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PDBsum entry 1ncs

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protein metals links
Transcription regulation PDB id
1ncs
Jmol PyMol
Contents
Protein chain
47 a.a. *
Metals
_ZN
* Residue conservation analysis
PDB id:
1ncs
Name: Transcription regulation
Title: Nmr study of swi5 zinc finger domain 1
Structure: Transcriptional factor swi5. Chain: a. Fragment: zinc finger DNA binding domain 1 of swi5. Synonym: peptide m30f. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: t7. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: t7 polymerase expression system
NMR struc: 46 models
Authors: R.N.Dutnall,D.Neuhaus,D.Rhodes
Key ref:
R.N.Dutnall et al. (1996). The solution structure of the first zinc finger domain of SWI5: a novel structural extension to a common fold. Structure, 4, 599-611. PubMed id: 8736557 DOI: 10.1016/S0969-2126(96)00064-0
Date:
26-Feb-96     Release date:   10-Jun-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.
47 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/S0969-2126(96)00064-0 Structure 4:599-611 (1996)
PubMed id: 8736557  
 
 
The solution structure of the first zinc finger domain of SWI5: a novel structural extension to a common fold.
R.N.Dutnall, D.Neuhaus, D.Rhodes.
 
  ABSTRACT  
 
BACKGROUND: The 2Cys-2His (C2-H2) zinc finger is a protein domain commonly used for sequence-specific DNA recognition. The zinc fingers of the yeast transcription factors SWI5 and ACE2 share strong sequence homology, which extends into a region N-terminal to the first finger, suggesting that the DNA-binding domains of these two proteins include additional structural elements. RESULTS: Structural analysis of the zinc fingers of SWI5 reveals that a 15 residue region N-terminal to the finger motifs forms part of the structure of the first finger domain, adding a beta strand and a helix not previously observed in other zinc finger structures. Sequence analysis suggests that other zinc finger proteins may also have this structure. Biochemical studies show that this additional structure increases DNA-binding affinity. CONCLUSIONS: The structural analysis presented reveals a novel zinc finger structure in which additional structural elements have been added to the C2-H2 zinc finger fold. This additional structure may enhance stability and has implications for DNA recognition by extending the potential DNA-binding surface of a single zinc finger domain.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Stereo view of backbone N, Cα, C atom trace of the lowest energy structure of peptide m30F. The Cα atom of every fifth residue is shown as a black sphere and the backbone N atoms of slowly exchanging NH groups are shown in cyan. The side chain heavy atoms of the zinc ligands are coloured as in Figure 4a. Figure 5. Stereo view of backbone N, Cα, C atom trace of the lowest energy structure of peptide m30F. The Cα atom of every fifth residue is shown as a black sphere and the backbone N atoms of slowly exchanging NH groups are shown in cyan. The side chain heavy atoms of the zinc ligands are coloured as in [3]Figure 4a.
Figure 8.
Figure 8. Model of the first zinc finger of SWI5 docked to B-form DNA. A schematic representation of the zinc finger structure is shown prepared as in Figure 4a. The sequence of the DNA is that of the primary binding site of SWI5 and the two DNA-strands are coloured differently for contrast. The protein N and C termini and zinc ion are marked as well as the 5′ and 3′ ends of the DNA strand (dark blue) to which the additional helix makes its closest approach. The DNA-recognition helix of the canonical zinc finger is positioned to contact a base triplet on the cyan strand. This arrangement positions the additional helix near the opposite (dark blue) strand across the major groove, at a suitable distance (≈7 å) for basic residues on the surface of the helix to reach phosphate groups of the DNA backbone. Figure 8. Model of the first zinc finger of SWI5 docked to B-form DNA. A schematic representation of the zinc finger structure is shown prepared as in [3]Figure 4a. The sequence of the DNA is that of the primary binding site of SWI5 and the two DNA-strands are coloured differently for contrast. The protein N and C termini and zinc ion are marked as well as the 5′ and 3′ ends of the DNA strand (dark blue) to which the additional helix makes its closest approach. The DNA-recognition helix of the canonical zinc finger is positioned to contact a base triplet on the cyan strand. This arrangement positions the additional helix near the opposite (dark blue) strand across the major groove, at a suitable distance (≈7 å) for basic residues on the surface of the helix to reach phosphate groups of the DNA backbone.
 
  The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 599-611) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18190927 R.P.Grant, N.J.Marshall, J.C.Yang, M.B.Fasken, S.M.Kelly, M.T.Harreman, D.Neuhaus, A.H.Corbett, and M.Stewart (2008).
Structure of the N-terminal Mlp1-binding domain of the Saccharomyces cerevisiae mRNA-binding protein, Nab2.
  J Mol Biol, 376, 1048-1059.
PDB codes: 2jps 2v75
11395410 C.O.Pabo, E.Peisach, and R.A.Grant (2001).
Design and selection of novel Cys2His2 zinc finger proteins.
  Annu Rev Biochem, 70, 313-340.  
10642181 E.T.Young, N.Kacherovsky, and C.Cheng (2000).
An accessory DNA binding motif in the zinc finger protein Adr1 assists stable binding to DNA and can be replaced by a third finger.
  Biochemistry, 39, 567-574.  
  10793143 L.Feng, B.Wang, B.Driscoll, and A.Jong (2000).
Identification and characterization of Saccharomyces cerevisiae Cdc6 DNA-binding properties.
  Mol Biol Cell, 11, 1673-1685.  
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.  
10409653 H.J.McBride, Y.Yu, and D.J.Stillman (1999).
Distinct regions of the Swi5 and Ace2 transcription factors are required for specific gene activation.
  J Biol Chem, 274, 21029-21036.  
  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.  
9736626 M.D.Allen, K.Yamasaki, M.Ohme-Takagi, M.Tateno, and M.Suzuki (1998).
A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.
  EMBO J, 17, 5484-5496.
PDB codes: 1gcc 2gcc 3gcc
9519295 S.Tan, and T.J.Richmond (1998).
Eukaryotic transcription factors.
  Curr Opin Struct Biol, 8, 41-48.  
  9111337 H.J.McBride, R.M.Brazas, Y.Yu, K.Nasmyth, and D.J.Stillman (1997).
Long-range interactions at the HO promoter.
  Mol Cell Biol, 17, 2669-2678.  
9033593 J.G.Omichinski, P.V.Pedone, G.Felsenfeld, A.M.Gronenborn, and G.M.Clore (1997).
The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode.
  Nat Struct Biol, 4, 122-132.
PDB codes: 1yui 1yuj
  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.  
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 codes are shown on the right.

 

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