Q24459 (PCL_DROME) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Polycomb protein Pcl

Alternative name(s):
Polycomblike protein

Gene names

Name:	Pcl
ORF Names:	CG5109

Organism

Drosophila melanogaster (Fruit fly) [Reference proteome]

Taxonomic identifier

7227 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Protostomia › Ecdysozoa › Panarthropoda › Arthropoda › Mandibulata › Pancrustacea › Hexapoda › Insecta › Dicondylia › Pterygota › Neoptera › Endopterygota › Diptera › Brachycera › Muscomorpha › Eremoneura › Cyclorrhapha › Schizophora › Acalyptratae › Ephydroidea › Drosophilidae › Drosophilinae › Drosophilini › Drosophilina › Drosophiliti › Drosophila › Sophophora › melanogaster group › melanogaster subgroup

Protein attributes

Sequence length	1043 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Polycomb group (PcG) protein. While PcG proteins are generally required to maintain the transcriptionally repressive state of homeotic genes throughout development, this protein is specifically required during the first 6 hours of embryogenesis to establish the repressed state. Component of the Esc/E(z) complex, which methylates 'Lys-9' and 'Lys-27' residues of histone H3, leading to transcriptional repression of the affected target gene. The Esc/E(z) complex is necessary but not sufficient for the repression of homeotic target genes, suggesting that the recruitment of the distinct PRC1 complex is also required. Required for the correct spatial expression of the homeotic genes of the Antennapedia and Bithorax complexes. Ref.1
Subunit structure	Component of a form of the Esc/E(z) complex present specifically during early embryogenesis which is composed of Caf1, esc, E(z), Su(z)12, Pcl and Rpd3. This complex is distinct from the PRC1 complex, which contains many other PcG proteins like Pc, Ph, Psc, Su(z)2. The two complexes however cooperate and interact together during the first 3 hours of development to establish PcG silencing. Interacts with corto in vitro. Ref.5 Ref.6
Subcellular location	Nucleus. Chromosome. Note: Associated with chromatin. Colocalizes with many PcG sites on polytene chromosomes. It also associates with many unique sites on polytene chromosomes. Ref.1
Developmental stage	Ubiquitous expression in embryos. Ref.1
Domain	The PHD-type zinc fingers mediate the interaction with E(z). Ref.8 Ref.9 In contrast to vertebrate homologs (PHF1, PHF19 and MTF2), the Tudor domain does not bind H3K36me3 (Ref.8 and Ref.9). Ref.8 Ref.9
Sequence similarities	Belongs to the Polycomblike family. Contains 2 PHD-type zinc fingers. Contains 1 Tudor domain.
Sequence caution	The sequence AAA64457.1 differs from that shown. Reason: Frameshift at position 807.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Chromosome Nucleus
Domain	Repeat Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Chromatin regulator Developmental protein Repressor
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	chromatin modification Inferred from direct assay Ref.1. Source: UniProtKB negative regulation of transcription, DNA-dependent Inferred from direct assay Ref.6Ref.1. Source: UniProtKB neurogenesis Inferred from mutant phenotype PubMed 21549331. Source: FlyBase transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	chromosome Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from direct assay Ref.1. Source: UniProtKB
Molecular_function	DNA binding Inferred from direct assay Ref.1. Source: UniProtKB chromatin binding Inferred from direct assay Ref.1. Source: FlyBase sequence-specific DNA binding transcription factor activity Inferred from direct assay Ref.5Ref.6Ref.1. Source: UniProtKB zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
E(z)	P42124	11	EBI-430086,EBI-112315
Rpd3	Q94517	5	EBI-430086,EBI-302197

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1043

1043

Polycomb protein Pcl

PRO_0000059339

Regions

Domain

349 – 404

56

Tudor

Zinc finger

424 – 472

49

PHD-type 1

Zinc finger

512 – 560

49

PHD-type 2

Compositional bias

237 – 256

20

Ser-rich

Compositional bias

278 – 347

70

Pro-rich

Amino acid modifications

Modified residue

805

1

Phosphoserine Ref.7

Modified residue

806

1

Phosphoserine Ref.7

Experimental info

Mutagenesis

517

1

C → S or A: Abolishes interaction with E(z). Ref.5

Mutagenesis

527 – 530

4

MLQC → QQQA: Abolishes interaction with E(z). Ref.5

Sequence conflict

93

1

S → N in AAA64457. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

1043

Helix Strand Turn

Details...

Beta strand

341 – 345

5

Beta strand

356 – 360

5

Beta strand

366 – 374

9

Beta strand

379 – 383

5

Beta strand

388 – 391

4

Turn

393 – 395

3

Sequences

	Sequence		Length	Mass (Da)
	Q24459 [UniParc]. Last modified May 10, 2004. Version 2. Checksum: BD3325D7835EEAC3	FASTA	1,043	114,638
	10 20 30 40 50 60 MMNNHFHLQH DHPPQNVAHP FMQQPSTAVP SAPPATYGYL AQPAGQQPQW MTTTYQILPP 70 80 90 100 110 120 SVGPATVAKR YYATTGPQTT HPTHPSTIQI TNSFAQQSTP PKQQAATSCS PFKANNIRII 130 140 150 160 170 180 STAPSVYSLN KPPQEAHSTY APVQSYYLPS GGGQTAGQIN LLAASGTGKQ LQPPPLVPVT 190 200 210 220 230 240 NSTSPPSTVV LDRINICINN HYTETPTSLS SSLTTAQQPS PIIPAIQHKA ILPLIDSSTA 250 260 270 280 290 300 DSSSCSSSSV SSSSYSGTAT TSAAVVIVDE PDSTTTTPQT PPTTPEAMSS PGKSSPSPPL 310 320 330 340 350 360 LATQSLLKGV NSMKPSFKTV EAAPPTPPTP PSPPPPPPAP PVAAPSPAVT YALQEDVFIK 370 380 390 400 410 420 CNDGRFYLGT IIDQTSDQYL IRFDDQSEQW CEPDKLRKLG GGSSITAGGG GASTTESTNT 430 440 450 460 470 480 SPSGPMCVAC KRSDIEDVVE ICERCGRGYH RGCTVEIVTG SGIWSCKRCA KPMKMQQPVS 490 500 510 520 530 540 HKITKPAGIC RQLPYHADKL SWDEKHRVNE EQIYCYCGKP GKFDHNMLQC CKCRNWFHTQ 550 560 570 580 590 600 CMQNFKKKLL RGDMFFVFCC TVCNNGIEFV RRMQIEWVDV LHIALYNLRK HQHQKYHHLL 610 620 630 640 650 660 NDIWPFILEQ RHQLPICEKW RTLPETALME RLKQTLKDYS DRFVCGREFK RAPAFYALRH 670 680 690 700 710 720 SGPPHIPKVF LEPHEELSDE LLEKRFKLML MPEEPDEGAN ELPKRVPKDV YEFNTDEDDP 730 740 750 760 770 780 VETSEDEIPI KQIIEKAKKQ AAQKADKHDE LPLKPDLADD NANDGDPGKL PAPIPPLLDA 790 800 810 820 830 840 NSSRKRKAFR LSKRYDNSRN HCDLSSDENS SSSRGTSSLD LIIPPPVNFL GRNNPFLMAT 850 860 870 880 890 900 PKKASQGRSI SVGTGVGVNG IINSIFKLKG TSKEQPRMVR TIKRRLSAKD ITIGPNQEVR 910 920 930 940 950 960 RRRTRRLTTA IEVISTTTIN PIPSHYLPIY AKDLQPPAPP MGKPTHGRLL RQRPQKQSPS 970 980 990 1000 1010 1020 QSRRNSTSST ATSSSSNGIG APGHSMLDLK QSVNKYFGGA MNRIDAGEPF AIRAKRRMGN 1030 1040 GQVQYLVEWG GDTATTAIGL LGN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular characterisation of the Polycomblike gene of Drosophila melanogaster, a trans-acting negative regulator of homeotic gene expression." Lonie A., D'andrea R., Paro R., Saint R. Development 120:2629-2636(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE. Tissue: Embryo.
[2]	"The genome sequence of Drosophila melanogaster." Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D. , Zhang Q., Chen L.X., Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C. Science 287:2185-2195(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Berkeley.
[3]	"Annotation of the Drosophila melanogaster euchromatic genome: a systematic review." Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S., Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E., Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P., Bettencourt B.R., Celniker S.E., de Grey A.D.N.J. , Drysdale R.A., Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E. Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002) [PubMed] [Europe PMC] [Abstract] Cited for: GENOME REANNOTATION. Strain: Berkeley.
[4]	"A Drosophila full-length cDNA resource." Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M., George R.A., Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H., Rubin G.M., Celniker S.E. Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: Berkeley. Tissue: Embryo.
[5]	"Polycomblike PHD fingers mediate conserved interaction with enhancer of zeste protein." O'Connell S., Wang L., Robert S., Jones C.A., Saint R., Jones R.S. J. Biol. Chem. 276:43065-43073(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH E(Z), MUTAGENESIS OF CYS-517 AND 527-MET--CYS-530.
[6]	"A 1-megadalton ESC/E(Z) complex from Drosophila that contains polycomblike and RPD3." Tie F., Prasad-Sinha J., Birve A., Rasmuson-Lestander A., Harte P.J. Mol. Cell. Biol. 23:3352-3362(2003) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN AN ESC/E(Z) COMPLEX WITH CAF1; ESC; E(Z); SU(Z)12 AND RPD3.
[7]	"Phosphoproteome analysis of Drosophila melanogaster embryos." Zhai B., Villen J., Beausoleil S.A., Mintseris J., Gygi S.P. J. Proteome Res. 7:1675-1682(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-805 AND SER-806, MASS SPECTROMETRY. Tissue: Embryo.
[8]	"Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity." Ballare C., Lange M., Lapinaite A., Martin G.M., Morey L., Pascual G., Liefke R., Simon B., Shi Y., Gozani O., Carlomagno T., Benitah S.A., Di Croce L. Nat. Struct. Mol. Biol. 19:1257-1265(2012) [PubMed] [Europe PMC] [Abstract] Cited for: DOMAIN.
[9]	"Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1." Musselman C.A., Avvakumov N., Watanabe R., Abraham C.G., Lalonde M.E., Hong Z., Allen C., Roy S., Nunez J.K., Nickoloff J., Kulesza C.A., Yasui A., Cote J., Kutateladze T.G. Nat. Struct. Mol. Biol. 19:1266-1272(2012) [PubMed] [Europe PMC] [Abstract] Cited for: DOMAIN.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L35153 mRNA. Translation: AAA64457.1. Frameshift.
AE013599 Genomic DNA. Translation: AAF57748.2.
AY075585 mRNA. Translation: AAL68389.1.

RefSeq

NP_001261067.1. NM_001274138.1.
NP_476672.1. NM_057324.5.

UniGene

Dm.4284.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2XK0	NMR	-	A	339-404	[»]

ProteinModelPortal

Q24459.

SMR

Q24459. Positions 350-404, 426-469, 512-566.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q24459. 5 interactions.

MINT

MINT-5227221.

Proteomic databases

PaxDb

Q24459.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblMetazoa

FBtr0086735; FBpp0085914; FBgn0003044.
FBtr0329998; FBpp0303033; FBgn0003044.

GeneID

37069.

KEGG

dme:Dmel_CG5109.

UCSC

CG5109-RA. d. melanogaster.

Organism-specific databases

FlyBase

FBgn0003044. Pcl.

Phylogenomic databases

eggNOG

NOG244542.

GeneTree

ENSGT00390000009222.

InParanoid

Q24459.

KO

K11485.

OMA

DEIPIKQ.

OrthoDB

EOG44XGXT.

PhylomeDB

Q24459.

Gene expression databases

Bgee

Q24459.

GermOnline

CG5109. Drosophila melanogaster.

Family and domain databases

Gene3D

3.30.40.10. 2 hits.

InterPro

IPR025894. Mtf2_C_dom.
IPR002999. Tudor.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]

Pfam

PF14061. Mtf2_C. 1 hit.
[Graphical view]

SMART

SM00249. PHD. 2 hits.
SM00333. TUDOR. 1 hit.
[Graphical view]

SUPFAM

SSF57903. FYVE_PHD_ZnF. 2 hits.

PROSITE

PS50304. TUDOR. False negative.
PS01359. ZF_PHD_1. 2 hits.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q24459.

GenomeRNAi

37069.

NextBio

801791.

Entry information

Entry name

PCL_DROME

Accession

Primary (citable) accession number: Q24459
Secondary accession number(s): Q8T8P9, Q9V8C2

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2004
Last sequence update:	May 10, 2004
Last modified:	May 1, 2013
This is version 106 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Drosophila annotation project