1ZW8

Solution structure of a ZAP1 zinc-responsive domain provides insights into metalloregulatory transcriptional repression in Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution structure of a Zap1 zinc-responsive domain provides insights into metalloregulatory transcriptional repression in Saccharomyces cerevisiae.

Wang, Z.Feng, L.S.Matskevich, V.Venkataraman, K.Parasuram, P.Laity, J.H.

(2006) J Mol Biol 357: 1167-1183

  • DOI: 10.1016/j.jmb.2006.01.010
  • Primary Citation of Related Structures:  
    1ZW8

  • PubMed Abstract: 
  • The Zap1 transcription factor controls expression of genes that regulate zinc homeostasis in Saccharomyces cerevisiae. The solution structure of two zinc fingers (zf1-2(CA3)) derived from a zinc-responsive domain of Zap1 (zf1-2) has been determined. Under zinc-limiting conditions, zinc finger 2 (zf2) from this domain has been shown to be a constitutive transcriptional activator ...

    The Zap1 transcription factor controls expression of genes that regulate zinc homeostasis in Saccharomyces cerevisiae. The solution structure of two zinc fingers (zf1-2(CA3)) derived from a zinc-responsive domain of Zap1 (zf1-2) has been determined. Under zinc-limiting conditions, zinc finger 2 (zf2) from this domain has been shown to be a constitutive transcriptional activator. Moreover, repression of zf2 function in zinc-replete cells required zinc coordination to both canonical finger 1 (zf1) and zf2 metal sites, suggesting zf1-zf2 cooperativity underlies Zap1 metalloregulation. A structural basis for this cooperativity is identified here. Favorable inter-helical contacts in zf1-2(CA3) extend the individual finger hydrophobic cores through the zf1-zf2 interface. Tryptophan residues at position 5 in each finger provide numerous non-helical inter-finger contacts reminiscent of those observed in GLI1 zinc fingers 1 and 2. The molecular mechanism for zf1-dependent repression of zf2 transcriptional activation is explored further using NMR and CD titration studies. While zf1 independently forms a betabetaalpha solution structure, the majority of zf2 ensemble solution states do not adopt the canonical betabetaalpha zinc finger fold without zf1-zf2 interactions. Cooperative effects on Zn(II) affinities stemming from these finger-finger interactions are observed also in calorimetric studies, in which the 160(+/-20)nM (zf1) and 250(+/-40)nM (zf2) K(d) values for each individual finger increased substantially in the context of the zf1-2 protein (apparent K(dzf1-2WT)=4.6(+/-1.2)nM). On the basis of the above observations, we propose a mechanism for Zap1 transcriptional regulation in which zf1-zf2 interactions stabilize the betabetaalpha folded "repressed state" of the zf2 activation domain in the presence of cellular Zn(II) excess. Moreover, in contrast to earlier reports of <<1 labile zinc ion/Escherichia coli cell, the zf1-zf2 zinc affinities determined calorimetrically are consistent with Zn(II) levels >>1 labile zinc ion/eukaryotic cell.


    Related Citations: 
    • Zinc fingers can act as Zn(II) sensors to regulate transcriptional activation domain function
      Bird, A.J., McCal, K., Kramer, M., Blankman, E., Winge, D.R., Eid, D.J.
      (2003) EMBO J 22: 5137
    • Zap1p, a metalloregulatory protein involved in zinc-responsive transcriptional regulation in Saccharomyces cerevisiae
      Zhao, H., Eide, D.J.
      (1997) Mol Cell 17: 5044

    Organizational Affiliation

    Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110-2499, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc-responsive transcriptional regulator ZAP1A64Saccharomyces cerevisiaeMutation(s): 3 
Gene Names: ZAP1
UniProt
Find proteins for P47043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47043 
Go to UniProtKB:  P47043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47043
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations