spacer
spacer

PDBsum entry 1zfd

Go to PDB code: 
protein metals links
Zinc finger DNA binding domain PDB id
1zfd
Jmol
Contents
Protein chain
32 a.a. *
Metals
_ZN
* Residue conservation analysis
PDB id:
1zfd
Name: Zinc finger DNA binding domain
Title: Swi5 zinc finger domain 2, nmr, 45 structures
Structure: Swi5. Chain: a. Fragment: zinc finger domain 2. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: t7 promoter
NMR struc: 45 models
Authors: D.Neuhaus,Y.Nakaseko,J.W.R.Schwabe,D.Rhodes,A.Klug
Key ref:
D.Neuhaus et al. (1992). Solution structures of two zinc-finger domains from SWI5 obtained using two-dimensional 1H nuclear magnetic resonance spectroscopy. A zinc-finger structure with a third strand of beta-sheet. J Mol Biol, 228, 637-651. PubMed id: 1453468 DOI: 10.1016/0022-2836(92)90846-C
Date:
04-Apr-96     Release date:   14-Oct-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08153  (SWI5_YEAST) -  Transcriptional factor SWI5
Seq:
Struc:
 
Seq:
Struc:
709 a.a.
32 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     2 terms  

 

 
DOI no: 10.1016/0022-2836(92)90846-C J Mol Biol 228:637-651 (1992)
PubMed id: 1453468  
 
 
Solution structures of two zinc-finger domains from SWI5 obtained using two-dimensional 1H nuclear magnetic resonance spectroscopy. A zinc-finger structure with a third strand of beta-sheet.
D.Neuhaus, Y.Nakaseko, J.W.Schwabe, A.Klug.
 
  ABSTRACT  
 
This paper describes the detailed three-dimensional structures of two zinc-finger domains from the yeast transcription factor SWI5, calculated using the results of the n.m.r. experiments described in the accompanying paper. The structure of finger 2 is essentially similar to those previously obtained by others for isolated, synthetic single zinc-finger domains in solution, and for the three zinc-finger peptide Zif268 in its crystalline complex with DNA. The N-terminal half of the sequence forms a two-stranded, irregular beta-sheet containing both of the metal-binding cysteine residues, while the remainder of the structure forms a helix. Approximately the first half of this helix is alpha-helical, whereas the C-terminal portion, including the two metal-binding histidine residues, is 3(10) helical. Four invariant hydrophobic residues form a core to the structure. In contrast to all previously described structures of zinc-finger domains, finger 1 has an additional strand in the beta-sheet, formed by residues N-terminal to the formal start of the finger motif. This additional strand plays a role in stabilising the folded form of finger 1, since a two-finger peptide lacking the N-terminal residues showed folded structure in finger 2 but not in finger 1.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Schematic representation of the structures of ingers 1 panels and B) and 2 (panels C and D) from SW15, prepared using the program Molscript (Kraulis, 1991). In each case, the structure having the lowest NOE violations is shown. iews A and C are related to views B and D by a 90'' rotation bout the vertical. In addition to the schematic representtion of the backbone, bonds are shown between the non-hydrogen atoms of the side-chains of the metal binding an conserved hydrophobic residues, nd these rsidues are labelled (not that, because the arrows representing the /3sheet do not necessarily pass through the actual c'' atom positions, the C''-CB bonds of some side-chains have been extended with broken lines so as to meet the bacbone representation artificially).
Figure 6.
Figure 6. Stereoview of a local ackbone superimposition in the turn regio (Cvs44 to Cys49) between the two P-strands of fingr 2 of SWIS; as in Fig. 3,45 structures are shown. Atoms Nj: NH, C'', e and 0' re shown for all residues, tog&her with the zinc ions and he non-hydrogen side-chain atoms of Cys44, Pro47 and Cys49. The conformation is clearly that of tpe II p-turn, characterized by the hydrogen bond between His46 C = 0 and Cys49 ?u'H (indicated hy the broken line) and by the relative orientation of the Pro47-Gly48 peptide bond.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1992, 228, 637-651) copyright 1992.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22157959 F.E.Loughlin, L.F.Gebert, H.Towbin, A.Brunschweiger, J.Hall, and F.H.Allain (2012).
Structural basis of pre-let-7 miRNA recognition by the zinc knuckles of pluripotency factor Lin28.
  Nat Struct Mol Biol, 19, 84-89.
PDB code: 2li8
20478078 A.Klug (2010).
The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation.
  Q Rev Biophys, 43, 1.  
20192761 A.Klug (2010).
The discovery of zinc fingers and their applications in gene regulation and genome manipulation.
  Annu Rev Biochem, 79, 213-231.  
18073212 R.Gamsjaeger, M.K.Swanton, F.J.Kobus, E.Lehtomaki, J.A.Lowry, A.H.Kwan, J.M.Matthews, and J.P.Mackay (2008).
Structural and biophysical analysis of the DNA binding properties of myelin transcription factor 1.
  J Biol Chem, 283, 5158-5167.
PDB code: 2jyd
17360614 S.A.Beasley, V.A.Hristova, and G.S.Shaw (2007).
Structure of the Parkin in-between-ring domain provides insights for E3-ligase dysfunction in autosomal recessive Parkinson's disease.
  Proc Natl Acad Sci U S A, 104, 3095-3100.
PDB code: 2jmo
14978306 P.Gutiérrez, M.J.Osborne, N.Siddiqui, J.F.Trempe, C.Arrowsmith, and K.Gehring (2004).
Structure of the archaeal translation initiation factor aIF2 beta from Methanobacterium thermoautotrophicum: implications for translation initiation.
  Protein Sci, 13, 659-667.
PDB code: 1nee
15234987 R.J.Simpson, S.H.Yi Lee, N.Bartle, E.Y.Sum, J.E.Visvader, J.M.Matthews, J.P.Mackay, and M.Crossley (2004).
A classic zinc finger from friend of GATA mediates an interaction with the coiled-coil of transforming acidic coiled-coil 3.
  J Biol Chem, 279, 39789-39797.
PDB code: 1srk
12842043 A.H.Kwan, D.A.Gell, A.Verger, M.Crossley, J.M.Matthews, and J.P.Mackay (2003).
Engineering a protein scaffold from a PHD finger.
  Structure, 11, 803-813.
PDB codes: 1mm2 1mm3
12657633 C.A.Plambeck, A.H.Kwan, D.J.Adams, B.J.Westman, L.van der Weyden, R.L.Medcalf, B.J.Morris, and J.P.Mackay (2003).
The structure of the zinc finger domain from human splicing factor ZNF265 fold.
  J Biol Chem, 278, 22805-22811.
PDB code: 1n0z
12654914 K.Kwon, C.Cao, and J.T.Stivers (2003).
A novel zinc snap motif conveys structural stability to 3-methyladenine DNA glycosylase I.
  J Biol Chem, 278, 19442-19446.
PDB code: 1nku
12736264 R.J.Simpson, E.D.Cram, R.Czolij, J.M.Matthews, M.Crossley, and J.P.Mackay (2003).
CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions.
  J Biol Chem, 278, 28011-28018.
PDB code: 1p7a
11226167 A.D.Capili, D.C.Schultz, F.J.RauscherIII, and K.L.Borden (2001).
Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains.
  EMBO J, 20, 165-177.
PDB code: 1fp0
11179890 J.H.Laity, B.M.Lee, and P.E.Wright (2001).
Zinc finger proteins: new insights into structural and functional diversity.
  Curr Opin Struct Biol, 11, 39-46.  
11018257 I.W.Manfield, L.A.Reynolds, J.Gittins, and G.G.Kneale (2000).
The DNA-binding domain of the gene regulatory protein AreA extends beyond the minimal zinc-finger region conserved between GATA proteins.
  Biochim Biophys Acta, 1493, 325-332.  
10672011 J.M.Matthews, K.Kowalski, C.K.Liew, B.K.Sharpe, A.H.Fox, M.Crossley, and J.P.MacKay (2000).
A class of zinc fingers involved in protein-protein interactions biophysical characterization of CCHC fingers from fog and U-shaped.
  Eur J Biochem, 267, 1030-1038.  
10940247 S.A.Wolfe, L.Nekludova, and C.O.Pabo (2000).
DNA recognition by Cys2His2 zinc finger proteins.
  Annu Rev Biophys Biomol Struct, 29, 183-212.  
10228174 C.M.Fletcher, T.V.Pestova, C.U.Hellen, and G.Wagner (1999).
Structure and interactions of the translation initiation factor eIF1.
  EMBO J, 18, 2631-2637.
PDB code: 2if1
9705310 F.W.Muskett, T.A.Frenkiel, J.Feeney, R.B.Freedman, M.D.Carr, and R.A.Williamson (1998).
High resolution structure of the N-terminal domain of tissue inhibitor of metalloproteinases-2 and characterization of its interaction site with matrix metalloproteinase-3.
  J Biol Chem, 273, 21736-21743.
PDB code: 2tmp
  9774660 L.T.Bhoite, and D.J.Stillman (1998).
Residues in the Swi5 zinc finger protein that mediate cooperative DNA binding with the Pho2 homeodomain protein.
  Mol Cell Biol, 18, 6436-6446.  
9698361 X.Chen, A.Agarwal, and D.P.Giedroc (1998).
Structural and functional heterogeneity among the zinc fingers of human MRE-binding transcription factor-1.
  Biochemistry, 37, 11152-11161.  
  9300483 M.Schmiedeskamp, P.Rajagopal, and R.E.Klevit (1997).
NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1.
  Protein Sci, 6, 1835-1848.  
9369471 M.Schmiedeskamp, and R.E.Klevit (1997).
Paramagnetic cobalt as a probe of the orientation of an accessory DNA-binding region of the yeast ADR1 zinc-finger protein.
  Biochemistry, 36, 14003-14011.  
8610125 P.V.Pedone, R.Ghirlando, G.M.Clore, A.M.Gronenborn, G.Felsenfeld, and J.G.Omichinski (1996).
The single Cys2-His2 zinc finger domain of the GAGA protein flanked by basic residues is sufficient for high-affinity specific DNA binding.
  Proc Natl Acad Sci U S A, 93, 2822-2826.  
8736557 R.N.Dutnall, D.Neuhaus, and D.Rhodes (1996).
The solution structure of the first zinc finger domain of SWI5: a novel structural extension to a common fold.
  Structure, 4, 599-611.
PDB code: 1ncs
7625690 A.Klug (1995).
Gene regulatory proteins and their interaction with DNA.
  Ann N Y Acad Sci, 758, 143-160.  
  8846787 K.L.Borden, J.M.Lally, S.R.Martin, N.J.O'Reilly, L.D.Etkin, and P.S.Freemont (1995).
Novel topology of a zinc-binding domain from a protein involved in regulating early Xenopus development.
  EMBO J, 14, 5947-5956.
PDB code: 1fre
  7729428 K.L.Borden, M.N.Boddy, J.Lally, N.J.O'Reilly, S.Martin, K.Howe, E.Solomon, and P.S.Freemont (1995).
The solution structure of the RING finger domain from the acute promyelocytic leukaemia proto-oncoprotein PML.
  EMBO J, 14, 1532-1541.
PDB code: 1bor
8750235 V.V.Svetlov, and T.G.Cooper (1995).
Review: compilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae.
  Yeast, 11, 1439-1484.  
8092710 B.E.Bernstein, R.C.Hoffman, and R.E.Klevit (1994).
Sequence-specific DNA recognition by Cys2, His2 zinc fingers.
  Ann N Y Acad Sci, 726, 92.  
7520819 C.M.Fletcher, R.A.Harrison, P.J.Lachmann, and D.Neuhaus (1994).
Structure of a soluble, glycosylated form of the human complement regulatory protein CD59.
  Structure, 2, 185-199.
PDB codes: 1cdq 1cdr 1cds
7922039 D.N.Jones, M.A.Searles, G.L.Shaw, M.E.Churchill, S.S.Ner, J.Keeler, A.A.Travers, and D.Neuhaus (1994).
The solution structure and dynamics of the DNA-binding domain of HMG-D from Drosophila melanogaster.
  Structure, 2, 609-627.
PDB code: 1hma
8078776 M.Suzuki, M.Gerstein, and N.Yagi (1994).
Stereochemical basis of DNA recognition by Zn fingers.
  Nucleic Acids Res, 22, 3397-3405.  
  8318900 R.C.Hoffman, S.J.Horvath, and R.E.Klevit (1993).
Structures of DNA-binding mutant zinc finger domains: implications for DNA binding.
  Protein Sci, 2, 951-965.
PDB codes: 1ard 1are 1arf
  8355698 R.M.Brazas, and D.J.Stillman (1993).
Identification and purification of a protein that binds DNA cooperatively with the yeast SWI5 protein.
  Mol Cell Biol, 13, 5524-5537.  
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.