Probable histone-binding protein lin-53

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Reviewed, UniProtKB/Swiss-Prot P90916 (LIN53_CAEEL)

Last modified December 15, 2009. Version 70. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Probable histone-binding protein lin-53
Alternative name(s):
    Abnormal cell lineage protein 53
    Synthetic multivulva protein p48

Gene names

Name:	lin-53
Synonyms:	rba-2
ORF Names:	K07A1.12

Organism

Caenorhabditis elegans [Complete proteome]

Taxonomic identifier

6239 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Nematoda › Chromadorea › Rhabditida › Rhabditoidea › Rhabditidae › Peloderinae › Caenorhabditis

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Protein attributes

Sequence length	417 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA By similarity. Synthetic multivulva class B (synMuvB) protein. SynMuvB proteins are required to repress the induction of vulval development by Ras signaling and probably act by forming the multiprotein DRM complex that repress transcription.
Subunit structure	Binds directly to helix 1 of the histone fold of histone H4, a region that is not accessible when H4 is in chromatin By similarity. Probable component of the NuRD complex, composed of at least lin-35, lin-53 and hda-1. Component of the DRM complex, at least composed of lin-9, lin-35, lin-37, lin-52, lin-53, lin-54- dpl-1 and efl-1.
Subcellular location	Nucleus Ref.1.
Developmental stage	Ubiquitously expressed in embryos and newly hatched larvae. Expressed in all P_3-8.p cells at the time of vulval induction. Ref.1
Sequence similarities	Belongs to the WD repeat RBAP46/RBAP48/MSI1 family. Contains 6 WD repeats.

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Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Repeat WD repeat
Molecular function	Chromatin regulator Developmental protein Repressor
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW embryonic development ending in birth or egg hatching Ref.1 Inferred from mutant phenotype. Source: UniProtKB hermaphrodite genitalia development Ref.1 Inferred from mutant phenotype. Source: UniProtKB negative regulation of transcription Ref.4 Non-traceable author statement. Source: UniProtKB negative regulation of vulval development Inferred from mutant phenotype. Source: WormBase nematode larval development Inferred from mutant phenotype. Source: WormBase transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	DRM complex Ref.4 Inferred from direct assay. Source: UniProtKB
Molecular function	histone deacetylase binding Ref.1 Inferred from physical interaction. Source: UniProtKB
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
hda-1	O17695	1	EBI-324314,EBI-318045
lin-35	O01682	1	EBI-324314,EBI-321470

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 417

417

Probable histone-binding protein lin-53

PRO_0000051059

Regions

Repeat

118 – 158

WD 1

Repeat

170 – 210

WD 2

Repeat

220 – 260

WD 3

Repeat

263 – 303

WD 4

Repeat

307 – 347

WD 5

Repeat

364 – 404

WD 6

Experimental info

Mutagenesis

292

L → F in semidominant alleles n883 and n2978; causes development of multiple vulvas. Ref.1

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Sequences

Sequence

Length

Mass (Da)

Tools

P90916-1 [UniParc].

Last modified February 7, 2006. Version 2.
Checksum: AE388CFB048CE51B
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FASTA

417

47,166

        10         20         30         40         50         60 
MATLEDGTSE DRVANDEYKI WKKNTPFLYD LVMTHALEWP SLSVQWLPDV AKDNSDHTIH 

        70         80         90        100        110        120 
RLILGTHTSD EQNHLLISKI CMPTDDAQFD ASRYDTERSE YGGFGAVNGK VEPDIRINHE 

       130        140        150        160        170        180 
GEVNRARYMP QKSNIIATKS PHADVYIFDY LKHSAVPRDN TFNPLIRLKG HTKEGYGLSW 

       190        200        210        220        230        240 
NPNKEGLILS ASDDQTVCHW DINANQNVAG ELQAKDVFKG HESVVEDVAW HVLHDGVFGS 

       250        260        270        280        290        300 
VGDDKKLLIW DVRTSTPGHC IDAHSAEVNC LAFNPYSEFI LATGSADKTV ALWDLRNLRM 

       310        320        330        340        350        360 
KLHSFESHRD EIFQVQWSPH NETILASSGT DKRLHVWDLS KIGEDQSAED AEDGPPELLF 

       370        380        390        400        410 
IHGGHTAKIS DFSWNPNEPW VVCSVSEDNI LQVWQMADNI YNEVDEETPA DVVERQQ

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"lin-35 and lin-53, two genes that antagonize a C. elegans Ras pathway, encode proteins similar to Rb and its binding protein RbAp48." Lu X., Horvitz H.R. Cell 95:981-991(1998) [PubMed: 9875852] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INTERACTION WITH LIN-35 AND HDA-1, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, MUTAGENESIS OF LEU-292.
[2]	"Genome sequence of the nematode C. elegans: a platform for investigating biology." The C. elegans sequencing consortium Science 282:2012-2018(1998) [PubMed: 9851916] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Bristol N2.
[3]	"NURD-complex genes antagonise Ras-induced vulval development in Caenorhabditis elegans." Solari F., Ahringer J. Curr. Biol. 10:223-226(2000) [PubMed: 10704416] [Abstract] Cited for: FUNCTION.
[4]	"Some C. elegans class B synthetic multivulva proteins encode a conserved LIN-35 Rb-containing complex distinct from a NuRD-like complex." Harrison M.M., Ceol C.J., Lu X., Horvitz H.R. Proc. Natl. Acad. Sci. U.S.A. 103:16782-16787(2006) [PubMed: 17075059] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE DRM COMPLEX.
+	Additional computationally mapped references.

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Cross-references

Sequence databases
	AF116530 mRNA. Translation: AAD05571.1. AL023833, Z81097 Genomic DNA. Translation: CAA19477.1. Z81097, AL023833 Genomic DNA. Translation: CAB03178.1.
PIR	T23391.
RefSeq	NP_492552.1.
UniGene	Cel.19610
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	P90916. 5 interactions.
STRING	P90916.
Genome annotation databases
Ensembl	K07A1.12.1; K07A1.12.1; K07A1.12; Caenorhabditis elegans. [Genome view] K07A1.12.2; K07A1.12.2; K07A1.12; Caenorhabditis elegans. [Genome view]
GeneID	172802.
KEGG	cel:K07A1.12.
UCSC	K07A1.12.1. c. elegans.
Organism-specific databases
CTD	172802.
WormBase	WBGene00003036. lin-53.
WormPep	K07A1.12. CE16234. [WorfDB]
Phylogenomic databases
HOGENOM	HBG435352.
InParanoid	P90916.
OMA	NDEEPDI.
Gene expression databases
ArrayExpress	P90916.
Family and domain databases
InterPro	IPR020472. G-protein_beta_WD-40_rep_reg. IPR015943. WD40/YVTN_repeat-like_dom. IPR001680. WD40_repeat. IPR011046. WD40_repeat-like_dom. IPR019782. WD40_repeat_2. IPR019775. WD40_repeat_CS. IPR017986. WD40_repeat_dom. IPR019781. WD40_repeat_sg. [Graphical view]
Gene3D	G3DSA:2.130.10.10. WD40/YVTN_repeat-like. 1 hit.
Pfam	PF00400. WD40. 5 hits. [Graphical view]
PRINTS	PR00320. GPROTEINBRPT.
SMART	SM00320. WD40. 6 hits. [Graphical view]
PROSITE	PS00678. WD_REPEATS_1. 2 hits. PS50082. WD_REPEATS_2. 5 hits. PS50294. WD_REPEATS_REGION. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	877063.

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Entry information

Entry name

LIN53_CAEEL

Accession

Primary (citable) accession number: P90916
Secondary accession number(s): A2JDY3, O62411

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	February 7, 2006
Last modified:	December 15, 2009
This is version 70 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Caenorhabditis annotation project

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Relevant documents

Caenorhabditis elegans

Caenorhabditis elegans: entries, gene names and cross-references to WormPep

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents