PDBsum entry 5znf

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protein metals links
Zinc finger DNA binding domain PDB id
Protein chain
30 a.a. *
* Residue conservation analysis
PDB id:
Name: Zinc finger DNA binding domain
Title: Alternating zinc fingers in the human male associated protein zfy: 2d nmr structure of an even finger and implications for "jumping-linker" DNA recognition
Structure: Zinc finger. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
NMR struc: 13 models
Authors: M.Kochoyan,H.T.Keutmann,M.A.Weiss
Key ref:
M.Kochoyan et al. (1991). Alternating zinc fingers in the human male associated protein ZFY: 2D NMR structure of an even finger and implications for "jumping-linker" DNA recognition. Biochemistry, 30, 3371-3386. PubMed id: 1849423 DOI: 10.1021/bi00228a004
22-Aug-91     Release date:   31-Jan-94    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P08048  (ZFY_HUMAN) -  Zinc finger Y-chromosomal protein
801 a.a.
30 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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


DOI no: 10.1021/bi00228a004 Biochemistry 30:3371-3386 (1991)
PubMed id: 1849423  
Alternating zinc fingers in the human male associated protein ZFY: 2D NMR structure of an even finger and implications for "jumping-linker" DNA recognition.
M.Kochoyan, T.F.Havel, D.T.Nguyen, C.E.Dahl, H.T.Keutmann, M.A.Weiss.
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].

Literature references that cite this PDB file's key reference

  PubMed id Reference
12616630 C.Isernia, E.Bucci, M.Leone, L.Zaccaro, P.Di Lello, G.Digilio, S.Esposito, M.Saviano, B.Di Blasio, C.Pedone, P.V.Pedone, and R.Fattorusso (2003).
NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein.
  Chembiochem, 4, 171-180.
PDB code: 1njq
11080638 C.K.Liew, K.Kowalski, A.H.Fox, A.Newton, B.K.Sharpe, M.Crossley, and J.P.Mackay (2000).
Solution structures of two CCHC zinc fingers from the FOG family protein U-shaped that mediate protein-protein interactions.
  Structure, 8, 1157-1166.
PDB codes: 1fu9 1fv5
10479738 X.Gao, and T.C.Wong (1999).
The study of the conformation and interaction of two tachykinin peptides in membrane mimicking systems by NMR spectroscopy and pulsed field gradient diffusion.
  Biopolymers, 50, 555-568.  
9558319 Q.X.Hua, W.H.Jia, B.P.Bullock, J.F.Habener, and M.A.Weiss (1998).
Transcriptional activator-coactivator recognition: nascent folding of a kinase-inducible transactivation domain predicts its structure on coactivator binding.
  Biochemistry, 37, 5858-5866.  
9242690 D.G.Kehres, G.S.Subramanyan, V.S.Hung, G.W.Rogers, and D.R.Setzer (1997).
Energetically unfavorable interactions among the zinc fingers of transcription factor IIIA when bound to the 5 S rRNA gene.
  J Biol Chem, 272, 20152-20161.  
9253405 M.P.Foster, D.S.Wuttke, I.Radhakrishnan, D.A.Case, J.M.Gottesfeld, and P.E.Wright (1997).
Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA.
  Nat Struct Biol, 4, 605-608.
PDB code: 1tf3
8662611 O.Rowland, and J.Segall (1996).
Interaction of wild-type and truncated forms of transcription factor IIIA from Saccharomyces cerevisiae with the 5 S RNA gene.
  J Biol Chem, 271, 12103-12110.  
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
7796266 K.Ogata, S.Morikawa, H.Nakamura, H.Hojo, S.Yoshimura, R.Zhang, S.Aimoto, Y.Ametani, Z.Hirata, and A.Sarai (1995).
Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb.
  Nat Struct Biol, 2, 309-320.
PDB codes: 1mbe 1mbf 1mbg 1mbh 1mbj 1mbk
  7935395 A.J.Franklin, T.L.Jetton, K.D.Shelton, and M.A.Magnuson (1994).
BZP, a novel serum-responsive zinc finger protein that inhibits gene transcription.
  Mol Cell Biol, 14, 6773-6788.  
8125104 A.Martin-Ponthieu, D.Wouters-Tyrou, B.Pudlo, E.Buisine, and P.Sautière (1994).
Isolation and characterization of a small putative zinc finger protein from cuttlefish epididymal sperm cells.
  Eur J Biochem, 220, 463-468.  
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.  
7664053 G.C.Pérez-Alvarado, C.Miles, J.W.Michelsen, H.A.Louis, D.R.Winge, M.C.Beckerle, and M.F.Summers (1994).
Structure of the carboxy-terminal LIM domain from the cysteine rich protein CRP.
  Nat Struct Biol, 1, 388-398.
PDB code: 1ctl
  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
  1425585 G.H.Jacobs (1992).
Determination of the base recognition positions of zinc fingers from sequence analysis.
  EMBO J, 11, 4507-4517.  
1438283 K.R.Clemens, X.Liao, V.Wolf, P.E.Wright, and J.M.Gottesfeld (1992).
Definition of the binding sites of individual zinc fingers in the transcription factor IIIA-5S RNA gene complex.
  Proc Natl Acad Sci U S A, 89, 10822-10826.  
1408784 L.Fairall, and D.Rhodes (1992).
A new approach to the analysis of DNase I footprinting data and its application to the TFIIIA/5S DNA complex.
  Nucleic Acids Res, 20, 4727-4731.  
  1304355 M.F.Summers, L.E.Henderson, M.R.Chance, J.W.Bess, T.L.South, P.R.Blake, I.Sagi, G.Perez-Alvarado, R.C.Sowder, and D.R.Hare (1992).
Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution-state structure of the nucleocapsid protein from HIV-1.
  Protein Sci, 1, 563-574.
PDB code: 1aaf
1324755 M.S.Lee, A.G.Palmer, and P.E.Wright (1992).
Relationship between 1H and 13C NMR chemical shifts and the secondary and tertiary structure of a zinc finger peptide.
  J Biomol NMR, 2, 307-322.  
1511742 M.S.Lee, R.J.Mortishire-Smith, and P.E.Wright (1992).
The zinc finger motif. Conservation of chemical shifts and correlation with structure.
  FEBS Lett, 309, 29-32.  
  1639074 N.Morellet, N.Jullian, H.De Rocquigny, B.Maigret, J.L.Darlix, and B.P.Roques (1992).
Determination of the structure of the nucleocapsid protein NCp7 from the human immunodeficiency virus type 1 by 1H NMR.
  EMBO J, 11, 3059-3065.  
1549601 Q.X.Hua, M.Kochoyan, and M.A.Weiss (1992).
Structure and dynamics of des-pentapeptide-insulin in solution: the molten-globule hypothesis.
  Proc Natl Acad Sci U S A, 89, 2379-2383.
PDB code: 1his
1594580 S.F.Michael, V.J.Kilfoil, M.H.Schmidt, B.T.Amann, and J.M.Berg (1992).
Metal binding and folding properties of a minimalist Cys2His2 zinc finger peptide.
  Proc Natl Acad Sci U S A, 89, 4796-4800.  
1924304 M.Kochoyan, H.T.Keutmann, and M.A.Weiss (1991).
Architectural rules of the zinc-finger motif: comparative two-dimensional NMR studies of native and "aromatic-swap" domains define a "weakly polar switch".
  Proc Natl Acad Sci U S A, 88, 8455-8459.  
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.