Phosphorylated by the cyclin-CDK complex PCL1-PHO85.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP36102.
PRIDEiP36102.

PTM databases

iPTMnetiP36102.

Interactioni

Subunit structurei

Homodimer. Interacts with the 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.UniRule annotation4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PAB1P041475EBI-12895,EBI-12823
PAN2P530105EBI-12895,EBI-12887

Protein-protein interaction databases

BioGridi34106. 53 interactors.
DIPiDIP-3987N.
IntActiP36102. 8 interactors.
MINTiMINT-480456.

Structurei

Secondary structure

1679
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 9Combined sources4
Helixi15 – 19Combined sources5
Helixi24 – 27Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4CYKNMR-A1-41[»]
4XR7X-ray3.80B/C/E/F/H/I/K/L226-679[»]
ProteinModelPortaliP36102.
SMRiP36102.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini299 – 549Protein kinaseUniRule annotationAdd BLAST251

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni560 – 679Interaction with PAN2UniRule annotation1 PublicationAdd BLAST120

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi143 – 163PABPC-interacting motif-2 (PAM-2)1 PublicationAdd BLAST21

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi114 – 201Asn-richAdd BLAST88

Domaini

The protein kinase domain is predicted to be catalytically inactive. However it still binds ATP and ATP-binding is required for mRNA degradation.UniRule annotation

Sequence similaritiesi

Belongs to the protein kinase superfamily. PAN3 family.UniRule annotation
Contains 1 C3H1-type zinc finger.UniRule annotation
Contains 1 protein kinase domain.UniRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri8 – 37C3H1-typeUniRule annotationAdd BLAST30

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000001504.
HOGENOMiHOG000007619.
InParanoidiP36102.
KOiK12572.
OMAiHQKNATI.
OrthoDBiEOG092C1R5J.

Family and domain databases

HAMAPiMF_03181. PAN3. 1 hit.
InterProiIPR011009. Kinase-like_dom.
IPR030844. PAN3.
IPR000719. Prot_kinase_dom.
IPR000571. Znf_CCCH.
[Graphical view]
SUPFAMiSSF56112. SSF56112. 1 hit.
PROSITEiPS50011. PROTEIN_KINASE_DOM. 1 hit.
PS50103. ZF_C3H1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P36102-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDKINPDWAK DIPCRNITIY GYCKKEKEGC PFKHSDNTTA TTINDVPPPI
60 70 80 90 100
DVGEATTPTM TSVPKFNAKV SASFTPMTVG SDSLTTVTNT TSAATNATGN
110 120 130 140 150
IAMAATSATA STVNPMINPI VNSSLVNNNN NNSNISISIP TTASSSNYDP
160 170 180 190 200
FNAPIFTPSS TSSIHTNANA HSFPFPSIAN SGGININATD DNSNNMSMAN
210 220 230 240 250
NVPPPMQPPP IESSNLKYPR IYPPPHSLLQ YHLYAPEQPS SLKSLLKPNE
260 270 280 290 300
RSADQLFIPN NIREDLTKKN LSILQVFPSS GKVIPSIVQD YFNLVPLNFN
310 320 330 340 350
NNDFLNKTTL FKVFSNYDGK AYVLKRLPNI DKSMNPNKIS KIYQIWSKIN
360 370 380 390 400
CTNLIKFRDI FQTTKFGDLS ICLVFDYYPN SLSLYDYHFV NFPKFPITNN
410 420 430 440 450
YLWIYLVQLT NVINSIHSQN LSIGNTLNWR KVLITGDPGR IKLSHCNFMD
460 470 480 490 500
LLFNDDTDTV VSSGGSTIEG QQQLDYKYLG ELLFNLSINI ENSNNNTAPK
510 520 530 540 550
EYRLEEITPQ SIDDMRQIDD KFKDVLKYLI SDNGDSKKSI HDLTSHFYDK
560 570 580 590 600
MFMVLESSQT YTEYMESVLS RELENGRLFR LVNKLNCIFG RIESRIDINW
610 620 630 640 650
SESGTKFPII LFYDYVFHQV DSNGKPIMDL THVLRCLNKL DAGIQEKLML
660 670
VTPDELNCII ISYKELKDLI ESTFRSITQ
Length:679
Mass (Da):76,455
Last modified:June 1, 1994 - v1
Checksum:iDE03E15BF4A5DA7C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z28025 Genomic DNA. Translation: CAA81860.1.
BK006944 Genomic DNA. Translation: DAA09129.1.
PIRiS37842.
RefSeqiNP_012900.1. NM_001179591.1.

Genome annotation databases

EnsemblFungiiYKL025C; YKL025C; YKL025C.
GeneIDi853843.
KEGGisce:YKL025C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z28025 Genomic DNA. Translation: CAA81860.1.
BK006944 Genomic DNA. Translation: DAA09129.1.
PIRiS37842.
RefSeqiNP_012900.1. NM_001179591.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4CYKNMR-A1-41[»]
4XR7X-ray3.80B/C/E/F/H/I/K/L226-679[»]
ProteinModelPortaliP36102.
SMRiP36102.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34106. 53 interactors.
DIPiDIP-3987N.
IntActiP36102. 8 interactors.
MINTiMINT-480456.

PTM databases

iPTMnetiP36102.

Proteomic databases

MaxQBiP36102.
PRIDEiP36102.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYKL025C; YKL025C; YKL025C.
GeneIDi853843.
KEGGisce:YKL025C.

Organism-specific databases

EuPathDBiFungiDB:YKL025C.
SGDiS000001508. PAN3.

Phylogenomic databases

GeneTreeiENSGT00390000001504.
HOGENOMiHOG000007619.
InParanoidiP36102.
KOiK12572.
OMAiHQKNATI.
OrthoDBiEOG092C1R5J.

Enzyme and pathway databases

BioCyciYEAST:G3O-31832-MONOMER.

Miscellaneous databases

PROiP36102.

Family and domain databases

HAMAPiMF_03181. PAN3. 1 hit.
InterProiIPR011009. Kinase-like_dom.
IPR030844. PAN3.
IPR000719. Prot_kinase_dom.
IPR000571. Znf_CCCH.
[Graphical view]
SUPFAMiSSF56112. SSF56112. 1 hit.
PROSITEiPS50011. PROTEIN_KINASE_DOM. 1 hit.
PS50103. ZF_C3H1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPAN3_YEAST
AccessioniPrimary (citable) accession number: P36102
Secondary accession number(s): D6VXQ9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: November 2, 2016
This is version 147 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1600 molecules/cell in log phase SD medium.1 Publication

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. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XI
    Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.