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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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi86 – 861L → A: Loss of nuclear export; when associated with A-90, A-93 and A-95. 1 Publication
Mutagenesisi90 – 901L → A: Loss of nuclear export; when associated with A-86, A-93 and A-95. 1 Publication
Mutagenesisi93 – 931M → A: Loss of nuclear export; when associated with A-86, A-90 and A-95. 1 Publication
Mutagenesisi95 – 951I → A: Loss of nuclear export; when associated with A-86, A-90 and A-93. 1 Publication
Mutagenesisi519 – 5191R → 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 Publication
Mutagenesisi520 – 5201R → 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 Publication
Mutagenesisi523 – 5231L → 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 Publication
Mutagenesisi527 – 5271E → 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 Publication
Mutagenesisi530 – 5301Y → 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 Publication
Mutagenesisi534 – 5341L → 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 Publication
Mutagenesisi539 – 55719YERRY…ALMDD → GSGSGSG in mut3; does not affect neither RNA-binding,interaction with the decapping machinery, nor localization to P-body. 1 PublicationAdd
BLAST
Mutagenesisi591 – 5911R → 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 Publication
Mutagenesisi595 – 5951R → 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 Publication
Mutagenesisi625 – 6251K → 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 Publication
Mutagenesisi626 – 6261K → 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 Publication

Organism-specific databases

PharmGKBiPA162398769.

Polymorphism and mutation databases

BioMutaiPATL1.
DMDMi182705251.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 770770Protein PAT1 homolog 1PRO_0000320963Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei177 – 1771PhosphoserineCombined sources
Modified residuei178 – 1781PhosphothreonineBy similarity
Modified residuei179 – 1791PhosphoserineCombined sources
Modified residuei184 – 1841PhosphoserineCombined sources
Modified residuei194 – 1941PhosphothreonineCombined sources
Modified residuei278 – 2781PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ86TB9.
MaxQBiQ86TB9.
PaxDbiQ86TB9.
PeptideAtlasiQ86TB9.
PRIDEiQ86TB9.

PTM databases

iPTMnetiQ86TB9.
PhosphoSiteiQ86TB9.

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
FHL3Q136433EBI-2562092,EBI-741101
GOLGA2Q083793EBI-2562092,EBI-618309
PSMA3P257883EBI-2562092,EBI-348380

Protein-protein interaction databases

BioGridi128613. 29 interactions.
IntActiQ86TB9. 8 interactions.
MINTiMINT-4717253.
STRINGi9606.ENSP00000300146.

Structurei

Secondary structure

1
770
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi518 – 54427Combined sources
Helixi548 – 5503Combined sources
Helixi551 – 57020Combined sources
Beta strandi574 – 5763Combined sources
Helixi582 – 5887Combined sources
Helixi591 – 60010Combined sources
Helixi601 – 6033Combined sources
Helixi606 – 61813Combined sources
Helixi620 – 6267Combined sources
Turni627 – 6304Combined sources
Helixi633 – 6364Combined sources
Helixi637 – 6448Combined sources
Helixi649 – 65911Combined sources
Turni663 – 6653Combined sources
Helixi677 – 6804Combined sources
Helixi683 – 70018Combined sources
Helixi712 – 72716Combined sources
Helixi730 – 7323Combined sources
Helixi743 – 7508Combined sources
Helixi753 – 76210Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2XEQX-ray3.10A/B/C/D517-767[»]
2XERX-ray2.95A/B/C517-767[»]
2XESX-ray2.10A/B517-767[»]
ProteinModelPortaliQ86TB9.
SMRiQ86TB9. Positions 517-765.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ86TB9.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 397397Involved in nuclear foci localizationAdd
BLAST
Regioni1 – 8484Region A; interaction with DDX6/RCKAdd
BLAST
Regioni85 – 388304Region N; interaction with decapping machineryAdd
BLAST
Regioni223 – 397175Involved in RNA-bindingAdd
BLAST
Regioni389 – 44860Region HAdd
BLAST
Regioni398 – 770373Involved in nuclear spleckles localizationAdd
BLAST
Regioni449 – 770322Region CAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi86 – 9510Nuclear export signal

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi155 – 338184Pro-richAdd
BLAST

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti160 – 1601Q → H in BAG54601 (PubMed:14702039).Curated
Sequence conflicti735 – 7351K → R in BAC04305 (PubMed:14702039).Curated
Sequence conflicti735 – 7351K → R in CAD89916 (PubMed:17974005).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 659659Missing in isoform 3. 1 PublicationVSP_031777Add
BLAST
Alternative sequencei1 – 143143Missing in isoform 2. 2 PublicationsVSP_031778Add
BLAST
Alternative sequencei242 – 27130Missing in isoform 4. 1 PublicationVSP_040576Add
BLAST
Alternative sequencei662 – 69837Missing in isoform 4. 1 PublicationVSP_040577Add
BLAST

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
EntryMethodResolution (Å)ChainPositionsPDBsum
2XEQX-ray3.10A/B/C/D517-767[»]
2XERX-ray2.95A/B/C517-767[»]
2XESX-ray2.10A/B517-767[»]
ProteinModelPortaliQ86TB9.
SMRiQ86TB9. Positions 517-765.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi128613. 29 interactions.
IntActiQ86TB9. 8 interactions.
MINTiMINT-4717253.
STRINGi9606.ENSP00000300146.

PTM databases

iPTMnetiQ86TB9.
PhosphoSiteiQ86TB9.

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.
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: September 7, 2016
This is version 99 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.