Q92541 (RTF1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
RNA polymerase-associated protein RTF1 homolog

Gene names

Name:	RTF1
Synonyms:	KIAA0252

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	710 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of MLL1; it promotes leukemogenesis though association with MLL-rearranged oncoproteins, such as MLL-MLLT3/AF9 and MLL-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Binds single-stranded DNA. Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex By similarity. Ref.7 Ref.8
Subunit structure	Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61; the association of RTF1 appears to be less stable than that of other subunits. At least in HeLa cells a N-terminal shorter form of RTF1 is also found in the complex. Ref.8
Subcellular location	Nucleus › nucleoplasm By similarity.
Domain	The Plus3 domain mediates single-stranded DNA-binding. Ref.13
Sequence similarities	Contains 1 Plus3 domain.
Caution	It is uncertain whether Met-1 or Met-41 is the initiator.
Sequence caution	The sequence AAH15052.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence BAA13382.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Biological process	Transcription Transcription regulation Wnt signaling pathway
Cellular component	Nucleus
Domain	Coiled coil
Ligand	DNA-binding
Molecular function	Activator
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA-dependent transcription, initiation Inferred from electronic annotation. Source: InterPro Wnt receptor signaling pathway Inferred from electronic annotation. Source: UniProtKB-KW endodermal cell fate commitment Inferred from sequence or structural similarity. Source: UniProtKB histone H3-K4 trimethylation Inferred from electronic annotation. Source: Compara negative regulation of transcription from RNA polymerase II promoter Inferred from sequence or structural similarity. Source: UniProtKB positive regulation of histone H3-K4 methylation Inferred from electronic annotation. Source: Compara positive regulation of transcription elongation from RNA polymerase II promoter Inferred from direct assay Ref.8. Source: UniProtKB positive regulation of transcription from RNA polymerase II promoter Inferred from direct assay Ref.8. Source: UniProtKB stem cell maintenance Inferred from direct assay Ref.7. Source: UniProtKB
Cellular_component	Cdc73/Paf1 complex Inferred from direct assay Ref.8. Source: UniProtKB nucleolus Inferred from electronic annotation. Source: Compara
Molecular_function	single-stranded DNA binding Inferred from direct assay Ref.13. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CDC73	Q6P1J9	12	EBI-1055239,EBI-930143
PAF1	Q8N7H5	16	EBI-1055239,EBI-2607770

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 710

710

RNA polymerase-associated protein RTF1 homolog

PRO_0000255936

Regions

Domain

353 – 484

132

Plus3

Coiled coil

526 – 560

35

Potential

Compositional bias

10 – 18

9

Poly-Ala

Compositional bias

135 – 173

39

Ser-rich

Compositional bias

174 – 345

172

Glu-rich

Compositional bias

214 – 307

94

Lys-rich

Amino acid modifications

Modified residue

53

1

Phosphoserine Ref.9 Ref.11

Modified residue

55

1

Phosphothreonine Ref.11

Modified residue

650

1

Phosphoserine Ref.9

Modified residue

697

1

Phosphoserine Ref.6 Ref.9

Experimental info

Mutagenesis

401

1

R → E: Loss of binding to single-stranded DNA. Ref.13

Mutagenesis

410

1

E → K: Reduced binding to single-stranded DNA. Ref.13

Mutagenesis

429

1

R → E: Loss of binding to single-stranded DNA. Ref.13

Mutagenesis

434

1

Q → A: Reduced binding to single-stranded DNA. Ref.13

Mutagenesis

435

1

R → E: Loss of binding to single-stranded DNA. Ref.13

Secondary structure

1

.

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710

Helix Strand Turn

Details...

Helix

356 – 360

5

Beta strand

362 – 364

3

Helix

366 – 372

7

Beta strand

373 – 377

5

Helix

378 – 382

5

Beta strand

386 – 392

7

Beta strand

395 – 397

3

Beta strand

399 – 417

19

Beta strand

420 – 430

11

Beta strand

433 – 438

6

Helix

439 – 441

3

Helix

449 – 462

14

Helix

469 – 478

10

Sequences

	Sequence		Length	Mass (Da)
	Q92541 [UniParc]. Last modified November 30, 2010. Version 4. Checksum: 54CC014655AA22B8	FASTA	710	80,313
	10 20 30 40 50 60 MRGRLCVGRA AAAAAAVAVP LAGGQEGSPG GGRRGSRGTT MVKKRKGRVV IDSDTEDSGS 70 80 90 100 110 120 DENLDQELLS LAKRKRSDSE EKEPPVSQPA ASSDSETSDS DDEWTFGSNK NKKKGKARKI 130 140 150 160 170 180 EKKGTMKKQA NKTASSGSSD KDSSAESSAP EEGEVSDSDS NSSSSSSDSD SSSEDEEFHD 190 200 210 220 230 240 GYGEDLMGDE EDRARLEQMT EKEREQELFN RIEKREVLKR RFEIKKKLKT AKKKEKKEKK 250 260 270 280 290 300 KKQEEEQEKK KLTQIQESQV TSHNKERRSK RDEKLDKKSQ AMEELKAERE KRKNRTAELL 310 320 330 340 350 360 AKKQPLKTSE VYSDDEEEEE DDKSSEKSDR SSRTSSSDEE EEKEEIPPKS QPVSLPEELN 370 380 390 400 410 420 RVRLSRHKLE RWCHMPFFAK TVTGCFVRIG IGNHNSKPVY RVAEITGVVE TAKVYQLGGT 430 440 450 460 470 480 RTNKGLQLRH GNDQRVFRLE FVSNQEFTES EFMKWKEAMF SAGMQLPTLD EINKKELSIK 490 500 510 520 530 540 EALNYKFNDQ DIEEIVKEKE RFRKAPPNYA MKKTQLLKEK AMAEDLGDQD KAKQIQDQLN 550 560 570 580 590 600 ELEERAEALD RQRTKNISAI SYINQRNREW NIVESEKALV AESHNMKNQQ MDPFTRRQCK 610 620 630 640 650 660 PTIVSNSRDP AVQAAILAQL NAKYGSGVLP DAPKEMSKGQ GKDKDLNSKS ASDLSEDLFK 670 680 690 700 710 VHDFDVKIDL QVPSSESKAL AITSKAPPAK DGAPRRSLNL EDYKKRRGLI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Analysis of the DNA sequence and duplication history of human chromosome 15." Zody M.C., Garber M., Sharpe T., Young S.K., Rowen L., O'Neill K., Whittaker C.A., Kamal M., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Kodira C.D., Madan A., Qin S., Yang X., Abbasi N., Abouelleil A. , Arachchi H.M., Baradarani L., Birditt B., Bloom S., Bloom T., Borowsky M.L., Burke J., Butler J., Cook A., DeArellano K., DeCaprio D., Dorris L. III, Dors M., Eichler E.E., Engels R., Fahey J., Fleetwood P., Friedman C., Gearin G., Hall J.L., Hensley G., Johnson E., Jones C., Kamat A., Kaur A., Locke D.P., Madan A., Munson G., Jaffe D.B., Lui A., Macdonald P., Mauceli E., Naylor J.W., Nesbitt R., Nicol R., O'Leary S.B., Ratcliffe A., Rounsley S., She X., Sneddon K.M.B., Stewart S., Sougnez C., Stone S.M., Topham K., Vincent D., Wang S., Zimmer A.R., Birren B.W., Hood L., Lander E.S., Nusbaum C. Nature 440:671-675(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[2]	"Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain." Nagase T., Seki N., Ishikawa K., Ohira M., Kawarabayasi Y., Ohara O., Tanaka A., Kotani H., Miyajima N., Nomura N. DNA Res. 3:321-329(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 9-710. Tissue: Brain.
[3]	"Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones." Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T. DNA Res. 9:99-106(2002) [PubMed] [Europe PMC] [Abstract] Cited for: SEQUENCE REVISION.
[4]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 14-710. Tissue: Uterus.
[5]	"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma.
[6]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-697, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[7]	"A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity." Ding L., Paszkowski-Rogacz M., Nitzsche A., Slabicki M.M., Heninger A.K., de Vries I., Kittler R., Junqueira M., Shevchenko A., Schulz H., Hubner N., Doss M.X., Sachinidis A., Hescheler J., Iacone R., Anastassiadis K., Stewart A.F., Pisabarro M.T. , Caldarelli A., Poser I., Theis M., Buchholz F. Cell Stem Cell 4:403-415(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[8]	"The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS." Kim J., Guermah M., Roeder R.G. Cell 140:491-503(2010) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE PAF1 COMPLEX, COMPOSITION OF THE PAF1 COMPLEX, FUNCTION OF THE PAF1 COMPLEX.
[9]	"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M. Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-53; SER-650 AND SER-697, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[10]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]	"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation." Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B. Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-53 AND THR-55, MASS SPECTROMETRY.
[12]	"Solution structure of the plus-3 domain of human KIAA0252 protein." RIKEN structural genomics initiative (RSGI) Submitted (JUN-2006) to the PDB data bank Cited for: STRUCTURE BY NMR OF 347-482.
[13]	"Structure and DNA binding of the human Rtf1 Plus3 domain." de Jong R.N., Truffault V., Diercks T., Ab E., Daniels M.A., Kaptein R., Folkers G.E. Structure 16:149-159(2008) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 353-484, DOMAIN PLUS3, DNA-BINDING, MUTAGENESIS OF ARG-401; GLU-410; ARG-429; GLN-434 AND ARG-435.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AC087721 Genomic DNA. No translation available.
D87440 mRNA. Translation: BAA13382.2. Different initiation.
BC015052 mRNA. Translation: AAH15052.1. Different initiation.

IPI

IPI00303832.

RefSeq

NP_055953.3. NM_015138.4.

UniGene

Hs.511096.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2BZE	NMR	-	A	353-484	[»]
2DB9	NMR	-	A	347-482	[»]
3U1U	X-ray	1.80	A/B	347-482	[»]

ProteinModelPortal

Q92541.

SMR

Q92541. Positions 347-482.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q92541. 13 interactions.

STRING

9606.ENSP00000374280.

PTM databases

PhosphoSite

Q92541.

Polymorphism databases

DMDM

118595726.

Proteomic databases

PaxDb

Q92541.

PRIDE

Q92541.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000389629; ENSP00000374280; ENSG00000137815.

GeneID

23168.

KEGG

hsa:23168.

UCSC

uc001zny.3. human.

Organism-specific databases

CTD

23168.

GeneCards

GC15P041709.

H-InvDB

HIX0012153.

HGNC

HGNC:28996. RTF1.

HPA

HPA006714.

MIM

611633. gene.

neXtProt

NX_Q92541.

PharmGKB

PA134961778.

HUGE

Search...

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG5296.

HOGENOM

HOG000231764.

HOVERGEN

HBG057331.

InParanoid

Q92541.

KO

K15178.

OMA

CKPTMVS.

OrthoDB

EOG4X97GV.

Gene expression databases

Bgee

Q92541.

CleanEx

HS_RTF1.

Genevestigator

Q92541.

GermOnline

ENSG00000137815. Homo sapiens.

Family and domain databases

InterPro

IPR004343. Plus-3.
IPR018144. Plus3-dom_subgr.
[Graphical view]

Pfam

PF03126. Plus-3. 1 hit.
[Graphical view]

SMART

SM00719. Plus3. 1 hit.
[Graphical view]

PROSITE

PS51360. PLUS3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

RTF1. human.

EvolutionaryTrace

Q92541.

GenomeRNAi

23168.

NextBio

44567.

PMAP-CutDB

Q92541.

SOURCE

Search...

Entry information

Entry name

RTF1_HUMAN

Accession

Primary (citable) accession number: Q92541
Secondary accession number(s): Q96BX6

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 31, 2006
Last sequence update:	November 30, 2010
Last modified:	April 3, 2013
This is version 98 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.