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UniProtKB - Q9UHX1 (PUF60_HUMAN)

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Protein

Poly(U)-binding-splicing factor PUF60

Gene

PUF60

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

Functioni

DNA- and RNA-binding protein, involved in several nuclear processes such as pre-mRNA splicing, apoptosis and transcription regulation. In association with FUBP1 regulates MYC transcription at the P2 promoter through the core-TFIIH basal transcription factor. Acts as a transcriptional repressor through the core-TFIIH basal transcription factor. Represses FUBP1-induced transcriptional activation but not basal transcription. Decreases ERCC3 helicase activity. Does not repress TFIIH-mediated transcription in xeroderma pigmentosum complementation group B (XPB) cells. Is also involved in pre-mRNA splicing. Promotes splicing of an intron with weak 3'-splice site and pyrimidine tract in a cooperative manner with U2AF2. Involved in apoptosis induction when overexpressed in HeLa cells. Isoform 6 failed to repress MYC transcription and inhibited FIR-induced apoptosis in colorectal cancer. Isoform 6 may contribute to tumor progression by enabling increased MYC expression and greater resistance to apoptosis in tumors than in normal cells. Modulates alternative splicing of several mRNAs. Binds to relaxed DNA of active promoter regions. Binds to the pyrimidine tract and 3'-splice site regions of pre-mRNA; binding is enhanced in presence of U2AF2. Binds to Y5 RNA in association with TROVE2. Binds to poly(U) RNA.6 Publications

Miscellaneous

Does not repress TFIIH-mediated transcription in xeroderma pigmentosum complementation group B (XPB) cells.

GO - Molecular functioni

  • cadherin binding Source: BHF-UCL
  • DNA binding Source: UniProtKB-KW
  • identical protein binding Source: IntAct
  • RNA binding Source: UniProtKB
Complete GO annotation...

GO - Biological processi

Complete GO annotation...

Keywordsi

Molecular functionDNA-binding, Repressor, Ribonucleoprotein, RNA-binding
Biological processApoptosis, mRNA processing, mRNA splicing, Transcription, Transcription regulation

Enzyme and pathway databases

ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Poly(U)-binding-splicing factor PUF60
Alternative name(s):
60 kDa poly(U)-binding-splicing factor
FUSE-binding protein-interacting repressor
Short name:
FBP-interacting repressor
Ro-binding protein 1
Short name:
RoBP1
Siah-binding protein 1
Short name:
Siah-BP1
Gene namesi
Name:PUF60
Synonyms:FIR, ROBPI, SIAHBP1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo
Proteomesi
  • UP000005640 Componenti: Chromosome 8

Organism-specific databases

HGNCiHGNC:17042. PUF60.

Subcellular locationi

  • Nucleus 2 Publications

    • Note: Colocalizes partially with TROVE2.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Verheij syndrome (VRJS)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA syndrome characterized by growth retardation, delayed psychomotor development, dysmorphic facial features, and skeletal, mainly vertebral, abnormalities. Additional variable features may include coloboma, renal defects, and cardiac defects.
See also OMIM:615583
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_070939169H → Y in VRJS; loss of function mutation; results in altered dosage of different PUF60 protein forms and abnormal splicing profile of several target genes. 1 PublicationCorresponds to variant dbSNP:rs398123001Ensembl.1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi22827.
MalaCardsiPUF60.
MIMi615583. phenotype.
OpenTargetsiENSG00000179950.
PharmGKBiPA162400364.

Polymorphism and mutation databases

DMDMi74761960.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002995191 – 559Poly(U)-binding-splicing factor PUF60Add BLAST559

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei60PhosphothreonineCombined sources1
Modified residuei112PhosphoserineCombined sources1
Modified residuei244PhosphoserineBy similarity1
Modified residuei251N6-acetyllysineCombined sources1
Modified residuei314PhosphothreonineCombined sources1
Modified residuei454N6-acetyllysineCombined sources1
Cross-linki458Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Isoform 5 (identifier: Q9UHX1-5)
Cross-linki14Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Isoform 6 (identifier: Q9UHX1-6)
Cross-linki14Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9UHX1.
PaxDbiQ9UHX1.
PeptideAtlasiQ9UHX1.
PRIDEiQ9UHX1.
TopDownProteomicsiQ9UHX1-3. [Q9UHX1-3]

PTM databases

iPTMnetiQ9UHX1.
PhosphoSitePlusiQ9UHX1.
SwissPalmiQ9UHX1.

Expressioni

Tissue specificityi

Isoform 2 is expressed in colonic epithelium and colorectal epithelium cancer (at protein level). Isoform 6 is expressed in colorectal epithelial cancer but below detection level in colonic epithelium. Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, spleen, thymus, prostate, testis, ovary, small intestine, colon and peripheral blood leukocytes.2 Publications

Gene expression databases

BgeeiENSG00000179950.
CleanExiHS_PUF60.
ExpressionAtlasiQ9UHX1. baseline and differential.
GenevisibleiQ9UHX1. HS.

Organism-specific databases

HPAiHPA045733.
HPA052096.
HPA059714.

Interactioni

Subunit structurei

Homodimer. Associates with the spliceosome. Found in a complex with TROVE2 and Y5 RNA. Found in a complex with FUBP1 and far upstream element (FUSE) DNA segment. Interacts directly with ERCC3. Interacts with CDK7, GTF2H1 and SFRS11. Does not interact with ERCC3 in xeroderma pigmentosum complementation group B (XPB) cells.5 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • cadherin binding Source: BHF-UCL
  • identical protein binding Source: IntAct
Complete GO annotation...

Protein-protein interaction databases

BioGridi116502. 132 interactors.
DIPiDIP-34636N.
IntActiQ9UHX1. 58 interactors.
MINTiMINT-1374433.
STRINGi9606.ENSP00000434359.

Structurei

Secondary structure

1559
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi118 – 128Combined sources11
Beta strandi130 – 134Combined sources5
Helixi142 – 149Combined sources8
Helixi150 – 152Combined sources3
Beta strandi155 – 160Combined sources6
Turni164 – 166Combined sources3
Beta strandi171 – 179Combined sources9
Helixi180 – 190Combined sources11
Beta strandi194 – 199Combined sources6
Beta strandi201 – 203Combined sources3
Helixi206 – 208Combined sources3
Helixi209 – 211Combined sources3
Helixi212 – 222Combined sources11
Helixi223 – 225Combined sources3
Beta strandi227 – 231Combined sources5
Beta strandi235 – 237Combined sources3
Helixi239 – 246Combined sources8
Beta strandi252 – 259Combined sources8
Turni261 – 263Combined sources3
Beta strandi266 – 276Combined sources11
Helixi277 – 287Combined sources11
Beta strandi293 – 296Combined sources4
Beta strandi298 – 301Combined sources4
Beta strandi306 – 309Combined sources4
Helixi445 – 448Combined sources4
Turni449 – 452Combined sources4
Helixi453 – 459Combined sources7
Beta strandi463 – 468Combined sources6
Helixi472 – 474Combined sources3
Helixi479 – 487Combined sources9
Turni488 – 490Combined sources3
Beta strandi493 – 506Combined sources14
Beta strandi510 – 521Combined sources12
Helixi522 – 532Combined sources11
Beta strandi536 – 541Combined sources6
Beta strandi543 – 547Combined sources5
Helixi549 – 553Combined sources5
Beta strandi557 – 559Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DNYNMR-A454-559[»]
2KXFNMR-A119-314[»]
2KXHNMR-A119-314[»]
2QFJX-ray2.10A/B118-316[»]
3DXBX-ray2.20A/B/C/D/E/F/G/H460-559[»]
3UE2X-ray1.23A443-559[»]
3US5X-ray1.38A443-559[»]
3UWTX-ray2.50A118-316[»]
ProteinModelPortaliQ9UHX1.
SMRiQ9UHX1.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UHX1.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini129 – 207RRM 1PROSITE-ProRule annotationAdd BLAST79
Domaini226 – 304RRM 2PROSITE-ProRule annotationAdd BLAST79
Domaini462 – 549RRM 3; atypicalPROSITE-ProRule annotationAdd BLAST88

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 516Inhibits homodimerizationAdd BLAST516
Regioni77 – 559Inhibits transcriptional repression, interaction with ERCC3 and apoptosis inductionAdd BLAST483

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi321 – 343Ala-richAdd BLAST23

Domaini

The third RNA recognition motif, called PUMP domain, is atypical and may rather mediate homodimerization and/or protein-protein interactions.

Sequence similaritiesi

Belongs to the RRM half pint family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0124. Eukaryota.
ENOG410XSGH. LUCA.
GeneTreeiENSGT00870000136413.
HOVERGENiHBG055622.
InParanoidiQ9UHX1.
KOiK12838.
OMAiIFDQGDL.
OrthoDBiEOG091G08UV.
PhylomeDBiQ9UHX1.
TreeFamiTF313987.

Family and domain databases

CDDicd12370. RRM1_PUF60. 1 hit.
cd12371. RRM2_PUF60. 1 hit.
cd12648. RRM3_UHM_PUF60. 1 hit.
InterProiView protein in InterPro
IPR006532. PolyU-bd.
IPR034209. PUF60_RRM1.
IPR034211. PUF60_RRM2.
IPR034212. PUF60_RRM3.
IPR000504. RRM_dom.
IPR003954. RRM_dom_euk.
PANTHERiPTHR24012:SF668. PTHR24012:SF668. 1 hit.
PfamiView protein in Pfam
PF00076. RRM_1. 2 hits.
SMARTiView protein in SMART
SM00360. RRM. 3 hits.
SM00361. RRM_1. 2 hits.
SUPFAMiSSF54928. SSF54928. 3 hits.
TIGRFAMsiTIGR01645. half-pint. 1 hit.
PROSITEiView protein in PROSITE
PS50102. RRM. 3 hits.

Sequences (6)i

Sequence statusi: Complete.

This entry describes 6 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9UHX1-1) [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
MATATIALQV NGQQGGGSEP AAAAAVVAAG DKWKPPQGTD SIKMENGQST 
        60         70         80         90        100
AAKLGLPPLT PEQQEALQKA KKYAMEQSIK SVLVKQTIAH QQQQLTNLQM 
       110        120        130        140        150
AAVTMGFGDP LSPLQSMAAQ RQRALAIMCR VYVGSIYYEL GEDTIRQAFA 
       160        170        180        190        200
PFGPIKSIDM SWDSVTMKHK GFAFVEYEVP EAAQLALEQM NSVMLGGRNI 
       210        220        230        240        250
KVGRPSNIGQ AQPIIDQLAE EARAFNRIYV ASVHQDLSDD DIKSVFEAFG 
       260        270        280        290        300
KIKSCTLARD PTTGKHKGYG FIEYEKAQSS QDAVSSMNLF DLGGQYLRVG 
       310        320        330        340        350
KAVTPPMPLL TPATPGGLPP AAAVAAAAAT AKITAQEAVA GAAVLGTLGT 
       360        370        380        390        400
PGLVSPALTL AQPLGTLPQA VMAAQAPGVI TGVTPARPPI PVTIPSVGVV 
       410        420        430        440        450
NPILASPPTL GLLEPKKEKE EEELFPESER PEMLSEQEHM SISGSSARHM 
       460        470        480        490        500
VMQKLLRKQE STVMVLRNMV DPKDIDDDLE GEVTEECGKF GAVNRVIIYQ 
       510        520        530        540        550
EKQGEEEDAE IIVKIFVEFS IASETHKAIQ ALNGRWFAGR KVVAEVYDQE 

RFDNSDLSA
Length:559
Mass (Da):59,875
Last modified:May 1, 2000 - v1
Checksum:i619F3C30D1C5951C
GO
Isoform 2 (identifier: Q9UHX1-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     101-117: Missing.

Show »
Length:542
Mass (Da):58,171
Checksum:i2C67EBE529A0922E
GO
Isoform 3 (identifier: Q9UHX1-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-43: Missing.

Show »
Length:516
Mass (Da):55,729
Checksum:iF52D8C619E874B55
GO
Isoform 4 (identifier: Q9UHX1-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-43: Missing.
     101-117: Missing.

Show »
Length:499
Mass (Da):54,025
Checksum:i77881512A09C3EFD
GO
Isoform 5 (identifier: Q9UHX1-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     9-37: Missing.

Show »
Length:530
Mass (Da):57,103
Checksum:i850251A390ECD30C
GO
Isoform 6 (identifier: Q9UHX1-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     9-37: Missing.
     101-117: Missing.

Show »
Length:513
Mass (Da):55,399
Checksum:i2A5BA6848E391E3A
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti3T → R in AAB41656 (Ref. 7) Curated1
Sequence conflicti123R → G in AAB41656 (Ref. 7) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_070939169H → Y in VRJS; loss of function mutation; results in altered dosage of different PUF60 protein forms and abnormal splicing profile of several target genes. 1 PublicationCorresponds to variant dbSNP:rs398123001Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0277171 – 43Missing in isoform 3 and isoform 4. 1 PublicationAdd BLAST43
Alternative sequenceiVSP_0277189 – 37Missing in isoform 5 and isoform 6. CuratedAdd BLAST29
Alternative sequenceiVSP_027719101 – 117Missing in isoform 2, isoform 4 and isoform 6. 3 PublicationsAdd BLAST17

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF217197 mRNA. Translation: AAF27522.2.
AF114818 mRNA. Translation: AAF23589.1.
AK292373 mRNA. Translation: BAF85062.1.
CR457143 mRNA. Translation: CAG33424.1.
CH471162 Genomic DNA. Translation: EAW82187.1.
CH471162 Genomic DNA. Translation: EAW82189.1.
BC008875 mRNA. Translation: AAH08875.1.
BC009734 mRNA. Translation: AAH09734.1.
BC011265 mRNA. Translation: AAH11265.1.
BC011979 mRNA. Translation: AAH11979.1.
U51586 mRNA. Translation: AAB41656.1.
AF190744 mRNA. Translation: AAF05605.1.
CCDSiCCDS47933.1. [Q9UHX1-2]
CCDS47934.1. [Q9UHX1-1]
CCDS47935.1. [Q9UHX1-3]
CCDS59514.1. [Q9UHX1-4]
CCDS59515.1. [Q9UHX1-6]
CCDS59516.1. [Q9UHX1-5]
RefSeqiNP_001129505.1. NM_001136033.2. [Q9UHX1-3]
NP_001258025.1. NM_001271096.1.
NP_001258026.1. NM_001271097.1. [Q9UHX1-6]
NP_001258027.1. NM_001271098.1.
NP_001258028.1. NM_001271099.1. [Q9UHX1-5]
NP_001258029.1. NM_001271100.1. [Q9UHX1-4]
NP_055096.2. NM_014281.4. [Q9UHX1-2]
NP_510965.1. NM_078480.2. [Q9UHX1-1]
XP_016868728.1. XM_017013239.1. [Q9UHX1-3]
XP_016868729.1. XM_017013240.1. [Q9UHX1-4]
UniGeneiHs.521924.

Genome annotation databases

EnsembliENST00000313352; ENSP00000322016; ENSG00000179950. [Q9UHX1-4]
ENST00000349157; ENSP00000322036; ENSG00000179950. [Q9UHX1-2]
ENST00000453551; ENSP00000402953; ENSG00000179950. [Q9UHX1-3]
ENST00000456095; ENSP00000395417; ENSG00000179950. [Q9UHX1-5]
ENST00000526683; ENSP00000434359; ENSG00000179950. [Q9UHX1-1]
ENST00000527197; ENSP00000431960; ENSG00000179950. [Q9UHX1-6]
ENST00000612237; ENSP00000478495; ENSG00000274081. [Q9UHX1-2]
ENST00000620341; ENSP00000484860; ENSG00000274081. [Q9UHX1-1]
ENST00000620953; ENSP00000478209; ENSG00000274081. [Q9UHX1-5]
ENST00000632444; ENSP00000487945; ENSG00000274081. [Q9UHX1-3]
ENST00000633206; ENSP00000487930; ENSG00000274081. [Q9UHX1-4]
GeneIDi22827.
KEGGihsa:22827.
UCSCiuc003yzq.5. human. [Q9UHX1-1]

Keywords - Coding sequence diversityi

Alternative splicing

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.

Entry informationi

Entry nameiPUF60_HUMAN
AccessioniPrimary (citable) accession number: Q9UHX1
Secondary accession number(s): A8K8K8
, Q969E7, Q96D94, Q96H63, Q99628, Q9NZA0, Q9UJY7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: May 1, 2000
Last modified: July 5, 2017
This is version 156 of the entry and version 1 of the sequence. See 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 8
    Human chromosome 8: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families