Protein skinhead-1 - Caenorhabditis elegans

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P34707 (SKN1_CAEEL) Reviewed, UniProtKB/Swiss-Prot

Last modified December 14, 2011. Version 112. History...

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

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Protein skinhead-1

Gene names

Name:	skn-1
ORF Names:	T19E7.2

Organism

Caenorhabditis elegans

Taxonomic identifier

6239 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	623 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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.

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 Reference proteome
Gene Ontology (GO)
Biological process	cell fate specification Inferred from mutant phenotype. Source: WormBase determination of adult lifespan Inferred from mutant phenotype. Source: WormBase embryo development ending in birth or egg hatching Inferred from mutant phenotype. Source: WormBase embryonic pattern specification Inferred from mutant phenotype. Source: WormBase mesendoderm development Traceable author statement. Source: WormBase nematode larval development 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 positive regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype. Source: WormBase reproduction Inferred from mutant phenotype. Source: WormBase response to heat Inferred from mutant phenotype. Source: WormBase response to herbicide Inferred from mutant phenotype. Source: WormBase response to oxidative stress Inferred from mutant phenotype. Source: WormBase
Cellular component	nucleus Non-traceable author statement. Source: UniProtKB
Molecular function	double-stranded DNA binding Inferred from direct assay. Source: WormBase protein binding Inferred from physical interaction. Source: UniProtKB sequence-specific DNA binding Inferred from direct assay Ref.5. Source: WormBase sequence-specific distal enhancer binding RNA polymerase II transcription factor activity Inferred from direct assay. Source: WormBase
Complete GO annotation...

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.

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...

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 [UniParc]. 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 [UniParc]. 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

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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

FO080233 Genomic DNA. Translation: CCD62212.1.
FO080233 Genomic DNA. Translation: CCD62213.1.
FO080233 Genomic DNA. Translation: CCD62214.1.
M84359 Genomic DNA. No translation available.

PIR

A42143.
F88694.

RefSeq

NP_741404.1. NM_171345.3.
NP_741405.1. NM_171346.2.
NP_741406.1. NM_171347.4.

UniGene

Cel.23037.

3D structure databases

PDBe
RCSB PDB
PDBj

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

ProteinModelPortal

P34707.

SMR

P34707. Positions 546-619.

ModBase

Search...

Protein-protein interaction databases

IntAct

P34707. 5 interactions.

MINT

MINT-1094083.

STRING

P34707.

Proteomic databases

PRIDE

P34707.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblMetazoa

T19E7.2a; T19E7.2a; T19E7.2.

GeneID

177343.

KEGG

cel:T19E7.2.

UCSC

T19E7.2b. c. elegans.

Organism-specific databases

CTD

177343.

WormBase

T19E7.2a; CE27591; WBGene00004804; skn-1.
T19E7.2b; CE31238; WBGene00004804; skn-1.
T19E7.2c; CE31239; WBGene00004804; skn-1.

Phylogenomic databases

eggNOG

KOG3863.

GeneTree

EMGT00050000008964.

HOGENOM

HBG383616.

InParanoid

P34707.

OMA

GLRWRDD.

Gene expression databases

ArrayExpress

P34707.

Family and domain databases

InterPro

IPR004827. bZIP.
IPR008917. Euk_TF_DNA-bd.
[Graphical view]

Gene3D

G3DSA:1.10.880.10. G3DSA:1.10.880.10. 1 hit.

SUPFAM

SSF47454. Euk_transcr_DNA. 1 hit.

PROSITE

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

ProtoNet

Search...

Other

NextBio

896360.

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:	December 14, 2011
This is version 112 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Caenorhabditis annotation project

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·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

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

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents