Protein skinhead-1 - Caenorhabditis elegans

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Reviewed, UniProtKB/Swiss-Prot P34707 (SKN1_CAEEL)

Last modified June 16, 2009. Version 87. History...

Clusters with 100%, 90%, 50% identity |

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

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Names and origin

Protein names

Recommended name:
Protein skinhead-1

Gene names

Name:	skn-1
ORF Names:	T19E7.2

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	623 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	Required to specify the fate of ventral blastomeres in the early embryo, and postembryonically for the development of the intestine. Directly regulates expression of zygotically expressed med-1 and med-2 to direct mesendoderm development. Ref.2 Ref.4
Subunit structure	Monomer. Ref.3
Subcellular location	Nucleus. Ref.3
Tissue specificity	Postembryonic intestinal cells. Ref.2
Developmental stage	Expressed both maternally and zygotically. Ref.2
Domain	Alternative DNA-binding strategy due to lack of a leucine zipper dimerization segment: DNA binding domain binds to its cognate half-site, an N-terminal arm recognizes adjacent 5' AT-rich sequences in the minor groove and the intervening residues stabilize interactions of these two subdomains with DNA.
Sequence similarities	Belongs to the bZIP family. Skn1 subfamily. Contains 1 bZIP domain.

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Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Ligand	DNA-binding
Molecular function	Developmental protein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	embryonic development ending in birth or egg hatching Inferred from mutant phenotype. Source: WormBase nematode larval development Ref.2 Inferred from mutant phenotype. Source: WormBase positive regulation of growth rate Inferred from mutant phenotype. Source: WormBase positive regulation of multicellular organism growth Inferred from mutant phenotype. Source: WormBase regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Non-traceable author statement. Source: UniProtKB
Molecular function	protein binding Inferred from physical interaction. Source: IntAct sequence-specific DNA binding Inferred from electronic annotation. Source: InterPro transcription factor activity Ref.2 Non-traceable author statement. Source: UniProtKB
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct
akt-1	Q17941	1	EBI-434984,EBI-1770718
akt-1	Q17941	1	EBI-434993,EBI-1770718
akt-2	Q9XTG7	1	EBI-434984,EBI-320656
akt-2	Q9XTG7	1	EBI-434993,EBI-320656
sgk-1	Q2PJ68	1	EBI-434993,EBI-1770776

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Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform a (identifier: P34707-1) This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform b (identifier: P34707-2) The sequence of this isoform differs from the canonical sequence as follows: 1-313: Missing. 314-389: FDNKQQHPVI...WLPTEVVPND → MSLPSDFASS...YSGVSSTFDR
Note: No experimental confirmation available.

Isoform c (identifier: P34707-3) The sequence of this isoform differs from the canonical sequence as follows: 1-90: Missing.
Note: No experimental confirmation available.

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 623

623

Protein skinhead-1

PRO_0000076639

Regions

DNA binding

597 – 612

Basic motif Ref.3

Natural variations

Alternative sequence

1 – 313

313

Missing in isoform b.

VSP_011488

Alternative sequence

1 – 90

Missing in isoform c.

VSP_011487

Alternative sequence

314 – 389

FDNKQ…VVPND → MSLPSDFASSLLASSTTTNT TNTAPAAVNSFDEQEEESKK ILNMYLQMFNQQQVDQHGHH HQHPYAYSGVSSTFDR in isoform b.

VSP_011489

Secondary structure

623

Helix Strand Turn

Details...

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Sequences

Sequence		Length	Mass (Da)
Isoform a [UniParc]. Last modified May 27, 2002. Version 2. Checksum: 31A70303AB7CC691 Show »	FASTA	623	70,709
10 20 30 40 50 60 MGGSSRRQRS TSATRRDDKR RRRQCFSSVA DDEEETTSIY GVSSIFIWIL ATSSLILVIS 70 80 90 100 110 120 SPSSNTSIQS SSYDRITTKH LLDNISPTFK MYTDSNNRNF DEVNHQHQQE QDFNGQSKYD 130 140 150 160 170 180 YPQFNRPMGL RWRDDQRMME YFMSNGPVET VPVMPILTEH PPASPFGRGP STERPTTSSR 190 200 210 220 230 240 YEYSSPSLED IDLIDVLWRS DIAGEKGTRQ VAPADQYECD LQTLTEKSTV APLTAEENAR 250 260 270 280 290 300 YEDLSKGFYN GFFESFNNNQ YQQKHQQQQR EQIKTPTLEH PTQKAELEDD LFDEDLAQLF 310 320 330 340 350 360 EDVSREEGQL NQLFDNKQQH PVINNVSLSE GIVYNQANLT EMQEMRDSCN QVSISTIPTT 370 380 390 400 410 420 STAQPETLFN VTDSQTVEQW LPTEVVPNDV FPTSNYAYIG MQNDSLQAVV SNGQIDYDHS 430 440 450 460 470 480 YQSTGQTPLS PLIIGSSGRQ QQTQTSPGSV TVTATATQSL FDPYHSQRHS FSDCTTDSSS 490 500 510 520 530 540 TCSRLSSESP RYTSESSTGT HESRFYGKLA PSSGSRYQRS SSPRSSQSSI KIARVVPLAS 550 560 570 580 590 600 GQRKRGRQSK DEQLASDNEL PVSAFQISEM SLSELQQVLK NESLSEYQRQ LIRKIRRRGK 610 620 NKVAARTCRQ RRTDRHDKMS HYI « Hide
Isoform b. Checksum: 21BD8A6536EE72B5 Show »	FASTA	310	34,588
10 20 30 40 50 60 MSLPSDFASS LLASSTTTNT TNTAPAAVNS FDEQEEESKK ILNMYLQMFN QQQVDQHGHH 70 80 90 100 110 120 HQHPYAYSGV SSTFDRVFPT SNYAYIGMQN DSLQAVVSNG QIDYDHSYQS TGQTPLSPLI 130 140 150 160 170 180 IGSSGRQQQT QTSPGSVTVT ATATQSLFDP YHSQRHSFSD CTTDSSSTCS RLSSESPRYT 190 200 210 220 230 240 SESSTGTHES RFYGKLAPSS GSRYQRSSSP RSSQSSIKIA RVVPLASGQR KRGRQSKDEQ 250 260 270 280 290 300 LASDNELPVS AFQISEMSLS ELQQVLKNES LSEYQRQLIR KIRRRGKNKV AARTCRQRRT 310 DRHDKMSHYI « Hide
Isoform c. Checksum: A911F45723ADCB13 Show »	FASTA	533	60,634
10 20 30 40 50 60 MYTDSNNRNF DEVNHQHQQE QDFNGQSKYD YPQFNRPMGL RWRDDQRMME YFMSNGPVET 70 80 90 100 110 120 VPVMPILTEH PPASPFGRGP STERPTTSSR YEYSSPSLED IDLIDVLWRS DIAGEKGTRQ 130 140 150 160 170 180 VAPADQYECD LQTLTEKSTV APLTAEENAR YEDLSKGFYN GFFESFNNNQ YQQKHQQQQR 190 200 210 220 230 240 EQIKTPTLEH PTQKAELEDD LFDEDLAQLF EDVSREEGQL NQLFDNKQQH PVINNVSLSE 250 260 270 280 290 300 GIVYNQANLT EMQEMRDSCN QVSISTIPTT STAQPETLFN VTDSQTVEQW LPTEVVPNDV 310 320 330 340 350 360 FPTSNYAYIG MQNDSLQAVV SNGQIDYDHS YQSTGQTPLS PLIIGSSGRQ QQTQTSPGSV 370 380 390 400 410 420 TVTATATQSL FDPYHSQRHS FSDCTTDSSS TCSRLSSESP RYTSESSTGT HESRFYGKLA 430 440 450 460 470 480 PSSGSRYQRS SSPRSSQSSI KIARVVPLAS GQRKRGRQSK DEQLASDNEL PVSAFQISEM 490 500 510 520 530 SLSELQQVLK NESLSEYQRQ LIRKIRRRGK NKVAARTCRQ RRTDRHDKMS HYI « Hide

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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], ALTERNATIVE SPLICING. Strain: Bristol N2.
[2]	"skn-1, a maternally expressed gene required to specify the fate of ventral blastomeres in the early C. elegans embryo." Bowerman B., Eaton B.A., Priess J.R. Cell 68:1061-1075(1992) [PubMed: 1547503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 49-623 (ISOFORM A), FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE. Strain: Bristol N2.
[3]	"Formation of a monomeric DNA binding domain by Skn-1 bZIP and homeodomain elements." Blackwell T.K., Bowerman B., Priess J.R., Weintraub H. Science 266:621-628(1994) [PubMed: 7939715] [Abstract] Cited for: SUBUNIT, SUBCELLULAR LOCATION, DNA-BINDING.
[4]	"Restriction of mesendoderm to a single blastomere by the combined action of SKN-1 and a GSK-3beta homolog is mediated by MED-1 and -2 in C. elegans." Maduro M.F., Meneghini M.D., Bowerman B., Broitman-Maduro G., Rothman J.H. Mol. Cell 7:475-485(2001) [PubMed: 11463373] [Abstract] Cited for: FUNCTION.
[5]	"A new DNA-binding motif in the Skn-1 binding domain-DNA complex." Rupert P.B., Daughdrill G.W., Bowerman B., Matthews B.W. Nat. Struct. Biol. 5:484-491(1998) [PubMed: 9628487] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 540-623.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

U42843 Genomic DNA. Translation: AAA83594.2.
U42843 Genomic DNA. Translation: AAM75365.1.
U42843 Genomic DNA. Translation: AAM75366.1.
M84359 Genomic DNA. No translation available.

PIR

A42143.
F88694.

RefSeq

NP_741404.1.

UniGene

Cel.23037

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SKN	X-ray	2.50	P	540-623	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P34707. 7 interactions.

Proteomic databases

PRIDE

P34707.

Genome annotation databases

Ensembl

T19E7.2. Caenorhabditis elegans. [Contig view]

GeneID

177343.

KEGG

cel:T19E7.2.

Organism-specific databases

WormBase

WBGene00004804. skn-1.

WormPep

T19E7.2a. CE27591. [WorfDB]
T19E7.2b. CE31238. [WorfDB]
T19E7.2c. CE31239. [WorfDB]

Gene expression databases

ArrayExpress

P34707.

Family and domain databases

InterPro

IPR013089. Kelch_related.
IPR004827. TF_bZIP.
[Graphical view]

PANTHER

PTHR23230. Kelch_related. 1 hit.

PROSITE

PS50217. BZIP. False negative.
PS00036. BZIP_BASIC. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

896360.

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Entry information

Entry name

SKN1_CAEEL

Accession

Primary (citable) accession number: P34707
Secondary accession number(s): Q8MPW2, Q8MPW3

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	May 27, 2002
Last modified:	June 16, 2009
This is version 87 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Alternative products

Sequence annotation (Features)

Molecule processing

Regions

Natural variations

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents