5ZNF

ALTERNATING ZINC FINGERS IN THE HUMAN MALE ASSOCIATED PROTEIN ZFY: 2D NMR STRUCTURE OF AN EVEN FINGER AND IMPLICATIONS FOR "JUMPING-LINKER" DNA RECOGNITION


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 13 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Alternating zinc fingers in the human male associated protein ZFY: 2D NMR structure of an even finger and implications for "jumping-linker" DNA recognition.

Kochoyan, M.Havel, T.F.Nguyen, D.T.Dahl, C.E.Keutmann, H.T.Weiss, M.A.

(1991) Biochemistry 30: 3371-3386

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ZFY, a sex-related Zn-finger protein encoded by the human Y chromosome, is distinguished from the general class of Zn-finger proteins by the presence of a two-finger repeat. Whereas odd-numbered domains and linkers fit a general consensus, even-numbe ...

    ZFY, a sex-related Zn-finger protein encoded by the human Y chromosome, is distinguished from the general class of Zn-finger proteins by the presence of a two-finger repeat. Whereas odd-numbered domains and linkers fit a general consensus, even-numbered domains and linkers exhibit systematic differences. Because this alternation may have fundamental implications for the mechanism of protein-DNA recognition, we have undertaken biochemical and structural studies of fragments of ZFY. We describe here the solution structure of a representative nonconsensus (even-numbered) Zn finger based on 2D NMR studies of a 30-residue peptide. Structural modeling by distance geometry and simulated annealing (DG/SA) demonstrates that this peptide folds as a miniglobular domain containing a C-terminal beta--hairpin and N-terminal alpha-helix (beta beta alpha motif). These features are similar to (but not identical with) those previously described in consensus-type Zn fingers (derived from ADR1 and Xfin); the similarities suggest that even and odd ZFY domains bind DNA by a common mechanism. A model of the protein-DNA complex (designated the "jumping-linker" model) is presented and discussed in terms of the ZFY two-finger repeat. In this model every other linker is proposed to cross the minor groove by means of a putative finger/linker submotif HX4HX3-hydrophobic residue-X3. Analogous use of a hydrophobic residue in a linker that spans the minor groove has recently been described in crystallographic and 3D NMR studies of homeodomain-DNA complexes. The proposed model of ZFY is supported in part by the hydroxyl radical footprint of the TFIIIA-DNA complex [Churchill, M.E.A., Tullius, T.D., & Klug, A. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 5528-5532].


    Related Citations: 
    • Alternating Zinc Fingers in the Human Male Associated Protein Zfy: Refinement of the NMR Structure of an Even Finger by Selective Deuterium Labeling and Implications for DNA Recognition
      Kochoyan, M.,Keutmann, H.T.,Weiss, M.A.
      (1991) Biochemistry 30: 7063
    • Architectural Rules of the Zinc-Finger Motif: Comparative Two-Dimensional NMR Studies of Native and "Aromatic-Swap" Domains Define a "Weakly Polar Switch"
      Kochoyan, M.,Keutmann, H.T.,Weiss, M.A.
      (1991) Proc.Natl.Acad.Sci.USA 88: 8455


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ZINC FINGER
A
30Homo sapiensMutation(s): 0 
Gene Names: ZFY
Find proteins for P08048 (Homo sapiens)
Go to Gene View: ZFY
Go to UniProtKB:  P08048
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 13 
  • Olderado: 5ZNF Olderado
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance