P90916 (LIN53_CAEEL) Reviewed, UniProtKB/Swiss-Prot

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

Taxonomic identifier

6239 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	417 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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. Ref.1 Ref.3 Ref.4
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 P3-8.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.

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 Reference proteome
Gene Ontology (GO)
Biological process	cell fate specification Inferred from mutant phenotype. Source: WormBase chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW embryo development ending in birth or egg hatching Inferred from mutant phenotype Ref.1. Source: UniProtKB embryonic digestive tract morphogenesis Inferred from genetic interaction. Source: WormBase hermaphrodite genitalia development Inferred from mutant phenotype Ref.1. Source: UniProtKB negative regulation of transcription, DNA-dependent Non-traceable author statement Ref.4. Source: UniProtKB negative regulation of vulval development Inferred from mutant phenotype. Source: WormBase nematode larval development Inferred from mutant phenotype. Source: WormBase tail tip morphogenesis Inferred from mutant phenotype. Source: WormBase transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	DRM complex Inferred from direct assay Ref.4. Source: UniProtKB
Molecular function	histone deacetylase binding Inferred from physical interaction Ref.1. Source: UniProtKB
Complete GO annotation...

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	41	WD 1
	Repeat	170 – 210	41	WD 2
	Repeat	220 – 260	41	WD 3
	Repeat	263 – 303	41	WD 4
	Repeat	307 – 347	41	WD 5
	Repeat	364 – 404	41	WD 6
Experimental info
	Mutagenesis	292	1	L → F in semidominant alleles n883 and n2978; causes development of multiple vulvas. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P90916 [UniParc]. Last modified February 7, 2006. Version 2. Checksum: AE388CFB048CE51B	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

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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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. NM_060151.5.
UniGene	Cel.19610.
3D structure databases
ProteinModelPortal	P90916.
SMR	P90916. Positions 6-403.
ModBase	Search...
Protein-protein interaction databases
IntAct	P90916. 5 interactions.
MINT	MINT-114323.
STRING	P90916.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblMetazoa	K07A1.12.1; K07A1.12.1; K07A1.12. K07A1.12.2; K07A1.12.2; K07A1.12.
GeneID	172802.
KEGG	cel:K07A1.12.
UCSC	K07A1.12.1. c. elegans.
Organism-specific databases
CTD	172802.
WormBase	K07A1.12; CE16234; WBGene00003036; lin-53.
Phylogenomic databases
eggNOG	meNOG04956.
GeneTree	EMGT00050000002914.
HOGENOM	HBG435352.
InParanoid	P90916.
OMA	NDEEPDI.
PhylomeDB	P90916.
Gene expression databases
ArrayExpress	P90916.
Family and domain databases
InterPro	IPR020472. G-protein_beta_WD-40_rep. IPR022052. Histone-bd_RBBP4. IPR015943. WD40/YVTN_repeat-like_dom. IPR001680. WD40_repeat. IPR011046. WD40_repeat-like_dom. IPR019775. WD40_repeat_CS. IPR017986. WD40_repeat_dom. [Graphical view]
Gene3D	G3DSA:2.130.10.10. WD40/YVTN_repeat-like. 1 hit.
KO	K10752.
Pfam	PF12265. CAF1C_H4-bd. 1 hit. PF00400. WD40. 5 hits. [Graphical view]
PRINTS	PR00320. GPROTEINBRPT.
SMART	SM00320. WD40. 6 hits. [Graphical view]
SUPFAM	SSF50978. WD40_like. 1 hit.
PROSITE	PS00678. WD_REPEATS_1. 2 hits. PS50082. WD_REPEATS_2. 5 hits. PS50294. WD_REPEATS_REGION. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	877063.

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:	January 25, 2012
This is version 86 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Caenorhabditis annotation project