PDBsum entry 1va2

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protein metals links
Transcription PDB id
Protein chain
31 a.a. *
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Solution structure of transcription factor sp1 DNA binding domain (zinc finger 2)
Structure: Transcription factor sp1. Chain: a. Fragment: zinc finger 2. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sp1. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 31 models
Authors: S.Oka,Y.Shiraishi,T.Yoshida,T.Ohkubo,Y.Sugiura,Y.Kobayashi
Key ref:
S.Oka et al. (2004). NMR structure of transcription factor Sp1 DNA binding domain. Biochemistry, 43, 16027-16035. PubMed id: 15609997 DOI: 10.1021/bi048438p
07-Feb-04     Release date:   08-Feb-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P08047  (SP1_HUMAN) -  Transcription factor Sp1
785 a.a.
31 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription from RNA polymerase II promoter   1 term 
  Biochemical function     nucleic acid binding     3 terms  


DOI no: 10.1021/bi048438p Biochemistry 43:16027-16035 (2004)
PubMed id: 15609997  
NMR structure of transcription factor Sp1 DNA binding domain.
S.Oka, Y.Shiraishi, T.Yoshida, T.Ohkubo, Y.Sugiura, Y.Kobayashi.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20565873 C.C.Chou, M.Rajasekaran, and C.Chen (2010).
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking.
  BMC Bioinformatics, 11, 334.  
20074339 J.E.Reid, K.J.Evans, N.Dyer, L.Wernisch, and S.Ott (2010).
Variable structure motifs for transcription factor binding sites.
  BMC Genomics, 11, 30.  
20060848 R.K.Kothinti, A.B.Blodgett, D.H.Petering, and N.M.Tabatabai (2010).
Cadmium down-regulation of kidney Sp1 binding to mouse SGLT1 and SGLT2 gene promoters: possible reaction of cadmium with the zinc finger domain of Sp1.
  Toxicol Appl Pharmacol, 244, 254-262.  
20073493 R.Kothinti, A.Blodgett, N.M.Tabatabai, and D.H.Petering (2010).
Zinc finger transcription factor Zn3-Sp1 reactions with Cd2+.
  Chem Res Toxicol, 23, 405-412.  
19319441 A.Nomura, and A.Okamoto (2009).
Photoresponsive tandem zinc finger peptide.
  Chem Commun (Camb), (), 1906-1908.  
19723341 X.Zu, L.Yu, Q.Sun, F.Liu, J.Wang, Z.Xie, Y.Wang, W.Xu, and Y.Jiang (2009).
SP1 enhances Zbtb7A gene expression via direct binding to GC box in HePG2 cells.
  BMC Res Notes, 2, 175.  
18648687 A.I.Anzellotti, and N.P.Farrell (2008).
Zinc metalloproteins as medicinal targets.
  Chem Soc Rev, 37, 1629-1651.  
18171589 U.Rana, R.Kothinti, J.Meeusen, N.M.Tabatabai, S.Krezoski, and D.H.Petering (2008).
Zinc binding ligands and cellular zinc trafficking: apo-metallothionein, glutathione, TPEN, proteomic zinc, and Zn-Sp1.
  J Inorg Biochem, 102, 489-499.  
18502777 Y.Osawa, K.Ikebukuro, H.Motoki, T.Matsuo, M.Horiuchi, and K.Sode (2008).
The simple and rapid detection of specific PCR products from bacterial genomes using Zn finger proteins.
  Nucleic Acids Res, 36, e68.  
17069580 J.R.Keys, M.R.Tallack, D.J.Hodge, S.O.Cridland, R.David, and A.C.Perkins (2007).
Genomic organisation and regulation of murine alpha haemoglobin stabilising protein by erythroid Kruppel-like factor.
  Br J Haematol, 136, 150-157.  
17925037 S.J.Bruce, B.B.Gardiner, L.J.Burke, M.M.Gongora, S.M.Grimmond, and A.C.Perkins (2007).
Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeBMP4 culture.
  BMC Genomics, 8, 365.  
16705186 A.M.Pilon, D.G.Nilson, D.Zhou, J.Sangerman, T.M.Townes, D.M.Bodine, and P.G.Gallagher (2006).
Alterations in expression and chromatin configuration of the alpha hemoglobin-stabilizing protein gene in erythroid Kruppel-like factor-deficient mice.
  Mol Cell Biol, 26, 4368-4377.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.