PDBsum entry 1sp1

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protein metals links
Zinc finger PDB id
Protein chain
29 a.a.
PDB id:
Name: Zinc finger
Title: Nmr structure of a zinc finger domain from transcription factor sp1f3, minimized average structure
Structure: Sp1f3. Chain: a. Fragment: zinc finger DNA binding domain. Synonym: transcription factor sp1. Engineered: yes. Other_details: does not bind DNA specifically as a single zinc finger
Source: Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: nucleoplasm
NMR struc: 1 models
Authors: V.A.Narayan,R.W.Kriwacki,J.P.Caradonna
Key ref:
V.A.Narayan et al. (1997). Structures of zinc finger domains from transcription factor Sp1. Insights into sequence-specific protein-DNA recognition. J Biol Chem, 272, 7801-7809. PubMed id: 9065444 DOI: 10.1074/jbc.272.12.7801
21-Nov-96     Release date:   21-Apr-97    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P08047  (SP1_HUMAN) -  Transcription factor Sp1
785 a.a.
29 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: 10.1074/jbc.272.12.7801 J Biol Chem 272:7801-7809 (1997)
PubMed id: 9065444  
Structures of zinc finger domains from transcription factor Sp1. Insights into sequence-specific protein-DNA recognition.
V.A.Narayan, R.W.Kriwacki, J.P.Caradonna.
The carboxyl terminus of transcription factor Sp1 contains three contiguous Cys2-His2 zinc finger domains with the consensus sequence Cys-X2-4-Cys-X12-His-X3-His. We have used standard homonuclear two-dimensional NMR techniques to solve the solution structures of synthetic peptides corresponding to the last two zinc finger domains (Sp1f2 and Sp1f3, respectively) of Sp1. Our studies indicate a classical Cys2-His2 type fold for both the domains differing from each other primarily in the conformation of Cys-X2-Cys (beta-type I turn) and Cys-X4-Cys (beta-type II turn) elements. There are, however, no significant differences in the metal binding properties between the Cys-X4-Cys (Sp1f2) and Cys-X2-Cys (Sp1f3) subclasses of zinc fingers. The free solution structures of Sp1f2 and Sp1f3 are very similar to those of the analogous fingers of Zif268 bound to DNA. There is NMR spectral evidence suggesting that the Arg-Asp buttressing interaction observed in the Zif-268.DNA complex is also preserved in unbound Sp1f2 and Sp1f3. Modeling Sp1-DNA complex by overlaying the Sp1f2 and Sp1f3 structures on Zif268 fingers 1 and 2, respectively, predicts the role of key amino acid residues, the interference/protection data, and supports the model of Sp1-DNA interaction proposed earlier.
  Selected figure(s)  
Figure 8.
Fig. 8. Summary of proposed DNA contacts between Sp1f2 and Sp1f3 with their respective 3-base pair subsites. The proposed amino acid-DNA base contacts are shown by a solid line. The other probable^ amino acid-DNA base interactions within the framework are indicated^ by dotted lines. Note the antiparallel orientation of peptide^ and DNA and absence of any direct contacts with the other C-rich strand of DNA duplex (not shown).
Figure 9.
Fig. 9. A, stereo presentation of the superposition of Sp1f2·avg·min (see "Experimental Procedures") and Zif268 finger 1. Residues 3-27 (excluding the loop between the two Cys residues) of Sp1f2·min·avg (dark) were superimposed on the corresponding residues of Zif268^ finger 1 (light). B, stereo presentation of the superposition of Sp1f3·avg·min (see "Experimental Procedures") and Zif268 finger 2. Residues 3-25 (excluding Pro9) of Sp1f3·min·avg (dark) were superimposed on the corresponding residues of Zif268 finger 2 (light).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1997, 272, 7801-7809) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20953893 E.A.Alemu, E.Sjøttem, H.Outzen, K.B.Larsen, T.Holm, G.Bjørkøy, and T.Johansen (2011).
Transforming growth factor-β-inducible early response gene 1 is a novel substrate for atypical protein kinase Cs.
  Cell Mol Life Sci, 68, 1953-1968.  
20439749 G.Y.Li, R.D.McCulloch, A.L.Fenton, M.Cheung, L.Meng, M.Ikura, and C.A.Koch (2010).
Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response.
  Proc Natl Acad Sci U S A, 107, 9129-9134.  
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.  
21152317 S.Chang, X.Jiao, J.P.Hu, Y.Chen, and X.H.Tian (2010).
Stability and folding behavior analysis of zinc-finger using simple models.
  Int J Mol Sci, 11, 4014-4034.  
19879314 Y.Zhao, L.Chen, S.Gao, P.Toselli, P.Stone, and W.Li (2010).
The critical role of the cellular thiol homeostasis in cadmium perturbation of the lung extracellular matrix.
  Toxicology, 267, 60-69.  
19292861 M.Araki, and A.Tamura (2009).
Solubility-dependent structural formation of a 25-residue, natively unfolded protein, induced by addition of a seven-residue peptide fragment.
  FEBS J, 276, 2336-2347.
PDB code: 2kfq
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.  
18632871 S.S.Tungteakkhun, M.Filippova, J.W.Neidigh, N.Fodor, and P.J.Duerksen-Hughes (2008).
The interaction between human papillomavirus type 16 and FADD is mediated by a novel E6 binding domain.
  J Virol, 82, 9600-9614.  
16402211 J.Miertus, W.Borozdin, V.Frecer, G.Tonini, S.Bertok, A.Amoroso, S.Miertus, and J.Kohlhase (2006).
A SALL4 zinc finger missense mutation predicted to result in increased DNA binding affinity is associated with cranial midline defects and mild features of Okihiro syndrome.
  Hum Genet, 119, 154-161.  
15523672 A.Al-Sarraj, R.M.Day, and G.Thiel (2005).
Specificity of transcriptional regulation by the zinc finger transcription factors Sp1, Sp3, and Egr-1.
  J Cell Biochem, 94, 153-167.  
15533246 M.A.Milona, J.E.Gough, and A.J.Edgar (2004).
Genomic structure and cloning of two transcript isoforms of human Sp8.
  BMC Genomics, 5, 86.  
12620113 J.Kaczynski, T.Cook, and R.Urrutia (2003).
Sp1- and Krüppel-like transcription factors.
  Genome Biol, 4, 206.  
14604442 M.A.Milona, J.E.Gough, and A.J.Edgar (2003).
Expression of alternatively spliced isoforms of human Sp7 in osteoblast-like cells.
  BMC Genomics, 4, 43.  
11742346 G.Polekhina, C.M.House, N.Traficante, J.P.Mackay, F.Relaix, D.A.Sassoon, M.W.Parker, and D.D.Bowtell (2002).
Siah ubiquitin ligase is structurally related to TRAF and modulates TNF-alpha signaling.
  Nat Struct Biol, 9, 68-75.
PDB code: 1k2f
11258905 M.Nagaoka, T.Kaji, M.Imanishi, Y.Hori, W.Nomura, and Y.Sugiura (2001).
Multiconnection of identical zinc finger: implication for DNA binding affinity and unit modulation of the three zinc finger domain.
  Biochemistry, 40, 2932-2941.  
11041860 J.S.You, M.Wang, and S.H.Lee (2000).
Functional characterization of zinc-finger motif in redox regulation of RPA-ssDNA interaction.
  Biochemistry, 39, 12953-12958.  
10799645 T.D.Stephens, C.J.Bunde, and B.J.Fillmore (2000).
Mechanism of action in thalidomide teratogenesis.
  Biochem Pharmacol, 59, 1489-1499.  
10077584 D.J.Segal, B.Dreier, R.R.Beerli, and C.F.Barbas (1999).
Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences.
  Proc Natl Acad Sci U S A, 96, 2758-2763.  
9578568 M.Yokono, N.Saegusa, K.Matsushita, and Y.Sugiura (1998).
Unique DNA binding mode of the N-terminal zinc finger of transcription factor Sp1.
  Biochemistry, 37, 6824-6832.  
  9744863 N.Gillemans, R.Tewari, F.Lindeboom, R.Rottier, Wit, M.Wijgerde, F.Grosveld, and S.Philipsen (1998).
Altered DNA-binding specificity mutants of EKLF and Sp1 show that EKLF is an activator of the beta-globin locus control region in vivo.
  Genes Dev, 12, 2863-2873.  
9519295 S.Tan, and T.J.Richmond (1998).
Eukaryotic transcription factors.
  Curr Opin Struct Biol, 8, 41-48.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.