1va3

From Proteopedia

(Difference between revisions)

Current revision

Solution Structure of Transcription Factor Sp1 DNA Binding Domain (Zinc Finger 3)

Structural highlights

1va3 is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SP1_HUMAN Transcription factor that can activate or repress transcription in response to physiological and pathological stimuli. Binds with high affinity to GC-rich motifs and regulates the expression of a large number of genes involved in a variety of processes such as cell growth, apoptosis, differentiation and immune responses. Highly regulated by post-translational modifications (phosphorylations, sumoylation, proteolytic cleavage, glycosylation and acetylation). Binds also the PDGFR-alpha G-box promoter. May have a role in modulating the cellular response to DNA damage. Implicated in chromatin remodeling. Plays a role in the recruitment of SMARCA4/BRG1 on the c-FOS promoter. Plays an essential role in the regulation of FE65 gene expression. In complex with ATF7IP, maintains telomerase activity in cancer cells by inducing TERT and TERC gene expression.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15]

Publication Abstract from PubMed

To understand the DNA recognition mechanism of zinc finger motifs of transcription factor Sp1, we have determined the solution structure of DNA-binding domain of the Sp1 by solution NMR techniques. The DNA-binding domain of Sp1 consists of three Cys(2)His(2)-type zinc finger motifs. They have typical betabetaalpha zinc finger folds and relatively random orientations. From DNA-binding analysis performed by NMR and comparison between structures determined here and previously reported structures of other zinc fingers, it was assumed that DNA recognition modes of fingers 2 and 3 would be similar to those of fingers of Zif268, in which each finger recognizes four base pairs strictly by using residues at positions -1, 2, 3, and 6 of the recognition helix. On the contrary, finger 1 can use only two residues for DNA recognition, Lys550 and His553 at positions -1 and 3 of the helix, and has more relaxed sequence and site specificity than other Cys(2)His(2) zinc fingers. It is proposed that this relaxed property of finger 1 allows transcription factor Sp1 to bind various DNA sequences with high affinity.

NMR structure of transcription factor Sp1 DNA binding domain.,Oka S, Shiraishi Y, Yoshida T, Ohkubo T, Sugiura Y, Kobayashi Y Biochemistry. 2004 Dec 28;43(51):16027-35. PMID:15609997^[16]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ding H, Benotmane AM, Suske G, Collen D, Belayew A. Functional interactions between Sp1 or Sp3 and the helicase-like transcription factor mediate basal expression from the human plasminogen activator inhibitor-1 gene. J Biol Chem. 1999 Jul 9;274(28):19573-80. PMID:10391891
↑ Yang X, Su K, Roos MD, Chang Q, Paterson AJ, Kudlow JE. O-linkage of N-acetylglucosamine to Sp1 activation domain inhibits its transcriptional capability. Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6611-6. Epub 2001 May 22. PMID:11371615 doi:http://dx.doi.org/10.1073/pnas.111099998
↑ Milanini-Mongiat J, Pouyssegur J, Pages G. Identification of two Sp1 phosphorylation sites for p42/p44 mitogen-activated protein kinases: their implication in vascular endothelial growth factor gene transcription. J Biol Chem. 2002 Jun 7;277(23):20631-9. Epub 2002 Mar 19. PMID:11904305 doi:http://dx.doi.org/10.1074/jbc.M201753200
↑ Bonello MR, Khachigian LM. Fibroblast growth factor-2 represses platelet-derived growth factor receptor-alpha (PDGFR-alpha) transcription via ERK1/2-dependent Sp1 phosphorylation and an atypical cis-acting element in the proximal PDGFR-alpha promoter. J Biol Chem. 2004 Jan 23;279(4):2377-82. Epub 2003 Oct 30. PMID:14593115 doi:http://dx.doi.org/10.1074/jbc.M308254200
↑ Hsu MC, Chang HC, Hung WC. HER-2/neu represses the metastasis suppressor RECK via ERK and Sp transcription factors to promote cell invasion. J Biol Chem. 2006 Feb 24;281(8):4718-25. Epub 2005 Dec 23. PMID:16377629 doi:http://dx.doi.org/10.1074/jbc.M510937200
↑ Vicart A, Lefebvre T, Imbert J, Fernandez A, Kahn-Perles B. Increased chromatin association of Sp1 in interphase cells by PP2A-mediated dephosphorylations. J Mol Biol. 2006 Dec 15;364(5):897-908. Epub 2006 Sep 16. PMID:17049555 doi:http://dx.doi.org/10.1016/j.jmb.2006.09.036
↑ Hung JJ, Wang YT, Chang WC. Sp1 deacetylation induced by phorbol ester recruits p300 to activate 12(S)-lipoxygenase gene transcription. Mol Cell Biol. 2006 Mar;26(5):1770-85. PMID:16478997 doi:http://dx.doi.org/10.1128/MCB.26.5.1770-1785.2006
↑ Zhang Y, Liao M, Dufau ML. Phosphatidylinositol 3-kinase/protein kinase Czeta-induced phosphorylation of Sp1 and p107 repressor release have a critical role in histone deacetylase inhibitor-mediated derepression [corrected] of transcription of the luteinizing hormone receptor gene. Mol Cell Biol. 2006 Sep;26(18):6748-61. PMID:16943418 doi:http://dx.doi.org/10.1128/MCB.00560-06
↑ Olofsson BA, Kelly CM, Kim J, Hornsby SM, Azizkhan-Clifford J. Phosphorylation of Sp1 in response to DNA damage by ataxia telangiectasia-mutated kinase. Mol Cancer Res. 2007 Dec;5(12):1319-30. doi: 10.1158/1541-7786.MCR-07-0374. PMID:18171990 doi:http://dx.doi.org/10.1158/1541-7786.MCR-07-0374
↑ Chung SS, Kim JH, Park HS, Choi HH, Lee KW, Cho YM, Lee HK, Park KS. Activation of PPARgamma negatively regulates O-GlcNAcylation of Sp1. Biochem Biophys Res Commun. 2008 Aug 8;372(4):713-8. doi:, 10.1016/j.bbrc.2008.05.096. Epub 2008 May 28. PMID:18513490 doi:http://dx.doi.org/10.1016/j.bbrc.2008.05.096
↑ Spengler ML, Guo LW, Brattain MG. Phosphorylation mediates Sp1 coupled activities of proteolytic processing, desumoylation and degradation. Cell Cycle. 2008 Mar 1;7(5):623-30. Epub 2007 Dec 4. PMID:18239466
↑ Iwahori S, Yasui Y, Kudoh A, Sato Y, Nakayama S, Murata T, Isomura H, Tsurumi T. Identification of phosphorylation sites on transcription factor Sp1 in response to DNA damage and its accumulation at damaged sites. Cell Signal. 2008 Oct;20(10):1795-803. doi: 10.1016/j.cellsig.2008.06.007. Epub, 2008 Jun 19. PMID:18619531 doi:http://dx.doi.org/10.1016/j.cellsig.2008.06.007
↑ Chuang JY, Wang YT, Yeh SH, Liu YW, Chang WC, Hung JJ. Phosphorylation by c-Jun NH2-terminal kinase 1 regulates the stability of transcription factor Sp1 during mitosis. Mol Biol Cell. 2008 Mar;19(3):1139-51. doi: 10.1091/mbc.E07-09-0881. Epub 2008, Jan 16. PMID:18199680 doi:http://dx.doi.org/10.1091/mbc.E07-09-0881
↑ Jochmann R, Thurau M, Jung S, Hofmann C, Naschberger E, Kremmer E, Harrer T, Miller M, Schaft N, Sturzl M. O-linked N-acetylglucosaminylation of Sp1 inhibits the human immunodeficiency virus type 1 promoter. J Virol. 2009 Apr;83(8):3704-18. doi: 10.1128/JVI.01384-08. Epub 2009 Feb 4. PMID:19193796 doi:http://dx.doi.org/10.1128/JVI.01384-08
↑ Yu HT, Chan WW, Chai KH, Lee CW, Chang RC, Yu MS, McLoughlin DM, Miller CC, Lau KF. Transcriptional regulation of human FE65, a ligand of Alzheimer's disease amyloid precursor protein, by Sp1. J Cell Biochem. 2010 Mar 1;109(4):782-93. doi: 10.1002/jcb.22457. PMID:20091743 doi:http://dx.doi.org/10.1002/jcb.22457
↑ Oka S, Shiraishi Y, Yoshida T, Ohkubo T, Sugiura Y, Kobayashi Y. NMR structure of transcription factor Sp1 DNA binding domain. Biochemistry. 2004 Dec 28;43(51):16027-35. PMID:15609997 doi:10.1021/bi048438p

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1va3"

@@ Line 1: / Line 1: @@
 ==Solution Structure of Transcription Factor Sp1 DNA Binding Domain (Zinc Finger 3)==
-<StructureSection load='1va3' size='340' side='right' caption='[[1va3]], [[NMR_Ensembles_of_Models | 31 NMR models]]' scene=''>
+<StructureSection load='1va3' size='340' side='right'caption='[[1va3]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1va3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VA3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VA3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1va3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VA3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1va1|1va1]], [[1va2|1va2]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1va3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1va3 OCA], [https://pdbe.org/1va3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1va3 RCSB], [https://www.ebi.ac.uk/pdbsum/1va3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1va3 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1va3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1va3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1va3 RCSB], [http://www.ebi.ac.uk/pdbsum/1va3 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SP1_HUMAN SP1_HUMAN]] Transcription factor that can activate or repress transcription in response to physiological and pathological stimuli. Binds with high affinity to GC-rich motifs and regulates the expression of a large number of genes involved in a variety of processes such as cell growth, apoptosis, differentiation and immune responses. Highly regulated by post-translational modifications (phosphorylations, sumoylation, proteolytic cleavage, glycosylation and acetylation). Binds also the PDGFR-alpha G-box promoter. May have a role in modulating the cellular response to DNA damage. Implicated in chromatin remodeling. Plays a role in the recruitment of SMARCA4/BRG1 on the c-FOS promoter. Plays an essential role in the regulation of FE65 gene expression. In complex with ATF7IP, maintains telomerase activity in cancer cells by inducing TERT and TERC gene expression.<ref>PMID:10391891</ref> <ref>PMID:11371615</ref> <ref>PMID:11904305</ref> <ref>PMID:14593115</ref> <ref>PMID:16377629</ref> <ref>PMID:17049555</ref> <ref>PMID:16478997</ref> <ref>PMID:16943418</ref> <ref>PMID:18171990</ref> <ref>PMID:18513490</ref> <ref>PMID:18239466</ref> <ref>PMID:18619531</ref> <ref>PMID:18199680</ref> <ref>PMID:19193796</ref> <ref>PMID:20091743</ref>
+[https://www.uniprot.org/uniprot/SP1_HUMAN SP1_HUMAN] Transcription factor that can activate or repress transcription in response to physiological and pathological stimuli. Binds with high affinity to GC-rich motifs and regulates the expression of a large number of genes involved in a variety of processes such as cell growth, apoptosis, differentiation and immune responses. Highly regulated by post-translational modifications (phosphorylations, sumoylation, proteolytic cleavage, glycosylation and acetylation). Binds also the PDGFR-alpha G-box promoter. May have a role in modulating the cellular response to DNA damage. Implicated in chromatin remodeling. Plays a role in the recruitment of SMARCA4/BRG1 on the c-FOS promoter. Plays an essential role in the regulation of FE65 gene expression. In complex with ATF7IP, maintains telomerase activity in cancer cells by inducing TERT and TERC gene expression.<ref>PMID:10391891</ref> <ref>PMID:11371615</ref> <ref>PMID:11904305</ref> <ref>PMID:14593115</ref> <ref>PMID:16377629</ref> <ref>PMID:17049555</ref> <ref>PMID:16478997</ref> <ref>PMID:16943418</ref> <ref>PMID:18171990</ref> <ref>PMID:18513490</ref> <ref>PMID:18239466</ref> <ref>PMID:18619531</ref> <ref>PMID:18199680</ref> <ref>PMID:19193796</ref> <ref>PMID:20091743</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1va3" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 23: / Line 24: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Kobayashi, Y]]
+[[Category: Large Structures]]
-[[Category: Ohkubo, T]]
+[[Category: Kobayashi Y]]
-[[Category: Oka, S]]
+[[Category: Ohkubo T]]
-[[Category: Shiraishi, Y]]
+[[Category: Oka S]]
-[[Category: Sugiura, Y]]
+[[Category: Shiraishi Y]]
-[[Category: Yoshida, T]]
+[[Category: Sugiura Y]]
-[[Category: C2h2 type zinc finger]]
+[[Category: Yoshida T]]
-[[Category: Dna-binding protein]]
-[[Category: Transcription]]
-[[Category: Transcription factor]]

1va3

From Proteopedia

Current revision

Solution Structure of Transcription Factor Sp1 DNA Binding Domain (Zinc Finger 3)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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