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PDBsum entry 1paa

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protein metals links
Transcription regulation PDB id
1paa
Jmol
Contents
Protein chain
30 a.a. *
Metals
_ZN
* Residue conservation analysis
PDB id:
1paa
Name: Transcription regulation
Title: Structure of a histidine-x4-histidine zinc finger domain: insights into adr1-uas1 protein-DNA recognition
Structure: Yeast transcription factor adr1. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
NMR struc: 10 models
Authors: B.E.Bernstein,R.C.Hoffman,S.J.Horvath,J.R.Herriott, R.E.Klevit
Key ref:
B.E.Bernstein et al. (1994). Structure of a histidine-X4-histidine zinc finger domain: insights into ADR1-UAS1 protein-DNA recognition. Biochemistry, 33, 4460-4470. PubMed id: 8161501 DOI: 10.1021/bi00181a005
Date:
15-Jul-94     Release date:   15-Oct-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07248  (ADR1_YEAST) -  Regulatory protein ADR1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1323 a.a.
30 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

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

 

 
DOI no: 10.1021/bi00181a005 Biochemistry 33:4460-4470 (1994)
PubMed id: 8161501  
 
 
Structure of a histidine-X4-histidine zinc finger domain: insights into ADR1-UAS1 protein-DNA recognition.
B.E.Bernstein, R.C.Hoffman, S.Horvath, J.R.Herriott, R.E.Klevit.
 
  ABSTRACT  
 
The solution structure for a mutant zinc finger peptide based on the sequence of the C-terminal ADR1 finger has been determined by two-dimensional NMR spectroscopy. The mutant peptide, called PAPA, has both proline residues from the wild-type sequence replaced with alanines. A nonessential cysteine was also replaced with alanine. The behavior of PAPA in solution implicates the prolines in the conformational heterogeneity reported earlier for the wild-type peptide [Xu, R. X., Horvath, S. J., & Klevit, R. E. (1991) Biochemistry 30, 3365-3371]. The solution structure of PAPA reveals several interesting features of the zinc finger motif. The residue immediately following the second cysteine ligand adopts a positive phi angle, which we propose is a common feature of this class of zinc fingers, regardless of whether this residue is a glycine. The NMR spectrum and resulting solution structure of PAPA suggest that a side-chain to side-chain hydrogen bond involving an arginine and an aspartic acid analogous to one observed in the Zif268 protein-DNA cocrystal structure exists in solution in the absence of DNA [Pavletich, N. P., & Pabo, C. O. (1991) Science 252, 809-817]. A model for the interaction between the two ADR1 zinc fingers and their DNA binding sites was built by superpositioning the refined solution structures of PAPA and ADR1b onto the Zif268 structure. This model offers structural explanations for a variety of mutations to the ADR1 zinc finger domains that have been shown to affect DNA-binding affinity or specificity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
15790571 E.Kellenberger, C.Dominguez, S.Fribourg, E.Wasielewski, D.Moras, A.Poterszman, R.Boelens, and B.Kieffer (2005).
Solution structure of the C-terminal domain of TFIIH P44 subunit reveals a novel type of C4C4 ring domain involved in protein-protein interactions.
  J Biol Chem, 280, 20785-20792.
PDB code: 1z60
12493736 E.Merithew, C.Stone, S.Eathiraj, and D.G.Lambright (2003).
Determinants of Rab5 interaction with the N terminus of early endosome antigen 1.
  J Biol Chem, 278, 8494-8500.  
10757981 M.Thompson, and N.W.Woodbury (2000).
Fluorescent and photochemical properties of a single zinc finger conjugated to a fluorescent DNA-binding probe.
  Biochemistry, 39, 4327-4338.  
  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.  
9053397 W.D.Kohn, C.T.Mant, and R.S.Hodges (1997).
Alpha-helical protein assembly motifs.
  J Biol Chem, 272, 2583-2586.  
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
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.  
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.