Q9VHA0 (SCM_DROME) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Polycomb protein Scm

Alternative name(s):
Sex comb on midleg protein

Gene names

Name:	Scm
ORF Names:	CG9495

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	877 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. Ref.7 UniProtKB Q9W3C1
Subunit structure	Scm associates with the PRC1 core complex containing PSC, PC, PH and Sce/RING1. Forms homotypic and heterotypic interactions. Interacts with the SAM domain of ph-p via its SAM domain in vitro. Interacts with corto in vitro. Ref.5 Ref.6 Ref.7 Ref.9
Subcellular location	Nucleus Probable.
Developmental stage	Expressed both maternally and zygotically. Levels are highest in 0-2 hours embryos and at lower levels during later embryonic and larval stages. A modest increase in expression is seen during the pupal stage. Expressed throughout the 9 hours embryo. After 12 hours expression is concentrated in the central nervous system. Ref.1
Domain	The SAM domain is essential for function. Ref.7
Sequence similarities	Belongs to the SCM family. Contains 1 FCS-type zinc finger. Contains 2 MBT repeats. Contains 1 SAM (sterile alpha motif) domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	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	axonogenesis Inferred from mutant phenotype PubMed 17164414. Source: FlyBase chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW gene silencing Inferred from mutant phenotype Ref.7. Source: UniProtKB germarium-derived female germ-line cyst encapsulation Inferred from mutant phenotype PubMed 14993188. Source: FlyBase negative regulation of transcription, DNA-dependent Traceable author statement Ref.7. Source: UniProtKB ovarian follicle cell stalk formation Inferred from mutant phenotype PubMed 14993188. Source: FlyBase transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	PRC1 complex Traceable author statement PubMed 15337121. Source: FlyBase
Molecular_function	zinc ion binding Non-traceable author statement Ref.1. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		4	EBI-89256,EBI-89256
corto	P41046	2	EBI-89256,EBI-300379
ph-p	P39769	5	EBI-89256,EBI-300360

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 877

877

Polycomb protein Scm

PRO_0000114333

Regions

Repeat

175 – 273

99

MBT 1

Repeat

281 – 382

102

MBT 2

Domain

806 – 876

71

SAM

Zinc finger

54 – 93

40

FCS-type

Compositional bias

7 – 49

43

Ser-rich

Compositional bias

672 – 750

79

Ser-rich

Compositional bias

751 – 776

26

Ala-rich

Amino acid modifications

Modified residue

546

1

Phosphothreonine Ref.8

Modified residue

549

1

Phosphoserine Ref.8

Modified residue

550

1

Phosphoserine Ref.8

Modified residue

585

1

Phosphoserine Ref.8

Experimental info

Mutagenesis

816

1

E → G: No effect on function. Shows self- and ph-p binding activity comparable to wild-type; when associated with V-846 and R-860. Ref.7

Mutagenesis

834

1

I → T: Complete loss of function. Significant loss of self-binding activity. Moderate loss of ph-p binding activity. Ref.5

Mutagenesis

836

1

G → D: Complete loss of function. Complete loss of self- and ph-p binding activity. Ref.5 Ref.7

Mutagenesis

836

1

G → S: Loss of self- and ph-p binding activity. Ref.5 Ref.7

Mutagenesis

840 – 841

2

LL → SS: Several-fold reduction of self-binding activity. Partial loss of ph-p binding activity. Ref.5

Mutagenesis

846

1

M → V: No effect on function. Shows self- and ph-p binding activity comparable to wild-type; when associated with G-816 and R-860. Ref.7

Mutagenesis

848

1

Missing: Complete loss of function. Significant loss of self-binding activity. Partial loss of ph-p binding activity. Ref.7

Mutagenesis

851

1

M → R: Complete loss of function. Complete loss of self- and ph-p binding activity. Ref.7

Mutagenesis

854

1

K → A: Partial loss of self- and ph-p binding activity. Ref.5

Mutagenesis

860

1

K → E: Complete loss of function. Partial loss of self-binding activity. Complete loss of ph-p binding activity. Ref.7

Mutagenesis

860

1

K → R: No effect on function. Shows self- and ph-p binding activity comparable to wild-type; when associated with G-816 and V-846. Ref.7

Secondary structure

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877

Helix Strand Turn

Details...

Helix

177 – 183

7

Helix

191 – 193

3

Beta strand

194 – 196

3

Beta strand

210 – 215

6

Beta strand

218 – 231

14

Beta strand

234 – 239

6

Beta strand

248 – 251

4

Helix

262 – 265

4

Helix

280 – 282

3

Helix

283 – 291

9

Helix

299 – 301

3

Beta strand

319 – 323

5

Beta strand

331 – 340

10

Beta strand

343 – 348

6

Helix

353 – 355

3

Beta strand

357 – 360

4

Helix

371 – 375

5

Helix

797 – 800

4

Helix

803 – 805

3

Helix

808 – 818

11

Helix

820 – 825

6

Helix

826 – 831

6

Helix

836 – 840

5

Helix

844 – 850

7

Helix

855 – 868

14

Sequences

	Sequence		Length	Mass (Da)
	Q9VHA0 [UniParc]. Last modified October 1, 2002. Version 2. Checksum: 7859FD0C7B91589E	FASTA	877	93,551
	10 20 30 40 50 60 MSGGRDSSTS SGSNSAAPGA STNATSSASA SASSTSTSAS PGSTTSPAST QRQRGRPAKR 70 80 90 100 110 120 ATCTWCGEGK LPLQYVLPTQ TGKKEFCSET CIAEFRKAYS KGACTQCDNV IRDGAPNKEF 130 140 150 160 170 180 CSIMCMNKHQ KKNCSTRHSG GSASGKGLAE SERKLLASGA PAPTGPFQYE SFHVFDWDAY 190 200 210 220 230 240 LEETGSEAAP AKCFKQAQNP PNNDFKIGMK LEALDPRNVT STCIATVVGV LGSRLRLRLD 250 260 270 280 290 300 GSDSQNDFWR LVDSTEIHAI GHCEKNGGML QPPLGFRMNA SSWPGYLCKI LNNAMVAPEE 310 320 330 340 350 360 IFQPEPPEPE ENLFKVGQKL EAVDKKNPQL ICCATVDAIK DDQIHVTFDG WRGAFDYWCN 370 380 390 400 410 420 YRSRDIFPAG WCARSCHPMQ PPGHKSRMDS SSSKQRCPRP RYTVVAESEA MVPASPATAH 430 440 450 460 470 480 FHPNCKGGPF INNSKLPCMV TGPTYQTLAK LCLQEVLAAS TDTQQLSKLL FALEGDVHIV 490 500 510 520 530 540 TAAGKNFTVK IPSPMRMKDD ESLAQFIETL CTTCRACANL ISLVHETEEC KKCANSRKRQ 550 560 570 580 590 600 LTQSATPPSS PVLADKRNRQ SNSATTSPSE KIIKQELAVK SPVESKSKTS TNNGKEPASQ 610 620 630 640 650 660 QNSNHSLNNN NNSASKSSNK VVIKSEPNGA NAQTSSTTQA LRKVRFQHHA NTNTNSSATN 670 680 690 700 710 720 GNQDTSQTTH VSTSHCSSSS TSSSTSLAGG SANTSTIGKY LAPLVAEVHP EQANVKPSNS 730 740 750 760 770 780 YYKSPTTLSS SASLPTSVST PFTGCQSASS TALAAGGVTA AKAATAPAGA AATAGASPSY 790 800 810 820 830 840 TAITSPVSTP TSALANSHLR SQPIDWTIEE VIQYIESNDN SLAVHGDLFR KHEIDGKALL 850 860 870 LLNSEMMMKY MGLKLGPALK ICNLVNKVNG RRNNLAL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The Drosophila polycomb group gene Sex comb on midleg (Scm) encodes a zinc finger protein with similarity to polyhomeotic protein." Bornemann D., Miller E., Simon J.A. Development 122:1621-1630(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], 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]	"A domain shared by the polycomb group proteins Scm and ph mediates heterotypic and homotypic interactions." Peterson A.J., Kyba M., Bornemann D., Morgan K., Brock H.W., Simon J.A. Mol. Cell. Biol. 17:6683-6692(1997) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PH-P, MUTAGENESIS OF ILE-834; GLY-836; 840-LEU-LEU-841 AND LYS-854.
[6]	"The Drosophila Corto protein interacts with Polycomb-group proteins and the GAGA factor." Salvaing J., Lopez A., Boivin A., Deutsch J.S., Peronnet F. Nucleic Acids Res. 31:2873-2882(2003) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH CORTO.
[7]	"Requirement for sex comb on midleg protein interactions in Drosophila polycomb group repression." Peterson A.J., Mallin D.R., Francis N.J., Ketel C.S., Stamm J., Voeller R.K., Kingston R.E., Simon J.A. Genetics 167:1225-1239(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, ASSOCIATION WITH PRC1 COMPLEX, MUTAGENESIS OF GLU-816; GLY-836; MET-846; MET-848; MET-851 AND LYS-860.
[8]	"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 THR-546; SER-549; SER-550 AND SER-585, MASS SPECTROMETRY. Tissue: Embryo.
[9]	"Structural organization of a Sex-comb-on-midleg/polyhomeotic copolymer." Kim C.A., Sawaya M.R., Cascio D., Kim W., Bowie J.U. J. Biol. Chem. 280:27769-27775(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 795-871, INTERACTION WITH PH-P.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U49793 mRNA. Translation: AAB57632.1.
AE014297 Genomic DNA. Translation: AAF54419.2.
BT001565 mRNA. Translation: AAN71320.1.

RefSeq

NP_001247006.1. NM_001260077.1.
NP_731385.1. NM_169299.1.

UniGene

Dm.6241.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1PK1	X-ray	1.80	B/D	795-871	[»]
1PK3	X-ray	1.85	A/B/C	795-871	[»]
2R57	X-ray	2.20	A	175-435	[»]
2R58	X-ray	2.00	A	175-435	[»]
2R5A	X-ray	2.30	A	175-435	[»]
2R5M	X-ray	2.65	A	175-435	[»]

ProteinModelPortal

Q9VHA0.

SMR

Q9VHA0. Positions 175-385, 795-869.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-17570N.

IntAct

Q9VHA0. 6 interactions.

MINT

MINT-266904.

Proteomic databases

PaxDb

Q9VHA0.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblMetazoa

FBtr0082102; FBpp0081580; FBgn0003334.
FBtr0306008; FBpp0297150; FBgn0003334.

GeneID

41168.

KEGG

dme:Dmel_CG9495.

Organism-specific databases

CTD

41168.

FlyBase

FBgn0003334. Scm.

Phylogenomic databases

eggNOG

NOG315447.

GeneTree

ENSGT00560000076796.

InParanoid

Q9VHA0.

KO

K11461.

OMA

FQYESFH.

OrthoDB

EOG400006.

PhylomeDB

Q9VHA0.

Gene expression databases

Bgee

Q9VHA0.

GermOnline

CG9495. Drosophila melanogaster.

Family and domain databases

Gene3D

1.10.150.50. 1 hit.

InterPro

IPR021987. DUF3588.
IPR004092. Mbt.
IPR001660. SAM.
IPR013761. SAM/pointed.
IPR021129. SAM_type1.
IPR012313. Znf_FCS.
IPR010507. Znf_MYM.
[Graphical view]

Pfam

PF12140. DUF3588. 1 hit.
PF02820. MBT. 2 hits.
PF00536. SAM_1. 1 hit.
PF06467. zf-FCS. 1 hit.
[Graphical view]

SMART

SM00561. MBT. 2 hits.
SM00454. SAM. 1 hit.
[Graphical view]

SUPFAM

SSF47769. SAM_homology. 1 hit.

PROSITE

PS51079. MBT. 2 hits.
PS50105. SAM_DOMAIN. 1 hit.
PS51024. ZF_FCS. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9VHA0.

GenomeRNAi

41168.

NextBio

822526.

Entry information

Entry name

SCM_DROME

Accession

Primary (citable) accession number: Q9VHA0
Secondary accession number(s): Q24191

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 2005
Last sequence update:	October 1, 2002
Last modified:	May 1, 2013
This is version 111 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Drosophila annotation project