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PDBsum entry 1mey
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protein dna_rna metals Protein-protein interface(s) links
Transferase/DNA PDB id
1mey

 

 

 

 

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Contents
Protein chains
83 a.a. *
28 a.a. *
DNA/RNA
Metals
_ZN ×8
_CL
Waters ×132
* Residue conservation analysis
PDB id:
1mey
Name: Transferase/DNA
Title: Crystal structure of a designed zinc finger protein bound to DNA
Structure: DNA (5'-d( Ap Tp Gp Ap Gp Gp Cp Ap Gp Ap Ap Cp T)-3'). Chain: a, d. Engineered: yes. DNA (5'-d( Tp Ap Gp Tp Tp Cp Tp Gp Cp Cp Tp (C38)p A)-3'). Chain: b, e. Engineered: yes. Consensus zinc finger. Chain: c, f, g. Engineered: yes
Source: Synthetic: yes. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Not given
Resolution:
2.20Å     R-factor:   0.224     R-free:   0.319
Authors: C.A.Kim,J.M.Berg
Key ref: C.A.Kim and J.M.Berg (1996). A 2.2 A resolution crystal structure of a designed zinc finger protein bound to DNA. Nat Struct Biol, 3, 940-945. PubMed id: 8901872
Date:
27-Sep-96     Release date:   12-Mar-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 83 a.a.
Protein chain
No UniProt id for this chain
Struc: 28 a.a.
Key:    Secondary structure  CATH domain

DNA/RNA chains
  A-T-G-A-G-G-C-A-G-A-A-C-T 13 bases
  T-A-G-T-T-C-T-G-C-C-T-C38-A 13 bases
  A-T-G-A-G-G-C-A-G-A-A-C-T 13 bases
  T-A-G-T-T-C-T-G-C-C-T-C38-A 13 bases

 

 
Nat Struct Biol 3:940-945 (1996)
PubMed id: 8901872  
 
 
A 2.2 A resolution crystal structure of a designed zinc finger protein bound to DNA.
C.A.Kim, J.M.Berg.
 
  ABSTRACT  
 
Considerable recent effort has been devoted to the design and selection of sequence-specific DNA binding proteins based on tandem arrays of Cys2His2 zinc finger domains. While the DNA binding properties of these designed proteins have been studied extensively, the structural basis for site-specific binding has not been examined experimentally. Here we report the crystal structure of a complex between a protein comprised of three consensus-sequence-based zinc finger domains and an oligonucleotide corresponding to a favourable DNA binding site. This structure reveals relatively simple modular interactions and structural adaptations that compensate for differences in contact residue side-chain lengths.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21470886 G.Nagy, B.Gyurcsik, E.A.Hoffmann, and T.Körtvélyesi (2011).
Theoretical design of a specific DNA-Zinc-finger protein interaction with semi-empirical quantum chemical methods.
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20852793 Y.Berezovskaya, C.T.Armstrong, A.L.Boyle, M.Porrini, D.N.Woolfson, and P.E.Barran (2011).
Metal binding to a zinc-finger peptide: a comparison between solution and the gas phase.
  Chem Commun (Camb), 47, 412-414.  
20197039 D.Jantz, and J.M.Berg (2010).
Probing the DNA-binding affinity and specificity of designed zinc finger proteins.
  Biophys J, 98, 852-860.  
20573777 K.Nowick, A.T.Hamilton, H.Zhang, and L.Stubbs (2010).
Rapid sequence and expression divergence suggest selection for novel function in primate-specific KRAB-ZNF genes.
  Mol Biol Evol, 27, 2606-2617.  
20167128 M.Hatayama, and J.Aruga (2010).
Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions.
  BMC Evol Biol, 10, 53.  
19574296 A.M.Van der Sloot, C.Kiel, L.Serrano, and F.Stricher (2009).
Protein design in biological networks: from manipulating the input to modifying the output.
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20041164 J.H.Thomas, R.O.Emerson, and J.Shendure (2009).
Extraordinary molecular evolution in the PRDM9 fertility gene.
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19488728 K.Kandavelou, and S.Chandrasegaran (2009).
Custom-designed molecular scissors for site-specific manipulation of the plant and mammalian genomes.
  Methods Mol Biol, 544, 617-636.  
19429892 N.A.Temiz, and C.J.Camacho (2009).
Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface.
  Nucleic Acids Res, 37, 4076-4088.  
19119423 R.O.Emerson, and J.H.Thomas (2009).
Adaptive evolution in zinc finger transcription factors.
  PLoS Genet, 5, e1000325.  
19394375 T.Sera (2009).
Zinc-finger-based artificial transcription factors and their applications.
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18328744 A.Zarebski, C.S.Velu, A.M.Baktula, T.Bourdeau, S.R.Horman, S.Basu, S.J.Bertolone, M.Horwitz, D.A.Hildeman, J.O.Trent, and H.L.Grimes (2008).
Mutations in growth factor independent-1 associated with human neutropenia block murine granulopoiesis through colony stimulating factor-1.
  Immunity, 28, 370-380.  
19368013 J.Shearer (2008).
Influence of sequential guanidinium methylation on the energetics of the guanidinium...guanine dimer and guanidinium...guanine...cytosine trimer: implications for the control of protein...DNA interactions by arginine methyltransferases.
  J Phys Chem B, 112, 16995-17002.  
18545224 T.Cathomen, and J.K.Joung (2008).
Zinc-finger nucleases: the next generation emerges.
  Mol Ther, 16, 1200-1207.  
18026168 T.I.Cornu, S.Thibodeau-Beganny, E.Guhl, S.Alwin, M.Eichtinger, J.Joung, and T.Cathomen (2008).
DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases.
  Mol Ther, 16, 352-358.  
17626045 K.Rothfels, O.Rowland, and J.Segall (2007).
Zinc fingers 1 and 7 of yeast TFIIIA are essential for assembly of a functional transcription complex on the 5 S RNA gene.
  Nucleic Acids Res, 35, 4869-4881.  
16606703 A.T.Hamilton, S.Huntley, M.Tran-Gyamfi, D.M.Baggott, L.Gordon, and L.Stubbs (2006).
Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes.
  Genome Res, 16, 584-594.  
16385466 D.Lugtenberg, H.G.Yntema, M.J.Banning, A.R.Oudakker, H.V.Firth, L.Willatt, M.Raynaud, T.Kleefstra, J.P.Fryns, H.H.Ropers, J.Chelly, C.Moraine, J.Gecz, J.van Reeuwijk, S.B.Nabuurs, B.B.de Vries, B.C.Hamel, A.P.de Brouwer, and H.van Bokhoven (2006).
ZNF674: a new kruppel-associated box-containing zinc-finger gene involved in nonsyndromic X-linked mental retardation.
  Am J Hum Genet, 78, 265-278.  
16906878 R.G.Endres, and N.S.Wingreen (2006).
Weight matrices for protein-DNA binding sites from a single co-crystal structure.
  Phys Rev E Stat Nonlin Soft Matter Phys, 73, 061921.  
16826557 S.H.Mishra, C.M.Shelley, D.J.Barrow, M.K.Darby, and M.W.Germann (2006).
Solution structures and characterization of human immunodeficiency virus Rev responsive element IIB RNA targeting zinc finger proteins.
  Biopolymers, 83, 352-364.
PDB codes: 2ab3 2ab7
15869395 A.Sarai, and H.Kono (2005).
Protein-DNA recognition patterns and predictions.
  Annu Rev Biophys Biomol Struct, 34, 379-398.  
16107335 B.Dreier, R.P.Fuller, D.J.Segal, C.V.Lund, P.Blancafort, A.Huber, B.Koksch, and C.F.Barbas (2005).
Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors.
  J Biol Chem, 280, 35588-35597.  
15128941 D.Jantz, and J.M.Berg (2004).
Reduction in DNA-binding affinity of Cys2His2 zinc finger proteins by linker phosphorylation.
  Proc Natl Acad Sci U S A, 101, 7589-7593.  
15557258 M.J.Lachenmann, J.E.Ladbury, X.Qian, K.Huang, R.Singh, and M.A.Weiss (2004).
Solvation and the hidden thermodynamics of a zinc finger probed by nonstandard repair of a protein crevice.
  Protein Sci, 13, 3115-3126.
PDB code: 1xrz
14610091 X.Chen, B.Zhang, P.M.Harmon, W.Schaffner, D.O.Peterson, and D.P.Giedroc (2004).
A novel cysteine cluster in human metal-responsive transcription factor 1 is required for heavy metal-induced transcriptional activation in vivo.
  J Biol Chem, 279, 4515-4522.  
12620113 J.Kaczynski, T.Cook, and R.Urrutia (2003).
Sp1- and Krüppel-like transcription factors.
  Genome Biol, 4, 206.  
14576293 T.G.Uil, H.J.Haisma, and M.G.Rots (2003).
Therapeutic modulation of endogenous gene function by agents with designed DNA-sequence specificities.
  Nucleic Acids Res, 31, 6064-6078.  
12433998 N.Dathan, L.Zaccaro, S.Esposito, C.Isernia, J.G.Omichinski, A.Riccio, C.Pedone, B.Di Blasio, R.Fattorusso, and P.V.Pedone (2002).
The Arabidopsis SUPERMAN protein is able to specifically bind DNA through its single Cys2-His2 zinc finger motif.
  Nucleic Acids Res, 30, 4945-4951.  
11395410 C.O.Pabo, E.Peisach, and R.A.Grant (2001).
Design and selection of novel Cys2His2 zinc finger proteins.
  Annu Rev Biochem, 70, 313-340.  
11554446 D.P.Giedroc, X.Chen, and J.L.Apuy (2001).
Metal response element (MRE)-binding transcription factor-1 (MTF-1): structure, function, and regulation.
  Antioxid Redox Signal, 3, 577-596.  
11752579 G.Narla, K.E.Heath, H.L.Reeves, D.Li, L.E.Giono, A.C.Kimmelman, M.J.Glucksman, J.Narla, F.J.Eng, A.M.Chan, A.C.Ferrari, J.A.Martignetti, and S.L.Friedman (2001).
KLF6, a candidate tumor suppressor gene mutated in prostate cancer.
  Science, 294, 2563-2566.  
11113203 M.Bibikova, D.Carroll, D.J.Segal, J.K.Trautman, J.Smith, Y.G.Kim, and S.Chandrasegaran (2001).
Stimulation of homologous recombination through targeted cleavage by chimeric nucleases.
  Mol Cell Biol, 21, 289-297.  
11050227 J.H.Laity, H.J.Dyson, and P.E.Wright (2000).
Molecular basis for modulation of biological function by alternate splicing of the Wilms' tumor suppressor protein.
  Proc Natl Acad Sci U S A, 97, 11932-11935.  
10954606 J.Smith, M.Bibikova, F.G.Whitby, A.R.Reddy, S.Chandrasegaran, and D.Carroll (2000).
Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains.
  Nucleic Acids Res, 28, 3361-3369.  
10773080 M.Schaub, A.Krol, and P.Carbon (2000).
Structural organization of Staf-DNA complexes.
  Nucleic Acids Res, 28, 2114-2121.  
10801972 N.C.Horton, and J.J.Perona (2000).
Crystallographic snapshots along a protein-induced DNA-bending pathway.
  Proc Natl Acad Sci U S A, 97, 5729-5734.
PDB codes: 1eoo 1eop
10940247 S.A.Wolfe, L.Nekludova, and C.O.Pabo (2000).
DNA recognition by Cys2His2 zinc finger proteins.
  Annu Rev Biophys Biomol Struct, 29, 183-212.  
10637336 S.Lee, and M.D.Garfinkel (2000).
Characterization of Drosophila OVO protein DNA binding specificity using random DNA oligomer selection suggests zinc finger degeneration.
  Nucleic Acids Res, 28, 826-834.  
10449725 D.J.McColl, C.D.Honchell, and A.D.Frankel (1999).
Structure-based design of an RNA-binding zinc finger.
  Proc Natl Acad Sci U S A, 96, 9521-9526.  
10077584 D.J.Segal, B.Dreier, R.R.Beerli, and C.F.Barbas (1999).
Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences.
  Proc Natl Acad Sci U S A, 96, 2758-2763.  
10561603 G.Caderas, S.Klauser, N.Liu, A.Bienz, and B.Gutte (1999).
Inhibition of HIV-1 enhancer-controlled transcription by artificial enhancer-binding peptides derived from bacteriophage 434 repressor.
  Eur J Biochem, 266, 599-607.  
10090291 H.Kono, and A.Sarai (1999).
Structure-based prediction of DNA target sites by regulatory proteins.
  Proteins, 35, 114-131.  
  10048326 H.Zhu, and W.Braun (1999).
Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins.
  Protein Sci, 8, 326-342.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
10200256 T.Kusakabe, A.V.Hine, S.G.Hyberts, and C.C.Richardson (1999).
The Cys4 zinc finger of bacteriophage T7 primase in sequence-specific single-stranded DNA recognition.
  Proc Natl Acad Sci U S A, 96, 4295-4300.  
9786867 H.Zhao, E.Butler, J.Rodgers, T.Spizzo, S.Duesterhoeft, and D.Eide (1998).
Regulation of zinc homeostasis in yeast by binding of the ZAP1 transcriptional activator to zinc-responsive promoter elements.
  J Biol Chem, 273, 28713-28720.  
9467467 J.L.Pomerantz, S.A.Wolfe, and C.O.Pabo (1998).
Structure-based design of a dimeric zinc finger protein.
  Biochemistry, 37, 965-970.  
9562555 M.Elrod-Erickson, T.E.Benson, and C.O.Pabo (1998).
High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition.
  Structure, 6, 451-464.
PDB codes: 1a1f 1a1g 1a1h 1a1i 1a1j 1a1k 1a1l
9501194 R.T.Nolte, R.M.Conlin, S.C.Harrison, and R.S.Brown (1998).
Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex.
  Proc Natl Acad Sci U S A, 95, 2938-2943.
PDB code: 1tf6
9698361 X.Chen, A.Agarwal, and D.P.Giedroc (1998).
Structural and functional heterogeneity among the zinc fingers of human MRE-binding transcription factor-1.
  Biochemistry, 37, 11152-11161.  
9546210 Y.Choo, and J.W.Schwabe (1998).
All wrapped up.
  Nat Struct Biol, 5, 253-255.  
9421515 Y.Choo (1998).
End effects in DNA recognition by zinc finger arrays.
  Nucleic Acids Res, 26, 554-557.  
9166794 C.A.Blasie, and J.M.Berg (1997).
Electrostatic interactions across a beta-sheet.
  Biochemistry, 36, 6218-6222.  
9005850 H.A.Greisman, and C.O.Pabo (1997).
A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites.
  Science, 275, 657-661.  
9204285 J.Heringa, and W.R.Taylor (1997).
Three-dimensional domain duplication, swapping and stealing.
  Curr Opin Struct Biol, 7, 416-421.  
9159121 M.Isalan, Y.Choo, and A.Klug (1997).
Synergy between adjacent zinc fingers in sequence-specific DNA recognition.
  Proc Natl Acad Sci U S A, 94, 5617-5621.  
  9300483 M.Schmiedeskamp, P.Rajagopal, and R.E.Klevit (1997).
NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1.
  Protein Sci, 6, 1835-1848.  
9369471 M.Schmiedeskamp, and R.E.Klevit (1997).
Paramagnetic cobalt as a probe of the orientation of an accessory DNA-binding region of the yeast ADR1 zinc-finger protein.
  Biochemistry, 36, 14003-14011.  
9251783 N.Pastor, L.Pardo, and H.Weinstein (1997).
Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein.
  Biophys J, 73, 640-652.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
9171100 S.Böhm, D.Frishman, and H.W.Mewes (1997).
Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins.
  Nucleic Acids Res, 25, 2464-2469.  
9110988 W.J.Friesen, and M.K.Darby (1997).
Phage display of RNA binding zinc fingers from transcription factor IIIA.
  J Biol Chem, 272, 10994-10997.  
9032060 Y.Choo, and A.Klug (1997).
Physical basis of a protein-DNA recognition code.
  Curr Opin Struct Biol, 7, 117-125.  
9266170 Y.Lu, and J.S.Valentine (1997).
Engineering metal-binding sites in proteins.
  Curr Opin Struct Biol, 7, 495-500.  
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 codes are shown on the right.

 

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