PDBsum entry 1zr9

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protein metals links
Transcription PDB id
Jmol PyMol
Protein chain
67 a.a. *
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Solution structure of a human c2h2-type zinc finger protein
Structure: Zinc finger protein 593. Chain: a. Synonym: zinc finger protein t86, zinc finger protein loc51042. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: znf593. Expressed in: cell-free synthesis. Other_details: wheat germ cell-free, in vitro expression
NMR struc: 20 models
Authors: B.L.Lytle,F.C.Peterson,B.F.Volkman,Center For Eukaryotic Structural Genomics (Cesg)
Key ref:
P.L.Hayes et al. (2008). The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominantly unstructured protein. Protein Sci, 17, 571-576. PubMed id: 18287285 DOI: 10.1110/ps.073290408
19-May-05     Release date:   07-Jun-05    
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Protein chain
Pfam   ArchSchema ?
O00488  (ZN593_HUMAN) -  Zinc finger protein 593
134 a.a.
67 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

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


DOI no: 10.1110/ps.073290408 Protein Sci 17:571-576 (2008)
PubMed id: 18287285  
The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominantly unstructured protein.
P.L.Hayes, B.L.Lytle, B.F.Volkman, F.C.Peterson.
Here, we report the solution structure of ZNF593, a protein identified in a functional study as a negative modulator of the DNA-binding activity of the Oct-2 transcription factor. ZNF593 contains a classic C(2)H(2) zinc finger domain flanked by about 40 disordered residues on each terminus. Although the protein contains a high degree of intrinsic disorder, the structure of the zinc finger domain was resolved by NMR spectroscopy without a need for N- or C-terminal truncations. The tertiary structure of the zinc finger domain is composed of a beta-hairpin that positions the cysteine side chains for zinc coordination, followed by an atypical kinked alpha-helix containing the two histidine side chain ligands. The structural topology of ZNF593 is similar to a fragment of the double-stranded RNA-binding protein Zfa and the C-terminal zinc finger of MBP-1, a human enhancer binding protein. The structure presented here will provide a guide for future functional studies of how ZNF593 negatively modulates the DNA-binding activity of Oct-2, a POU domain-containing transcription factor. Our work illustrates the unique capacity of NMR spectroscopy for structural analysis of folded domains in a predominantly disordered protein.
  Selected figure(s)  
Figure 1.
(A) Two-dimensional ^15N --^1H HSQC spectrum of ZNF593 before (black contours) and after (red contours) the addition of 2 mM EDTA. Resonance assignments are indicated by a one-letter amino acid code followed by the specified residue number. (B) Ensemble of 20 conformers of ZNF593. (Gray) The N- and C-terminal unstructured regions (residues 28 --42 and 76 --94), (green) [beta]-sheet, (orange) [alpha]-helices, (green sphere) the zinc ion. (C) Cross-eyed stereoview of ZNF593, with unstructured residues 1 --35 and 78 --116 omitted for clarity. (D) Backbone r.m.s.d. and ^15N --^1H heteronuclear NOEs values displayed as a function of amino acid sequence. Locations of secondary structure elements are indicated.
Figure 2.
(A) Ribbon diagrams of ZNF593 (PDB code: 1zr9), the second zinc finger of dsRNA-ZFa (residues 94 --128) (PDB code: 1zu1), the C-terminal zinc finger of MBP-1 (residues 30 --57) (PDB code: 1bbo), and ZFY-swap (PDB code: 7znf). (B) Multiple sequence alignments demonstrating residue conservation between similar zinc fingers. (Green residues) Conserved amino acids. (C) Positively charged residues located on the solvent-exposed side of the [alpha]-helix are compared between ZNF593 and double-stranded RNA-binding protein ZFa.
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2008, 17, 571-576) copyright 2008.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23212245 M.Altvater, Y.Chang, A.Melnik, L.Occhipinti, S.Schütz, U.Rothenbusch, P.Picotti, and V.G.Panse (2012).
Targeted proteomics reveals compositional dynamics of 60S pre-ribosomes after nuclear export.
  Mol Syst Biol, 8, 628.  
19116284 A.Andreeva, and A.G.Murzin (2008).
A fortuitous insight into a common mode of RNA recognition by the dsRNA-specific zinc fingers.
  Proc Natl Acad Sci U S A, 105, E128-E129.  
18718539 N.A.Ciaccio, M.L.Moreno, R.L.Bauer, and J.S.Laurence (2008).
High-yield expression in E. coli and refolding of the bZIP domain of activating transcription factor 5.
  Protein Expr Purif, 62, 235-243.  
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