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protein dna_rna ligands Protein-protein interface(s) links
Transcription/DNA PDB id
1cma
Jmol
Contents
Protein chains
104 a.a. *
DNA/RNA
Ligands
SAM ×2
Waters ×36
* Residue conservation analysis
PDB id:
1cma
Name: Transcription/DNA
Title: Met repressor/DNA complex + s-adenosyl-methionine
Structure: DNA (5'-d( Tp Tp Ap Gp Ap Cp Gp Tp Cp T)-3'). Chain: c. Engineered: yes. DNA (5'-d( Ap Gp Ap Cp Gp Tp Cp Tp A)-3'). Chain: d. Engineered: yes. Protein (met repressor). Chain: a, b
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.80Å     R-factor:   0.220    
Authors: W.S.Somers,S.E.V.Phillips
Key ref: W.S.Somers and S.E.Phillips (1992). Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands. Nature, 359, 387-393. PubMed id: 1406951 DOI: 10.1038/359387a0
Date:
24-Aug-92     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A8U6  (METJ_ECOLI) -  Met repressor
Seq:
Struc: 		105 a.a.
104 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     regulation of transcription   6 terms 
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1038/359387a0 Nature 359:387-393 (1992)
PubMed id: 1406951  
 
 
Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands.
W.S.Somers, S.E.Phillips.
 
  ABSTRACT  
 
The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognizes sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21123191 L.Huang, P.Yin, X.Zhu, Y.Zhang, and K.Ye (2011).
Crystal structure and centromere binding of the plasmid segregation protein ParB from pCXC100.
  Nucleic Acids Res, 39, 2954-2968.
PDB code: 3no7
21336656 N.Chopra, S.Agarwal, S.Verma, S.Bhatnagar, and R.Bhatnagar (2011).
Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function.
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20196619 A.M.Augustus, H.Sage, and L.D.Spicer (2010).
Binding of MetJ repressor to specific and nonspecific DNA and effect of S-adenosylmethionine on these interactions.
  Biochemistry, 49, 3289-3295.  
20010837 A.Sabogal, A.Y.Lyubimov, J.E.Corn, J.M.Berger, and D.C.Rio (2010).
THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves.
  Nat Struct Mol Biol, 17, 117-123.  
20569269 E.Diago-Navarro, A.M.Hernandez-Arriaga, J.López-Villarejo, A.J.Muñoz-Gómez, M.B.Kamphuis, R.Boelens, M.Lemonnier, and R.Díaz-Orejas (2010).
parD toxin-antitoxin system of plasmid R1--basic contributions, biotechnological applications and relationships with closely-related toxin-antitoxin systems.
  FEBS J, 277, 3097-3117.  
20581212 E.L.Benanti, and P.T.Chivers (2010).
Geobacter uraniireducens NikR displays a DNA binding mode distinct from other members of the NikR family.
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20334529 R.Rohs, X.Jin, S.M.West, R.Joshi, B.Honig, and R.S.Mann (2010).
Origins of specificity in protein-DNA recognition.
  Annu Rev Biochem, 79, 233-269.  
20144952 S.Campagne, O.Saurel, V.Gervais, and A.Milon (2010).
Structural determinants of specific DNA-recognition by the THAP zinc finger.
  Nucleic Acids Res, 38, 3466-3476.
PDB code: 2ko0
19520770 A.M.Hernández-Arriaga, T.S.Rubio-Lepe, M.Espinosa, and G.del Solar (2009).
Repressor CopG prevents access of RNA polymerase to promoter and actively dissociates open complexes.
  Nucleic Acids Res, 37, 4799-4811.  
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Structure, function, and targets of the transcriptional regulator SvtR from the hyperthermophilic archaeal virus SIRV1.
  J Biol Chem, 284, 22222-22237.
PDB code: 2kel
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Agrobacterium tumefaciens VirC2 enhances T-DNA transfer and virulence through its C-terminal ribbon-helix-helix DNA-binding fold.
  Proc Natl Acad Sci U S A, 106, 9643-9648.
PDB code: 2rh3
19244617 J.W.Locasale, A.A.Napoli, S.Chen, H.M.Berman, and C.L.Lawson (2009).
Signatures of protein-DNA recognition in free DNA binding sites.
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PDB codes: 1hq7 2b1b 2b1c 2b1d
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PDB code: 2rbf
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  PLoS ONE, 2, e273.  
17449623 C.Geslin, M.Gaillard, D.Flament, K.Rouault, M.Le Romancer, D.Prieur, and G.Erauso (2007).
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  J Bacteriol, 189, 4510-4519.  
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The N-terminal arm of the Helicobacter pylori Ni2+-dependent transcription factor NikR is required for specific DNA binding.
  J Biol Chem, 282, 20365-20375.  
17676053 E.R.Schreiter, and C.L.Drennan (2007).
Ribbon-helix-helix transcription factors: variations on a theme.
  Nat Rev Microbiol, 5, 710-720.  
17898804 J.Møller-Jensen, S.Ringgaard, C.P.Mercogliano, K.Gerdes, and J.Löwe (2007).
Structural analysis of the ParR/parC plasmid partition complex.
  EMBO J, 26, 4413-4422.
PDB code: 2jd3
18097417 M.A.Schumacher, T.C.Glover, A.J.Brzoska, S.O.Jensen, T.D.Dunham, R.A.Skurray, and N.Firth (2007).
Segrosome structure revealed by a complex of ParR with centromere DNA.
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PDB code: 2q2k
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The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding.
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Macrocyclic beta-sheet peptides that mimic protein quaternary structure through intermolecular beta-sheet interactions.
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Structural basis for the differential regulation of DNA by the methionine repressor MetJ.
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NikR-operator complex structure and the mechanism of repressor activation by metal ions.
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Helicobacter pylori protein HP0222 belongs to Arc/MetJ family of transcriptional regulators.
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The unstructured N-terminal tail of ParG modulates assembly of a quaternary nucleoprotein complex in transcription repression.
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16153161 G.N.Cohen, and G.N.Cohen (2005).
Looking back.
  Annu Rev Microbiol, 59, 1.  
  15927055 K.Sivaraman, A.S.Seshasayee, K.Swaminathan, G.Muthukumaran, and G.Pennathur (2005).
Promoter addresses: revelations from oligonucleotide profiling applied to the Escherichia coli genome.
  Theor Biol Med Model, 2, 20.  
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Role of the N-terminal region and of beta-sheet residue Thr29 on the activity of the omega2 global regulator from the broad-host range Streptococcus pyogenes plasmid pSM19035.
  Biol Chem, 386, 881-894.  
16225687 P.Z.Kozbial, and A.R.Mushegian (2005).
Natural history of S-adenosylmethionine-binding proteins.
  BMC Struct Biol, 5, 19.  
15190131 A.B.de la Hoz, F.Pratto, R.Misselwitz, C.Speck, W.Weihofen, K.Welfle, W.Saenger, H.Welfle, and J.C.Alonso (2004).
Recognition of DNA by omega protein from the broad-host range Streptococcus pyogenes plasmid pSM19035: analysis of binding to operator DNA with one to four heptad repeats.
  Nucleic Acids Res, 32, 3136-3147.  
15155740 D.Gu, Y.Zhou, V.Kallhoff, B.Baban, J.J.Tanner, and D.F.Becker (2004).
Identification and characterization of the DNA-binding domain of the multifunctional PutA flavoenzyme.
  J Biol Chem, 279, 31171-31176.  
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Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC.
  Nat Struct Biol, 10, 1002-1010.
PDB codes: 1omh 1osb 1qx0
14622405 A.P.Golovanov, D.Barillà, M.Golovanova, F.Hayes, and L.Y.Lian (2003).
ParG, a protein required for active partition of bacterial plasmids, has a dimeric ribbon-helix-helix structure.
  Mol Microbiol, 50, 1141-1153.
PDB code: 1p94
12444085 A.Yokota, K.Tsumoto, M.Shiroishi, H.Kondo, and I.Kumagai (2003).
The role of hydrogen bonding via interfacial water molecules in antigen-antibody complexation. The HyHEL-10-HEL interaction.
  J Biol Chem, 278, 5410-5418.
PDB codes: 1j1o 1j1p 1j1x
14515373 K.Bastard, A.Thureau, R.Lavery, and C.Prévost (2003).
Docking macromolecules with flexible segments.
  J Comput Chem, 24, 1910-1920.  
12682016 S.X.Cohen, M.Moulin, S.Hashemolhosseini, K.Kilian, M.Wegner, and C.W.Müller (2003).
Structure of the GCM domain-DNA complex: a DNA-binding domain with a novel fold and mode of target site recognition.
  EMBO J, 22, 1835-1845.
PDB code: 1odh
12514135 T.Kwon, J.H.Chang, E.Kwak, C.W.Lee, A.Joachimiak, Y.C.Kim, J.Lee, and Y.Cho (2003).
Mechanism of histone lysine methyl transfer revealed by the structure of SET7/9-AdoMet.
  EMBO J, 22, 292-303.
PDB codes: 1n6a 1n6c
12193609 G.del Solar, A.M.Hernández-Arriaga, F.X.Gomis-Rüth, M.Coll, and M.Espinosa (2002).
A genetically economical family of plasmid-encoded transcriptional repressors involved in control of plasmid copy number.
  J Bacteriol, 184, 4943-4951.  
11867549 M.A.Schumacher, M.C.Miller, S.Grkovic, M.H.Brown, R.A.Skurray, and R.G.Brennan (2002).
Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR.
  EMBO J, 21, 1210-1218.
PDB code: 1jt0
11809880 N.A.Pavlov, D.I.Cherny, I.V.Nazimov, A.I.Slesarev, and V.Subramaniam (2002).
Identification, cloning and characterization of a new DNA-binding protein from the hyperthermophilic methanogen Methanopyrus kandleri.
  Nucleic Acids Res, 30, 685-694.  
11827949 N.Rajewsky, N.D.Socci, M.Zapotocky, and E.D.Siggia (2002).
The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons.
  Genome Res, 12, 298-308.  
11226234 A.Berggrun, and R.T.Sauer (2001).
Contributions of distinct quaternary contacts to cooperative operator binding by Mnt repressor.
  Proc Natl Acad Sci U S A, 98, 2301-2305.  
11741530 C.W.Garvie, and C.Wolberger (2001).
Recognition of specific DNA sequences.
  Mol Cell, 8, 937-946.  
11454201 H.Afif, N.Allali, M.Couturier, and L.Van Melderen (2001).
The ratio between CcdA and CcdB modulates the transcriptional repression of the ccd poison-antidote system.
  Mol Microbiol, 41, 73-82.  
11717268 S.Grkovic, M.H.Brown, M.A.Schumacher, R.G.Brennan, and R.A.Skurray (2001).
The staphylococcal QacR multidrug regulator binds a correctly spaced operator as a pair of dimers.
  J Bacteriol, 183, 7102-7109.  
  10986458 C.W.Garvie, and S.E.Phillips (2000).
Direct and indirect readout in mutant Met repressor-operator complexes.
  Structure, 8, 905-914.
PDB codes: 1mj2 1mjm 1mjo 1mjp 1mjq
10734204 E.Pérez-Rueda, and J.Collado-Vides (2000).
The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12.
  Nucleic Acids Res, 28, 1838-1847.  
10696113 M.Lu, and T.A.Steitz (2000).
Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.
  Proc Natl Acad Sci U S A, 97, 2023-2028.
PDB code: 1dfu
  11104519 N.M.Luscombe, S.E.Austin, H.M.Berman, and J.M.Thornton (2000).
An overview of the structures of protein-DNA complexes.
  Genome Biol, 1, REVIEWS001.  
10727231 S.Deb, S.Bandyopadhyay, and S.Roy (2000).
DNA sequence dependent and independent conformational changes in multipartite operator recognition by lambda-repressor.
  Biochemistry, 39, 3377-3383.  
9890988 A.McGregor, J.B.Murray, C.J.Adams, P.G.Stockley, and B.A.Connolly (1999).
Secondary structure mapping of an RNA ligand that has high affinity for the MetJ repressor protein and interference modification analysis of the protein-RNA complex.
  J Biol Chem, 274, 2255-2262.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
10661868 M.Oberer, H.Lindner, O.Glatter, C.Kratky, and W.Keller (1999).
Thermodynamic properties and DNA binding of the ParD protein from the broad host-range plasmid RK2/RP4 killing system.
  Biol Chem, 380, 1413-1420.  
10391902 P.L.Lum, and J.F.Schildbach (1999).
Specific DNA recognition by F Factor TraY involves beta-sheet residues.
  J Biol Chem, 274, 19644-19648.  
  10595554 P.T.Chivers, and R.T.Sauer (1999).
NikR is a ribbon-helix-helix DNA-binding protein.
  Protein Sci, 8, 2494-2500.  
9712865 E.Pohl, R.K.Holmes, and W.G.Hol (1998).
Motion of the DNA-binding domain with respect to the core of the diphtheria toxin repressor (DtxR) revealed in the crystal structures of apo- and holo-DtxR.
  J Biol Chem, 273, 22420-22427.
PDB codes: 1bi0 1bi1 1bi2 1bi3
  9732276 F.W.Whipple, E.F.Hou, and A.Hochschild (1998).
Amino acid-amino acid contacts at the cooperativity interface of the bacteriophage lambda and P22 repressors.
  Genes Dev, 12, 2791-2802.  
9857196 F.X.Gomis-Rüth, M.Solá, P.Acebo, A.Párraga, A.Guasch, R.Eritja, A.González, M.Espinosa, G.del Solar, and M.Coll (1998).
The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator.
  EMBO J, 17, 7404-7415.
PDB codes: 1b01 2cpg
9860945 H.Rozenberg, D.Rabinovich, F.Frolow, R.S.Hegde, and Z.Shakked (1998).
Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets.
  Proc Natl Acad Sci U S A, 95, 15194-15199.
PDB codes: 423d 424d 425d
9430665 J.F.Schildbach, C.R.Robinson, and R.T.Sauer (1998).
Biophysical characterization of the TraY protein of Escherichia coli F factor.
  J Biol Chem, 273, 1329-1333.  
9748476 J.M.Berger (1998).
Structure of DNA topoisomerases.
  Biochim Biophys Acta, 1400, 3.  
9736626 M.D.Allen, K.Yamasaki, M.Ohme-Takagi, M.Tateno, and M.Suzuki (1998).
A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.
  EMBO J, 17, 5484-5496.
PDB codes: 1gcc 2gcc 3gcc
9668115 M.K.Shirra, and U.Hansen (1998).
LSF and NTF-1 share a conserved DNA recognition motif yet require different oligomerization states to form a stable protein-DNA complex.
  J Biol Chem, 273, 19260-19268.  
9736624 M.Newman, K.Lunnen, G.Wilson, J.Greci, I.Schildkraut, and S.E.Phillips (1998).
Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.
  EMBO J, 17, 5466-5476.
PDB code: 1dmu
9741623 Y.Shi, Y.F.Wang, L.Jayaraman, H.Yang, J.Massagué, and N.P.Pavletich (1998).
Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-beta signaling.
  Cell, 94, 585-594.
PDB code: 1mhd
9305935 A.H.Lauber, T.J.Barrett, M.Subramaniam, M.Schuchard, and T.C.Spelsberg (1997).
A DNA-binding element for a steroid receptor-binding factor is flanked by dual nuclear matrix DNA attachment sites in the c-myc gene promoter.
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9254598 D.N.Paolella, Y.Liu, M.A.Fabian, and A.Schepartz (1997).
Electrostatic mechanism for DNA bending by bZIP proteins.
  Biochemistry, 36, 10033-10038.  
9199797 J.A.Subirana, and T.Faria (1997).
Influence of sequence on the conformation of the B-DNA helix.
  Biophys J, 73, 333-338.  
9032054 M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.
  Curr Opin Struct Biol, 7, 76-85.  
9278422 M.A.Schumacher, A.Glasfeld, H.Zalkin, and R.G.Brennan (1997).
The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity.
  J Biol Chem, 272, 22648-22653.
PDB code: 1wet
9782775 M.Tateno, K.Yamasaki, N.Amano, J.Kakinuma, H.Koike, M.D.Allen, and M.Suzuki (1997).
DNA recognition by beta-sheets.
  Biopolymers, 44, 335-359.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
9103202 S.M.Soisson, B.MacDougall-Shackleton, R.Schleif, and C.Wolberger (1997).
Structural basis for ligand-regulated oligomerization of AraC.
  Science, 276, 421-425.
PDB codes: 2ara 2arc
9207015 W.Gong, M.O'Gara, R.M.Blumenthal, and X.Cheng (1997).
Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
  Nucleic Acids Res, 25, 2702-2715.
PDB code: 1boo
8733235 C.Günes, D.Staacke, B.von Wilcken-Bergmann, and B.Müller-Hill (1996).
Co-operative binding of two Trp repressor dimers to alpha- or beta-centred trp operators.
  Mol Microbiol, 20, 375-384.  
  8897612 C.J.Morton, and J.E.Ladbury (1996).
Water-mediated protein-DNA interactions: the relationship of thermodynamics to structural detail.
  Protein Sci, 5, 2115-2118.  
8805260 D.Moras, and A.Poterszman (1996).
Getting into the major groove. Protein-RNA interactions.
  Curr Biol, 6, 530-532.  
8679635 H.Thorogood, T.R.Waters, A.W.Parker, C.W.Wharton, and B.A.Connolly (1996).
Resonance Raman spectroscopy of 4-thiothymidine and oligodeoxynucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV.
  Biochemistry, 35, 8723-8733.  
8599757 L.Urpí, V.Tereshko, L.Malinina, T.Huynh-Dinh, and J.A.Subirana (1996).
Structural comparison between the d(CTAG) sequence in oligonucleotides and trp and met repressor-operator complexes.
  Nat Struct Biol, 3, 325-328.
PDB codes: 249d 250d
  8824627 P.M.Silverman, and A.Sholl (1996).
Effect of traY amber mutations on F-plasmid traY promoter activity in vivo.
  J Bacteriol, 178, 5787-5789.  
8702525 R.Magnuson, H.Lehnherr, G.Mukhopadhyay, and M.B.Yarmolinsky (1996).
Autoregulation of the plasmid addiction operon of bacteriophage P1.
  J Biol Chem, 271, 18705-18710.  
8557624 S.Cal, and B.A.Connolly (1996).
The EcoRV modification methylase causes considerable bending of DNA upon binding to its recognition sequence GATATC.
  J Biol Chem, 271, 1008-1015.  
8809770 W.C.Nelson, and S.W.Matson (1996).
The F plasmid traY gene product binds DNA as a monomer or a dimer: structural and functional implications.
  Mol Microbiol, 20, 1179-1187.  
7773740 A.K.Aggarwal (1995).
Structure and function of restriction endonucleases.
  Curr Opin Struct Biol, 5, 11-19.  
7625690 A.Klug (1995).
Gene regulatory proteins and their interaction with DNA.
  Ann N Y Acad Sci, 758, 143-160.  
7567471 B.E.Withers, and J.C.Dunbar (1995).
DNA determinants in sequence-specific recognition by XmaI endonuclease.
  Nucleic Acids Res, 23, 3571-3577.  
7664107 D.Stanojevic, and G.L.Verdine (1995).
Deconstruction of GCN4/GCRE into a monomeric peptide-DNA complex.
  Nat Struct Biol, 2, 450-457.  
7540055 G.Siligardi, and A.F.Drake (1995).
The importance of extended conformations and, in particular, the PII conformation for the molecular recognition of peptides.
  Biopolymers, 37, 281-292.  
7716167 J.Janin (1995).
Elusive affinities.
  Proteins, 21, 30-39.  
  7735836 J.W.Schwabe, L.Chapman, and D.Rhodes (1995).
The oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation.
  Structure, 3, 201-213.  
7553867 M.A.Schumacher, K.Y.Choi, F.Lu, H.Zalkin, and R.G.Brennan (1995).
Mechanism of corepressor-mediated specific DNA binding by the purine repressor.
  Cell, 83, 147-155.
PDB code: 1dbq
7647248 M.A.Young, G.Ravishanker, D.L.Beveridge, and H.M.Berman (1995).
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
  Biophys J, 68, 2454-2468.  
8530394 M.Dlakic, and R.E.Harrington (1995).
Bending and torsional flexibility of G/C-rich sequences as determined by cyclization assays.
  J Biol Chem, 270, 29945-29952.  
7610037 M.Suzuki, and N.Yagi (1995).
Stereochemical basis of DNA bending by transcription factors.
  Nucleic Acids Res, 23, 2083-2091.  
  8139553 A.Andrianopoulos, and W.E.Timberlake (1994).
The Aspergillus nidulans abaA gene encodes a transcriptional activator that acts as a genetic switch to control development.
  Mol Cell Biol, 14, 2503-2515.  
  7987223 J.Guenot, R.J.Fletterick, and P.A.Kollman (1994).
A negative electrostatic determinant mediates the association between the Escherichia coli trp repressor and its operator DNA.
  Protein Sci, 3, 1276-1285.  
8302865 J.Liu, M.Sodeoka, W.S.Lane, and G.L.Verdine (1994).
Evidence for a non-alpha-helical DNA-binding motif in the Rel homology region.
  Proc Natl Acad Sci U S A, 91, 908-912.  
  8087557 K.Phillips, and S.E.Phillips (1994).
Electrostatic activation of Escherichia coli methionine repressor.
  Structure, 2, 309-316.  
8041727 L.Nekludova, and C.O.Pabo (1994).
Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes.
  Proc Natl Acad Sci U S A, 91, 6948-6952.  
  7915817 L.S.Frost, K.Ippen-Ihler, and R.A.Skurray (1994).
Analysis of the sequence and gene products of the transfer region of the F sex factor.
  Microbiol Rev, 58, 162-210.  
  8087558 M.Suzuki (1994).
A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules.
  Structure, 2, 317-326.  
8121798 P.P.Papp, and D.K.Chattoraj (1994).
Missing-base and ethylation interference footprinting of P1 plasmid replication initiator.
  Nucleic Acids Res, 22, 152-157.  
8139652 S.E.Phillips, and P.G.Stockley (1994).
Similarity of met and trp repressors.
  Nature, 368, 106.  
8092669 W.S.Somers, J.B.Rafferty, K.Phillips, S.Strathdee, Y.Y.He, T.McNally, I.Manfield, O.Navratil, I.G.Old, and I.Saint-Girons (1994).
The Met repressor-operator complex: DNA recognition by beta-strands.
  Ann N Y Acad Sci, 726, 105-117.  
  8076590 X.Cheng, K.Balendiran, I.Schildkraut, and J.E.Anderson (1994).
Structure of PvuII endonuclease with cognate DNA.
  EMBO J, 13, 3927-3935.
PDB code: 1pvi
8152370 Y.Luo, Q.Gao, and R.C.Deonier (1994).
Mutational and physical analysis of F plasmid traY protein binding to oriT.
  Mol Microbiol, 11, 459-469.  
8223636 A.J.Bendall, R.A.Sturm, P.A.Danoy, and P.L.Molloy (1993).
Broad binding-site specificity and affinity properties of octamer 1 and brain octamer-binding proteins.
  Eur J Biochem, 217, 799-811.  
8404814 D.E.Lewis, and J.Carey (1993).
Analysis of trp repressor-DNA interactions using gel electrophoresis.
  Electrophoresis, 14, 713-719.  
8412677 I.B.Vipond, and S.E.Halford (1993).
Structure-function correlation for the EcoRV restriction enzyme: from non-specific binding to specific DNA cleavage.
  Mol Microbiol, 9, 225-231.  
8221895 J.W.Schwabe, L.Chapman, J.T.Finch, and D.Rhodes (1993).
The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements.
  Cell, 75, 567-578.
PDB code: 1hcq
8290361 M.P.Laget, I.Callebaut, Y.de Launoit, D.Stehelin, and J.P.Mornon (1993).
Predicted common structural features of DNA-binding domains from Ets, Myb and HMG transcription factors.
  Nucleic Acids Res, 21, 5987-5996.  
  8392621 M.R.Chen, J.M.Middeldorp, and S.D.Hayward (1993).
Separation of the complex DNA binding domain of EBNA-1 into DNA recognition and dimerization subdomains of novel structure.
  J Virol, 67, 4875-4885.  
8516313 S.A.Bustos, and R.F.Schleif (1993).
Functional domains of the AraC protein.
  Proc Natl Acad Sci U S A, 90, 5638-5642.  
8343957 X.Cheng, S.Kumar, J.Posfai, J.W.Pflugrath, and R.J.Roberts (1993).
Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine.
  Cell, 74, 299-307.
PDB code: 1hmy
15336020 J.W.Schwabe (1992).
DNA between the sheets.
  Curr Biol, 2, 661-663.  
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