spacer
spacer

PDBsum entry 1fv5

Go to PDB code: 
protein metals links
Transcription PDB id
1fv5
Jmol
Contents
Protein chain
36 a.a.
Metals
_ZN
PDB id:
1fv5
Name: Transcription
Title: Solution structure of the first zinc finger from the drosophila u-shaped transcription factor
Structure: First zinc finger of u-shaped. Chain: a. Fragment: first zinc finger domain (residues 202-235). Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: C.K.Liew,K.Kowalski,A.H.Fox,A.Newton,B.K.Sharpe,M.Crossley, J.P.Mackay
Key ref:
C.K.Liew et al. (2000). Solution structures of two CCHC zinc fingers from the FOG family protein U-shaped that mediate protein-protein interactions. Structure, 8, 1157-1166. PubMed id: 11080638 DOI: 10.1016/S0969-2126(00)00527-X
Date:
18-Sep-00     Release date:   04-Oct-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9VPQ6  (USH_DROME) -  Zinc finger protein ush
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1191 a.a.
36 a.a.*
Key:    PfamA domain  PfamB 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: 10.1016/S0969-2126(00)00527-X Structure 8:1157-1166 (2000)
PubMed id: 11080638  
 
 
Solution structures of two CCHC zinc fingers from the FOG family protein U-shaped that mediate protein-protein interactions.
C.K.Liew, K.Kowalski, A.H.Fox, A.Newton, B.K.Sharpe, M.Crossley, J.P.Mackay.
 
  ABSTRACT  
 
BACKGROUND: Zinc finger domains have traditionally been regarded as sequence-specific DNA binding motifs. However, recent evidence indicates that many zinc fingers mediate specific protein-protein interactions. For instance, several zinc fingers from FOG family proteins have been shown to interact with the N-terminal zinc finger of GATA-1. RESULTS: We have used NMR spectroscopy to determine the first structures of two FOG family zinc fingers that are involved in protein-protein interactions: fingers 1 and 9 from U-shaped. These fingers resemble classical TFIIIA-like zinc fingers, with the exception of an unusual extended portion of the polypeptide backbone prior to the fourth zinc ligand. [15N,(1)H]-HSQC titrations have been used to define the GATA binding surface of USH-F1, and comparison with other FOG family proteins indicates that the recognition mechanism is conserved across species. The surface of FOG-type fingers that interacts with GATA-1 overlaps substantially with the surface through which classical fingers typically recognize DNA. This suggests that these fingers could not contact both GATA and DNA simultaneously. In addition, results from NMR, gel filtration, and sedimentation equilibrium experiments suggest that the interactions are of moderate affinity. CONCLUSIONS: Our results demonstrate unequivocally that zinc fingers comprising the classical betabetaalpha fold are capable of mediating specific contacts between proteins. The existence of this alternative function has implications for the prediction of protein function from sequence data and for the evolution of protein function.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Overlays of USH-F9 and the Sixth Finger from ZFYUSH-F9 is shown in blue, and the sixth finger from ZFY [23] is shown in red. The overlays are related by a 90 rotation about a horizontal axis in the plane of the page. The differences in side chain conformation in this region can be clearly seen

 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 1157-1166) copyright 2000.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19095651 J.A.Lowry, R.Gamsjaeger, S.Y.Thong, W.Hung, A.H.Kwan, G.Broitman-Maduro, J.M.Matthews, M.Maduro, and J.P.Mackay (2009).
Structural Analysis of MED-1 Reveals Unexpected Diversity in the Mechanism of DNA Recognition by GATA-type Zinc Finger Domains.
  J Biol Chem, 284, 5827-5835.
PDB code: 2kae
18253864 K.J.Brayer, and D.J.Segal (2008).
Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains.
  Cell Biochem Biophys, 50, 111-131.  
18202004 T.Kohinata, H.Nishino, and H.Fukuzawa (2008).
Significance of zinc in a regulatory protein, CCM1, which regulates the carbon-concentrating mechanism in Chlamydomonas reinhardtii.
  Plant Cell Physiol, 49, 273-283.  
16379012 E.Vinolo, H.Sebban, A.Chaffotte, A.Israël, G.Courtois, M.Véron, and F.Agou (2006).
A point mutation in NEMO associated with anhidrotic ectodermal dysplasia with immunodeficiency pathology results in destabilization of the oligomer and reduces lipopolysaccharide- and tumor necrosis factor-mediated NF-kappa B activation.
  J Biol Chem, 281, 6334-6348.  
15659346 A.B.Cantor, and S.H.Orkin (2005).
Coregulation of GATA factors by the Friend of GATA (FOG) family of multitype zinc finger proteins.
  Semin Cell Dev Biol, 16, 117-128.  
15698569 B.K.Sharpe, C.K.Liew, A.H.Kwan, J.A.Wilce, M.Crossley, J.M.Matthews, and J.P.Mackay (2005).
Assessment of the robustness of a serendipitous zinc binding fold: mutagenesis and protein grafting.
  Structure, 13, 257-266.
PDB codes: 1wo3 1wo4 1wo5 1wo6 1wo7
15234987 R.J.Simpson, S.H.Yi Lee, N.Bartle, E.Y.Sum, J.E.Visvader, J.M.Matthews, J.P.Mackay, and M.Crossley (2004).
A classic zinc finger from friend of GATA mediates an interaction with the coiled-coil of transforming acidic coiled-coil 3.
  J Biol Chem, 279, 39789-39797.
PDB code: 1srk
12842043 A.H.Kwan, D.A.Gell, A.Verger, M.Crossley, J.M.Matthews, and J.P.Mackay (2003).
Engineering a protein scaffold from a PHD finger.
  Structure, 11, 803-813.
PDB codes: 1mm2 1mm3
12620233 A.S.McCarty, G.Kleiger, D.Eisenberg, and S.T.Smale (2003).
Selective dimerization of a C2H2 zinc finger subfamily.
  Mol Cell, 11, 459-470.  
12736264 R.J.Simpson, E.D.Cram, R.Czolij, J.M.Matthews, M.Crossley, and J.P.Mackay (2003).
CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions.
  J Biol Chem, 278, 28011-28018.
PDB code: 1p7a
12527760 S.S.Krishna, I.Majumdar, and N.V.Grishin (2003).
Structural classification of zinc fingers: survey and summary.
  Nucleic Acids Res, 31, 532-550.  
11742346 G.Polekhina, C.M.House, N.Traficante, J.P.Mackay, F.Relaix, D.A.Sassoon, M.W.Parker, and D.D.Bowtell (2002).
Siah ubiquitin ligase is structurally related to TRAF and modulates TNF-alpha signaling.
  Nat Struct Biol, 9, 68-75.
PDB code: 1k2f
11983708 J.L.Sepulveda, S.Vlahopoulos, D.Iyer, N.Belaguli, and R.J.Schwartz (2002).
Combinatorial expression of GATA4, Nkx2-5, and serum response factor directs early cardiac gene activity.
  J Biol Chem, 277, 25775-25782.  
12110675 K.Kowalski, C.K.Liew, J.M.Matthews, D.A.Gell, M.Crossley, and J.P.Mackay (2002).
Characterization of the conserved interaction between GATA and FOG family proteins.
  J Biol Chem, 277, 35720-35729.
PDB code: 1jn7
11179890 J.H.Laity, B.M.Lee, and P.E.Wright (2001).
Zinc finger proteins: new insights into structural and functional diversity.
  Curr Opin Struct Biol, 11, 39-46.  
11404479 N.Fossett, S.G.Tevosian, K.Gajewski, Q.Zhang, S.H.Orkin, and R.A.Schulz (2001).
The Friend of GATA proteins U-shaped, FOG-1, and FOG-2 function as negative regulators of blood, heart, and eye development in Drosophila.
  Proc Natl Acad Sci U S A, 98, 7342-7347.  
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.