SCAN domain: Difference between revisions

Revision as of 22:17, 19 December 2019

"The SCAN domain is a highly conserved, leucine-rich motif of approximately 60 aa originally found within a subfamily of zinc finger proteins."^[1]

"The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization."^[2]

SRE-ZBP

The "SRE-ZBP [is] a human zinc finger protein that binds to the c-Fos serum response element (17)".^[3]

CTfin51

AW-1

AW-1 is ZNF174.^[4]

Gene ID: 7727 is ZNF174 zinc finger protein 174. "This gene encodes a protein with three Cys2-His2-type zinc fingers in the carboxy-terminus, a putative nuclear localization signal, and an amino-terminus SCAN box which forms homodimers. This protein is believed to function as a transcriptional repressor. Alternative splicing results in multiple transcript variants encoding distinct isoforms."^[5] Aka AW-1 and zinc finger and SCAN domain-containing protein 8.^[5]

Number 18 cDNA

pfam00096 proteins

"The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)."^[6]

"Proteins are generally composed of one or more functional regions, commonly termed domains. Different combinations of domains give rise to the diverse range of proteins found in nature. The identification of domains that occur within proteins can therefore provide insights into their function."^[6]

"Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pfam entries which are related by similarity of sequence, structure or profile-HMM."^[6]

"The data presented for each entry is based on the UniProt Reference Proteomes but information on individual UniProtKB sequences can still be found by entering the protein accession. Pfam full alignments are available from searching a variety of databases, either to provide different accessions (e.g. all UniProt and NCBI GI) or different levels of redundancy."^[6]

Family: zf-C2H2 (PF00096), "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter [2]."^[7]

References

↑ RefSeq (January 2011). "SCAND1 SCAN domain containing 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 19 December 2019.
↑ NCBI (2017). "Conserved Protein Domain Family SCAN". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 19 December 2019.
↑ Gina Pengue, Viola Calabro, Paola Cannada Bartoli, Alfredo Pagliuca and Luigi Lania (1994). "Repression of transcriptional activity at a distance by the evolutionarily conserved KRAB domain present in a subfamily of zinc finger proteins" (PDF). Nucleic Acids Research. 22 (15): 2908–14. Retrieved 19 December 2019.
↑ Leonard C. Edelstein and Tucker Collins (10 October 2005). "The SCAN domain family of zinc finger transcription factors". Gene. 359: 1–17. doi:10.1016/j.gene.2005.06.022. Retrieved 19 December 2019.
↑ ^5.0 ^5.1 RefSeq (December 2016). "ZNF174 zinc finger protein 174 [ Homo sapiens (human) ]". U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information. Retrieved 19 December 2019.
↑ ^6.0 ^6.1 ^6.2 ^6.3 S. El-Gebali, J. Mistry, A. Bateman, S.R. Eddy, A. Luciani, S.C. Potter, M. Qureshi, L.J. Richardson, G.A. Salazar, A. Smart, E.L.L. Sonnhammer, L. Hirsh, L. Paladin, D. Piovesan, S.C.E. Tosatto, R.D. Finn (September 2018). "Pfam 32.0 (September 2018, 17929 entries)". Meyerhofstraße 1 69117 Heidelberg, Germany: European Molecular Biology Laboratory (EMBL). Retrieved 19 December 2019.
↑ S Boehm, D Frishman and HW Mewes (June 1997). "Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins" (PDF). Nucleic Acids Research. 25 (12): 2464–9. doi:10.1093/nar/25.12.2464. PMID 9171100. Retrieved 19 December 2019.

External links

The Pfam protein families database in 2019, S. El-Gebali, J. Mistry, A. Bateman, S.R. Eddy, A. Luciani, S.C. Potter, M. Qureshi, L.J. Richardson, G.A. Salazar, A. Smart, E.L.L. Sonnhammer, L. Hirsh, L. Paladin, D. Piovesan, S.C.E. Tosatto, R.D. Finn, Nucleic Acids Research (2019) doi: 10.1093/nar/gky995.

Template:Sisterlinks

[RefSeq-1] RefSeq (January 2011). "SCAND1 SCAN domain containing 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 19 December 2019.

[NCBI-2] NCBI (2017). "Conserved Protein Domain Family SCAN". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 19 December 2019.

[Pengue-3] Gina Pengue, Viola Calabro, Paola Cannada Bartoli, Alfredo Pagliuca and Luigi Lania (1994). "Repression of transcriptional activity at a distance by the evolutionarily conserved KRAB domain present in a subfamily of zinc finger proteins" (PDF). Nucleic Acids Research. 22 (15): 2908–14. Retrieved 19 December 2019.

[Edelstein-4] Leonard C. Edelstein and Tucker Collins (10 October 2005). "The SCAN domain family of zinc finger transcription factors". Gene. 359: 1–17. doi:10.1016/j.gene.2005.06.022. Retrieved 19 December 2019.

[RefSeq2016-5] 5.0 ^5.1 RefSeq (December 2016). "ZNF174 zinc finger protein 174 [ Homo sapiens (human) ]". U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information. Retrieved 19 December 2019.

[Gebali-6] 6.0 ^6.1 ^6.2 ^6.3 S. El-Gebali, J. Mistry, A. Bateman, S.R. Eddy, A. Luciani, S.C. Potter, M. Qureshi, L.J. Richardson, G.A. Salazar, A. Smart, E.L.L. Sonnhammer, L. Hirsh, L. Paladin, D. Piovesan, S.C.E. Tosatto, R.D. Finn (September 2018). "Pfam 32.0 (September 2018, 17929 entries)". Meyerhofstraße 1 69117 Heidelberg, Germany: European Molecular Biology Laboratory (EMBL). Retrieved 19 December 2019.

[Boehm-7] S Boehm, D Frishman and HW Mewes (June 1997). "Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins" (PDF). Nucleic Acids Research. 25 (12): 2464–9. doi:10.1093/nar/25.12.2464. PMID 9171100. Retrieved 19 December 2019.

[1]

[2]

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[7]

@@ Line 37: / Line 37: @@
 ==AW-1==
+AW-1 is ZNF174.<ref name=Edelstein>{{ cite journal
+|author=Leonard C. Edelstein and Tucker Collins
+|title=The SCAN domain family of zinc finger transcription factors
+|journal=Gene
+|date=10 October 2005
+|volume=359
+|issue=
+|pages=1-17
+|url=https://www.sciencedirect.com/science/article/abs/pii/S0378111905003653
+|arxiv=
+|bibcode=
+|doi=10.1016/j.gene.2005.06.022
+|pmid=
+|accessdate=19 December 2019 }}</ref>
+Gene ID: 7727 is ZNF174 zinc finger protein 174. "This gene encodes a protein with three Cys2-His2-type zinc fingers in the carboxy-terminus, a putative nuclear localization signal, and an amino-terminus SCAN box which forms homodimers. This protein is believed to function as a transcriptional repressor. Alternative splicing results in multiple transcript variants encoding distinct isoforms."<ref name=RefSeq2016>{{ cite web
+|author=RefSeq
+|title=ZNF174 zinc finger protein 174 [ Homo sapiens (human) ]
+|publisher=National Center for Biotechnology Information
+|location=U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda MD, 20894 USA
+|date=December 2016
+|url=https://www.ncbi.nlm.nih.gov/gene/7727
+|accessdate=19 December 2019 }}</ref> Aka AW-1 and zinc finger and SCAN domain-containing protein 8.<ref name=RefSeq2016/>
 ==Number 18 cDNA==

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transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions 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