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Protein

Protein PAT1 homolog 1

Gene

PATL1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

RNA-binding protein involved in deadenylation-dependent decapping of mRNAs, leading to the degradation of mRNAs. Acts as a scaffold protein that connects deadenylation and decapping machinery. Required for cytoplasmic mRNA processing body (P-body) assembly. In case of infection, required for translation and replication of hepatitis C virus (HCV).5 Publications

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB
  • poly(G) binding Source: MGI
  • poly(U) RNA binding Source: MGI
  • RNA binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-430039. mRNA decay by 5' to 3' exoribonuclease.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein PAT1 homolog 1
Alternative name(s):
PAT1-like protein 1
Protein PAT1 homolog b
Short name:
Pat1b
Short name:
hPat1b
Gene namesi
Name:PATL1
ORF Names:OK/KNS-cl.5
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

HGNCiHGNC:26721. PATL1.

Subcellular locationi

  • CytoplasmP-body
  • Nucleus
  • NucleusPML body
  • Nucleus speckle

  • Note: Predominantly cytoplasmic. Shuttles between the nucleus and the cytoplasm in a CRM1-dependent manner. Enriched in splicing speckles. Localization to nuclear foci and speckles requires active transcription. Excluded from the nucleolus.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi86L → A: Loss of nuclear export; when associated with A-90, A-93 and A-95. 1 Publication1
Mutagenesisi90L → A: Loss of nuclear export; when associated with A-86, A-93 and A-95. 1 Publication1
Mutagenesisi93M → A: Loss of nuclear export; when associated with A-86, A-90 and A-95. 1 Publication1
Mutagenesisi95I → A: Loss of nuclear export; when associated with A-86, A-90 and A-93. 1 Publication1
Mutagenesisi519R → A in mut1; Abolishes RNA-binding, localization to P-body and interaction with the decapping machinery; when associated with A-520; A-591; A-595; A-625 and A-626. 1 Publication1
Mutagenesisi520R → A in mut1; Abolishes RNA-binding, localization to P-body and interaction with the decapping machinery; when associated with A-519; A-591; A-595; A-625 and A-626. 1 Publication1
Mutagenesisi523L → A in mut2; Abolishes interaction with the decapping machinery and localization to P-body; when associated with A-527; A-530 and S-534. 1 Publication1
Mutagenesisi527E → A in mut2; Abolishes interaction with the decapping machinery and localization to P-body; when associated with S-523; A-530 and S-534. 1 Publication1
Mutagenesisi530Y → A in mut2; Abolishes interaction with the decapping machinery and localization to P-body; when associated with S-523; A-527 and S-534. 1 Publication1
Mutagenesisi534L → S in mut2; Abolishes interaction with the decapping machinery and localization to P-body; when associated with S-523; A-527 and A-530. 1 Publication1
Mutagenesisi539 – 557YERRY…ALMDD → GSGSGSG in mut3; does not affect neither RNA-binding,interaction with the decapping machinery, nor localization to P-body. 1 PublicationAdd BLAST19
Mutagenesisi591R → A in mut1; Abolishes RNA-binding, localization to P-body and interaction with the decapping machinery; when associated with A-519; A-520; A-595; A-625 and A-626. 1 Publication1
Mutagenesisi595R → A in mut1; Abolishes RNA-binding, localization to P-body and interaction with the decapping machinery; when associated with A-519; A-520; A-591; A-625 and A-626. 1 Publication1
Mutagenesisi625K → A in mut1; Abolishes RNA-binding, localization to P-body and interaction with the decapping machinery; when associated with A-519; A-520; A-591; A-595 and A-626. 1 Publication1
Mutagenesisi626K → A in mut1; Abolishes RNA-binding, localization to P-body and interaction with the decapping machinery; when associated with A-519; A-520; A-591; A-595 and A-625. 1 Publication1

Organism-specific databases

OpenTargetsiENSG00000166889.
PharmGKBiPA162398769.

Polymorphism and mutation databases

BioMutaiPATL1.
DMDMi182705251.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003209631 – 770Protein PAT1 homolog 1Add BLAST770

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei177PhosphoserineCombined sources1
Modified residuei178PhosphothreonineBy similarity1
Modified residuei179PhosphoserineCombined sources1
Modified residuei184PhosphoserineCombined sources1
Modified residuei194PhosphothreonineCombined sources1
Modified residuei217Asymmetric dimethylarginineCombined sources1
Modified residuei223Asymmetric dimethylarginineCombined sources1
Modified residuei263Asymmetric dimethylarginineCombined sources1
Modified residuei278PhosphoserineCombined sources1
Modified residuei284Asymmetric dimethylarginineBy similarity1
Modified residuei385Omega-N-methylarginineBy similarity1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

EPDiQ86TB9.
MaxQBiQ86TB9.
PaxDbiQ86TB9.
PeptideAtlasiQ86TB9.
PRIDEiQ86TB9.

PTM databases

iPTMnetiQ86TB9.
PhosphoSitePlusiQ86TB9.

Expressioni

Tissue specificityi

Ubiquitous.1 Publication

Gene expression databases

BgeeiENSG00000166889.
CleanExiHS_PATL1.
GenevisibleiQ86TB9. HS.

Organism-specific databases

HPAiHPA039030.

Interactioni

Subunit structurei

Interacts (via region A) with DDX6/RCK. Interacts (via region H and region C) with LSM1 and LSM4. Interacts (via region N) with DCP1A, DCP2, EDC3, EDC4 and XRN1. Interacts with the CCR4-NOT complex. Interacts with the Lsm-containing SMN-Sm protein complex.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
FHL3Q136435EBI-2562092,EBI-741101
GOLGA2Q083793EBI-2562092,EBI-618309
PSMA3P257883EBI-2562092,EBI-348380

Protein-protein interaction databases

BioGridi128613. 29 interactors.
IntActiQ86TB9. 10 interactors.
MINTiMINT-4717253.
STRINGi9606.ENSP00000300146.

Structurei

Secondary structure

1770
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi518 – 544Combined sources27
Helixi548 – 550Combined sources3
Helixi551 – 570Combined sources20
Beta strandi574 – 576Combined sources3
Helixi582 – 588Combined sources7
Helixi591 – 600Combined sources10
Helixi601 – 603Combined sources3
Helixi606 – 618Combined sources13
Helixi620 – 626Combined sources7
Turni627 – 630Combined sources4
Helixi633 – 636Combined sources4
Helixi637 – 644Combined sources8
Helixi649 – 659Combined sources11
Turni663 – 665Combined sources3
Helixi677 – 680Combined sources4
Helixi683 – 700Combined sources18
Helixi712 – 727Combined sources16
Helixi730 – 732Combined sources3
Helixi743 – 750Combined sources8
Helixi753 – 762Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XEQX-ray3.10A/B/C/D517-767[»]
2XERX-ray2.95A/B/C517-767[»]
2XESX-ray2.10A/B517-767[»]
ProteinModelPortaliQ86TB9.
SMRiQ86TB9.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ86TB9.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 397Involved in nuclear foci localizationAdd BLAST397
Regioni1 – 84Region A; interaction with DDX6/RCKAdd BLAST84
Regioni85 – 388Region N; interaction with decapping machineryAdd BLAST304
Regioni223 – 397Involved in RNA-bindingAdd BLAST175
Regioni389 – 448Region HAdd BLAST60
Regioni398 – 770Involved in nuclear spleckles localizationAdd BLAST373
Regioni449 – 770Region CAdd BLAST322

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi86 – 95Nuclear export signal10

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi155 – 338Pro-richAdd BLAST184

Domaini

The region A, also named N-term, mediates the interaction with DDX6/RCK and is required for cytoplasmic mRNA processing body assembly.
The region C, also named Pat-C, is required for RNA-binding and mediates the binding with the Lsm-containing SMN-Sm protein complex and the decapping machinery. It folds into an alpha-alpha superhelix, exposing conserved and basic residues on one side of the domain.

Sequence similaritiesi

Belongs to the PAT1 family.Curated

Phylogenomic databases

eggNOGiKOG4592. Eukaryota.
ENOG4110Q9I. LUCA.
GeneTreeiENSGT00520000055649.
HOGENOMiHOG000115461.
HOVERGENiHBG104422.
InParanoidiQ86TB9.
KOiK12617.
OMAiYTVEKMY.
OrthoDBiEOG091G0MYC.
PhylomeDBiQ86TB9.
TreeFamiTF323322.

Family and domain databases

InterProiIPR019167. Topo_II-assoc_PAT1.
[Graphical view]
PfamiPF09770. PAT1. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q86TB9-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MFRYESLEDC PLDEDEDAFQ GLGEEDEEID QFNDDTFGSG AVDDDWQEAH
60 70 80 90 100
ERLAELEEKL PVAVNEQTGN GERDEMDLLG DHEENLAERL SKMVIENELE
110 120 130 140 150
DPAIMRAVQT RPVLQPQPGS LNSSIWDGSE VLRRIRGPLL AQEMPTVSVL
160 170 180 190 200
EYALPQRPPQ GPEDDRDLSE RALPRRSTSP IIGSPPVRAV PIGTPPKQMA
210 220 230 240 250
VPSFTQQILC PKPVHVRPPM PPRYPAPYGE RMSPNQLCSV PNSSLLGHPF
260 270 280 290 300
PPSVPPVLSP LQRAQLLGGA QLQPGRMSPS QFARVPGFVG SPLAAMNPKL
310 320 330 340 350
LQGRVGQMLP PAPGFRAFFS APPSATPPPQ QHPPGPGPHL QNLRSQAPMF
360 370 380 390 400
RPDTTHLHPQ HRRLLHQRQQ QNRSQHRNLN GAGDRGSHRS SHQDHLRKDP
410 420 430 440 450
YANLMLQREK DWVSKIQMMQ LQSTDPYLDD FYYQNYFEKL EKLSAAEEIQ
460 470 480 490 500
GDGPKKERTK LITPQVAKLE HAYKPVQFEG SLGKLTVSSV NNPRKMIDAV
510 520 530 540 550
VTSRSEDDET KEKQVRDKRR KTLVIIEKTY SLLLDVEDYE RRYLLSLEEE
560 570 580 590 600
RPALMDDRKH KICSMYDNLR GKLPGQERPS DDHFVQIMCI RKGKRMVARI
610 620 630 640 650
LPFLSTEQAA DILMTTARNL PFLIKKDAQD EVLPCLLSPF SLLLYHLPSV
660 670 680 690 700
SITSLLRQLM NLPQSAATPA LSNPHLTAVL QNKFGLSLLL ILLSRGEDLQ
710 720 730 740 750
SSDPATESTQ NNQWTEVMFM ATRELLRIPQ AALAKPISIP TNLVSLFSRY
760 770
VDRQKLNLLE TKLQLVQGIR
Length:770
Mass (Da):86,850
Last modified:February 26, 2008 - v2
Checksum:i65F7038C4AAC356B
GO
Isoform 2 (identifier: Q86TB9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-143: Missing.

Show »
Length:627
Mass (Da):70,639
Checksum:iDF1CAE822EF7C076
GO
Isoform 3 (identifier: Q86TB9-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-659: Missing.

Show »
Length:111
Mass (Da):12,340
Checksum:i46794530E9E99090
GO
Isoform 4 (identifier: Q86TB9-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     242-271: Missing.
     662-698: Missing.

Note: No experimental confirmation available.
Show »
Length:703
Mass (Da):79,908
Checksum:iA4FEE89882057391
GO

Sequence cautioni

The sequence CAD89916 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti160Q → H in BAG54601 (PubMed:14702039).Curated1
Sequence conflicti735K → R in BAC04305 (PubMed:14702039).Curated1
Sequence conflicti735K → R in CAD89916 (PubMed:17974005).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0317771 – 659Missing in isoform 3. 1 PublicationAdd BLAST659
Alternative sequenceiVSP_0317781 – 143Missing in isoform 2. 2 PublicationsAdd BLAST143
Alternative sequenceiVSP_040576242 – 271Missing in isoform 4. 1 PublicationAdd BLAST30
Alternative sequenceiVSP_040577662 – 698Missing in isoform 4. 1 PublicationAdd BLAST37

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB065087 mRNA. Translation: BAB93524.1.
AK094193 mRNA. Translation: BAC04305.1.
AK127943 mRNA. Translation: BAG54601.1.
AL831992 mRNA. Translation: CAD89916.1. Different initiation.
AP000442 Genomic DNA. No translation available.
AP000640 Genomic DNA. No translation available.
BC065264 mRNA. Translation: AAH65264.2.
BC109038 mRNA. Translation: AAI09039.1.
BC109039 mRNA. Translation: AAI09040.1.
BC111047 mRNA. Translation: AAI11048.1.
CCDSiCCDS44613.1. [Q86TB9-1]
RefSeqiNP_689929.2. NM_152716.2. [Q86TB9-1]
UniGeneiHs.591960.

Genome annotation databases

EnsembliENST00000300146; ENSP00000300146; ENSG00000166889. [Q86TB9-1]
GeneIDi219988.
KEGGihsa:219988.
UCSCiuc001noe.6. human. [Q86TB9-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB065087 mRNA. Translation: BAB93524.1.
AK094193 mRNA. Translation: BAC04305.1.
AK127943 mRNA. Translation: BAG54601.1.
AL831992 mRNA. Translation: CAD89916.1. Different initiation.
AP000442 Genomic DNA. No translation available.
AP000640 Genomic DNA. No translation available.
BC065264 mRNA. Translation: AAH65264.2.
BC109038 mRNA. Translation: AAI09039.1.
BC109039 mRNA. Translation: AAI09040.1.
BC111047 mRNA. Translation: AAI11048.1.
CCDSiCCDS44613.1. [Q86TB9-1]
RefSeqiNP_689929.2. NM_152716.2. [Q86TB9-1]
UniGeneiHs.591960.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XEQX-ray3.10A/B/C/D517-767[»]
2XERX-ray2.95A/B/C517-767[»]
2XESX-ray2.10A/B517-767[»]
ProteinModelPortaliQ86TB9.
SMRiQ86TB9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi128613. 29 interactors.
IntActiQ86TB9. 10 interactors.
MINTiMINT-4717253.
STRINGi9606.ENSP00000300146.

PTM databases

iPTMnetiQ86TB9.
PhosphoSitePlusiQ86TB9.

Polymorphism and mutation databases

BioMutaiPATL1.
DMDMi182705251.

Proteomic databases

EPDiQ86TB9.
MaxQBiQ86TB9.
PaxDbiQ86TB9.
PeptideAtlasiQ86TB9.
PRIDEiQ86TB9.

Protocols and materials databases

DNASUi219988.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000300146; ENSP00000300146; ENSG00000166889. [Q86TB9-1]
GeneIDi219988.
KEGGihsa:219988.
UCSCiuc001noe.6. human. [Q86TB9-1]

Organism-specific databases

CTDi219988.
GeneCardsiPATL1.
H-InvDBHIX0009657.
HGNCiHGNC:26721. PATL1.
HPAiHPA039030.
MIMi614660. gene.
neXtProtiNX_Q86TB9.
OpenTargetsiENSG00000166889.
PharmGKBiPA162398769.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4592. Eukaryota.
ENOG4110Q9I. LUCA.
GeneTreeiENSGT00520000055649.
HOGENOMiHOG000115461.
HOVERGENiHBG104422.
InParanoidiQ86TB9.
KOiK12617.
OMAiYTVEKMY.
OrthoDBiEOG091G0MYC.
PhylomeDBiQ86TB9.
TreeFamiTF323322.

Enzyme and pathway databases

ReactomeiR-HSA-430039. mRNA decay by 5' to 3' exoribonuclease.

Miscellaneous databases

ChiTaRSiPATL1. human.
EvolutionaryTraceiQ86TB9.
GenomeRNAii219988.
PROiQ86TB9.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000166889.
CleanExiHS_PATL1.
GenevisibleiQ86TB9. HS.

Family and domain databases

InterProiIPR019167. Topo_II-assoc_PAT1.
[Graphical view]
PfamiPF09770. PAT1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPATL1_HUMAN
AccessioniPrimary (citable) accession number: Q86TB9
Secondary accession number(s): B3KXT9
, Q2TA86, Q6P166, Q8N9M6, Q8NI63
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 26, 2008
Last sequence update: February 26, 2008
Last modified: November 30, 2016
This is version 102 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 11
    Human chromosome 11: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

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.