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PDBsum entry 2pub
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Transcription/DNA PDB id
2pub

 

 

 

 

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Contents
Protein chain
338 a.a. *
DNA/RNA
Ligands
ADE
Waters ×53
* Residue conservation analysis
PDB id:
2pub
Name: Transcription/DNA
Title: Crystal structure of the laci family member, purr, bound to dna: minor groove binding by alpha helices
Structure: DNA (5'- d( Tp Ap Cp Gp Cp Ap Ap Ap Cp Gp Tp Tp Tp Gp Cp Gp T )-3'). Chain: b. Engineered: yes. Purine repressor. Chain: a. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Escherichia coli. Organism_taxid: 562. Gene: purr. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.70Å     R-factor:   0.171    
Authors: R.G.Schumacher,K.Y.Choi,H.Zalkin,M.A.Brennan
Key ref: M.A.Schumacher et al. (1994). Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices. Science, 266, 763-770. PubMed id: 7973627 DOI: 10.1126/science.7973627
Date:
04-Oct-97     Release date:   06-May-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0ACP7  (PURR_ECOLI) -  HTH-type transcriptional repressor PurR from Escherichia coli (strain K12)
Seq:
Struc: 		341 a.a.
338 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chain
  T-A-C-G-C-A-A-A-C-G-T-T-T-G-C-G-T 17 bases

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1126/science.7973627 Science 266:763-770 (1994)
PubMed id: 7973627  
 
 
Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices.
M.A.Schumacher, K.Y.Choi, H.Zalkin, R.G.Brennan.
 
  ABSTRACT  
 
The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A resolution by x-ray crystallography. The bipartite structure of PurR consists of an amino-terminal DNA-binding domain and a larger carboxyl-terminal corepressor binding and dimerization domain that is similar to that of the bacterial periplasmic binding proteins. The DNA-binding domain contains a helix-turn-helix motif that makes base-specific contacts in the major groove of the DNA. Base contacts are also made by residues of symmetry-related alpha helices, the "hinge" helices, which bind deeply in the minor groove. Critical to hinge helix-minor groove binding is the intercalation of the side chains of Leu54 and its symmetry-related mate, Leu54', into the central CpG-base pair step. These residues thereby act as "leucine levers" to pry open the minor groove and kink the purF operator by 45 degrees.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21106498 M.A.Schumacher, M.Sprehe, M.Bartholomae, W.Hillen, and R.G.Brennan (2011).
Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators.
  Nucleic Acids Res, 39, 2931-2942.
PDB codes: 3oqm 3oqn 3oqo
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
  Nucleic Acids Res, 39, 744-754.
PDB code: 3ndh
20581202 A.Daddaoua, T.Krell, C.Alfonso, B.Morel, and J.L.Ramos (2010).
Compartmentalized glucose metabolism in Pseudomonas putida is controlled by the PtxS repressor.
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21085639 F.M.Camas, E.J.Alm, and J.F.Poyatos (2010).
Local gene regulation details a recognition code within the LacI transcriptional factor family.
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20512969 L.Milk, R.Daber, and M.Lewis (2010).
Functional rules for lac repressor-operator associations and implications for protein-DNA interactions.
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20061473 P.Himes, S.J.McBryant, and L.Kroos (2010).
Two regions of Bacillus subtilis transcription factor SpoIIID allow a monomer to bind DNA.
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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.
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20062058 S.Djuranovic, M.K.Zinchenko, J.K.Hur, A.Nahvi, J.L.Brunelle, E.J.Rogers, and R.Green (2010).
Allosteric regulation of Argonaute proteins by miRNAs.
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The Tumbleweed: towards a synthetic proteinmotor.
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Signatures of protein-DNA recognition in free DNA binding sites.
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PDB codes: 1hq7 2b1b 2b1c 2b1d
20001804 K.Gurova (2009).
New hopes from old drugs: revisiting DNA-binding small molecules as anticancer agents.
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19540845 R.Daber, and M.Lewis (2009).
A novel molecular switch.
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18344359 H.S.Kim, H.Yi, J.Myung, K.R.Piper, and S.K.Farrand (2008).
Opine-based Agrobacterium competitiveness: dual expression control of the agrocinopine catabolism (acc) operon by agrocinopines and phosphate levels.
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The role of DNA-binding specificity in the evolution of bacterial regulatory networks.
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18388862 P.Rondard, S.Huang, C.Monnier, H.Tu, B.Blanchard, N.Oueslati, F.Malhaire, Y.Li, E.Trinquet, G.Labesse, J.P.Pin, and J.Liu (2008).
Functioning of the dimeric GABA(B) receptor extracellular domain revealed by glycan wedge scanning.
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18469102 S.El Qaidi, and J.Plumbridge (2008).
Switching control of expression of ptsG from the Mlc regulon to the NagC regulon.
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18829719 S.Jamal Rahi, P.Virnau, L.A.Mirny, and M.Kardar (2008).
Predicting transcription factor specificity with all-atom models.
  Nucleic Acids Res, 36, 6209-6217.  
18536016 S.Meinhardt, and L.Swint-Kruse (2008).
Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformatics-based predictions generate true positives and false negatives.
  Proteins, 73, 941-957.  
18922190 V.E.Angarica, A.G.Pérez, A.T.Vasconcelos, J.Collado-Vides, and B.Contreras-Moreira (2008).
Prediction of TF target sites based on atomistic models of protein-DNA complexes.
  BMC Bioinformatics, 9, 436.  
17211887 A.T.Macias, N.K.Banavali, and A.D.MacKerell (2007).
DNA bending induced by carbocyclic sugar analogs constrained to the north conformation.
  Biopolymers, 85, 438-449.  
17372346 B.Loll, M.Kowalczyk, C.Alings, A.Chieduch, J.Bardowski, W.Saenger, and J.Biesiadka (2007).
Structure of the transcription regulator CcpA from Lactococcus lactis.
  Acta Crystallogr D Biol Crystallogr, 63, 431-436.
PDB code: 2o20
17214883 F.Spyrakis, P.Cozzini, C.Bertoli, A.Marabotti, G.E.Kellogg, and A.Mozzarelli (2007).
Energetics of the protein-DNA-water interaction.
  BMC Struct Biol, 7, 4.  
17652321 K.Yamasaki, T.Akiba, T.Yamasaki, and K.Harata (2007).
Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1.
  Nucleic Acids Res, 35, 5073-5084.
PDB codes: 2o49 2o4a
  17401189 R.K.Singh, G.J.Palm, S.Panjikar, and W.Hinrichs (2007).
Structure of the apo form of the catabolite control protein A (CcpA) from Bacillus megaterium with a DNA-binding domain.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 253-257.
PDB code: 2jcg
17436321 S.Tungtur, S.M.Egan, and L.Swint-Kruse (2007).
Functional consequences of exchanging domains between LacI and PurR are mediated by the intervening linker sequence.
  Proteins, 68, 375-388.  
17401341 Y.Xu, R.Tashiro, and H.Sugiyama (2007).
Photochemical determination of different DNA structures.
  Nat Protoc, 2, 78-87.  
17158705 J.Deutscher, C.Francke, and P.W.Postma (2006).
How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria.
  Microbiol Mol Biol Rev, 70, 939.  
16475182 J.Seetharaman, D.Kumaran, J.B.Bonanno, S.K.Burley, and S.Swaminathan (2006).
Crystal structure of a putative HTH-type transcriptional regulator yxaF from Bacillus subtilis.
  Proteins, 63, 1087-1091.
PDB code: 1sgm
16698780 M.Zacharias (2006).
Minor groove deformability of DNA: a molecular dynamics free energy simulation study.
  Biophys J, 91, 882-891.  
16962967 P.Prabakaran, J.G.Siebers, S.Ahmad, M.M.Gromiha, M.G.Singarayan, and A.Sarai (2006).
Classification of protein-DNA complexes based on structural descriptors.
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16755587 V.Chaptal, V.Gueguen-Chaignon, S.Poncet, C.Lecampion, P.Meyer, J.Deutscher, A.Galinier, S.Nessler, and S.Moréra (2006).
Structural analysis of B. subtilis CcpA effector binding site.
  Proteins, 64, 814-816.
PDB code: 2fep
16519689 W.Müller, N.Horstmann, W.Hillen, and H.Sticht (2006).
The transcription regulator RbsR represents a novel interaction partner of the phosphoprotein HPr-Ser46-P in Bacillus subtilis.
  FEBS J, 273, 1251-1261.  
16416452 Y.Xu, and H.Sugiyama (2006).
Photochemical approach to probing different DNA structures.
  Angew Chem Int Ed Engl, 45, 1354-1362.  
16061804 A.B.Datta, S.Panjikar, M.S.Weiss, P.Chakrabarti, and P.Parrack (2005).
Structure of lambda CII: implications for recognition of direct-repeat DNA by an unusual tetrameric organization.
  Proc Natl Acad Sci U S A, 102, 11242-11247.
PDB code: 1xwr
15653643 C.Y.Chen, T.P.Ko, T.W.Lin, C.C.Chou, C.J.Chen, and A.H.Wang (2005).
Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d.
  Nucleic Acids Res, 33, 430-438.
PDB codes: 1wto 1wtp 1wtq 1wtr 1wtv 1wtw 1wtx 1xyi
15369672 M.A.Schumacher, G.S.Allen, M.Diel, G.Seidel, W.Hillen, and R.G.Brennan (2004).
Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P.
  Cell, 118, 731-741.
PDB codes: 1rzr 1sxg 1sxh 1sxi
15465864 M.Slutsky, and L.A.Mirny (2004).
Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.
  Biophys J, 87, 4021-4035.  
15549109 R.T.Batey, S.D.Gilbert, and R.K.Montange (2004).
Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine.
  Nature, 432, 411-415.
PDB codes: 1u8d 4fe5
15289461 S.Semsey, M.Y.Tolstorukov, K.Virnik, V.B.Zhurkin, and S.Adhya (2004).
DNA trajectory in the Gal repressosome.
  Genes Dev, 18, 1898-1907.  
12837784 A.K.Bera, J.Zhu, H.Zalkin, and J.L.Smith (2003).
Functional dissection of the Bacillus subtilis pur operator site.
  J Bacteriol, 185, 4099-4109.
PDB code: 1p4a
12065400 C.G.Kalodimos, A.M.Bonvin, R.K.Salinas, R.Wechselberger, R.Boelens, and R.Kaptein (2002).
Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain.
  EMBO J, 21, 2866-2876.
PDB code: 1l1m
11917033 L.A.Mirny, and M.S.Gelfand (2002).
Structural analysis of conserved base pairs in protein-DNA complexes.
  Nucleic Acids Res, 30, 1704-1711.  
11910022 L.Swint-Kruse, C.Larson, B.M.Pettitt, and K.S.Matthews (2002).
Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR.
  Protein Sci, 11, 778-794.  
  11257552 A.Schlösser, A.Weber, and H.Schrempf (2001).
Synthesis of the Streptomyces lividans maltodextrin ABC transporter depends on the presence of the regulator MalR.
  FEMS Microbiol Lett, 196, 77-83.  
11179887 C.E.Bell, and M.Lewis (2001).
The Lac repressor: a second generation of structural and functional studies.
  Curr Opin Struct Biol, 11, 19-25.  
11353825 C.G.Kalodimos, G.E.Folkers, R.Boelens, and R.Kaptein (2001).
Strong DNA binding by covalently linked dimeric Lac headpiece: evidence for the crucial role of the hinge helices.
  Proc Natl Acad Sci U S A, 98, 6039-6044.  
11741530 C.W.Garvie, and C.Wolberger (2001).
Recognition of specific DNA sequences.
  Mol Cell, 8, 937-946.  
11296236 D.M.van Aalten, C.C.DiRusso, and J.Knudsen (2001).
The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR.
  EMBO J, 20, 2041-2050.
PDB codes: 1h9g 1h9t
11301006 H.Choi, S.Kim, P.Mukhopadhyay, S.Cho, J.Woo, G.Storz, and S.E.Ryu (2001).
Structural basis of the redox switch in the OxyR transcription factor.
  Cell, 105, 103-113.
PDB codes: 1i69 1i6a
11557150 H.Ludwig, and J.Stülke (2001).
The Bacillus subtilis catabolite control protein CcpA exerts all its regulatory functions by DNA-binding.
  FEMS Microbiol Lett, 203, 125-129.  
11139621 J.Plumbridge (2001).
DNA binding sites for the Mlc and NagC proteins: regulation of nagE, encoding the N-acetylglucosamine-specific transporter in Escherichia coli.
  Nucleic Acids Res, 29, 506-514.  
11114939 K.A.Egland, and E.P.Greenberg (2001).
Quorum sensing in Vibrio fischeri: analysis of the LuxR DNA binding region by alanine-scanning mutagenesis.
  J Bacteriol, 183, 382-386.  
11353844 L.H.Weaver, K.Kwon, D.Beckett, and B.W.Matthews (2001).
Corepressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator.
  Proc Natl Acad Sci U S A, 98, 6045-6050.
PDB code: 1hxd
11266612 L.Swint-Kruse, C.R.Elam, J.W.Lin, D.R.Wycuff, and K.Shive Matthews (2001).
Plasticity of quaternary structure: twenty-two ways to form a LacI dimer.
  Protein Sci, 10, 262-276.  
11726698 T.D.Schneider (2001).
Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.
  Nucleic Acids Res, 29, 4881-4891.  
10986270 A.J.Turinsky, T.R.Moir-Blais, F.J.Grundy, and T.M.Henkin (2000).
Bacillus subtilis ccpA gene mutants specifically defective in activation of acetoin biosynthesis.
  J Bacteriol, 182, 5611-5614.  
  10981702 A.Schlösser, T.Aldekamp, and H.Schrempf (2000).
Binding characteristics of CebR, the regulator of the ceb operon required for cellobiose/cellotriose uptake in Streptomyces reticuli.
  FEMS Microbiol Lett, 190, 127-132.  
10856250 E.Gillitzer, G.Chen, and A.Stenlund (2000).
Separate domains in E1 and E2 proteins serve architectural and productive roles for cooperative DNA binding.
  EMBO J, 19, 3069-3079.  
10666630 J.Tebbe, P.Orth, E.K.Küster-Schöck, W.Hillen, W.Saenger, and W.Hinrichs (2000).
Crystallization and preliminary X-ray analyses of catabolite control protein A, free and in complex with its DNA-binding site.
  Acta Crystallogr D Biol Crystallogr, 56, 67-69.  
10733977 L.Pardo, M.Campillo, D.Bosch, N.Pastor, and H.Weinstein (2000).
Binding mechanisms of TATA box-binding proteins: DNA kinking is stabilized by specific hydrogen bonds.
  Biophys J, 78, 1988-1996.  
11097914 M.E.Davey, and F.J.de Bruijn (2000).
A homologue of the tryptophan-rich sensory protein TspO and FixL regulate a novel nutrient deprivation-induced Sinorhizobium meliloti locus.
  Appl Environ Microbiol, 66, 5353-5359.  
10760140 M.N.Alekshun, Y.S.Kim, and S.B.Levy (2000).
Mutational analysis of MarR, the negative regulator of marRAB expression in Escherichia coli, suggests the presence of two regions required for DNA binding.
  Mol Microbiol, 35, 1394-1404.  
10613893 N.A.Spiridonov, and D.B.Wilson (2000).
A celR mutation affecting transcription of cellulase genes in Thermobifida fusca.
  J Bacteriol, 182, 252-255.  
  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.  
10896472 P.B.Rupert, and A.R.Ferré-D'amaré (2000).
SRPrises in RNA-protein recognition.
  Structure, 8, R99-104.  
11087395 Q.He, U.M.Ohndorf, and S.J.Lippard (2000).
Intercalating residues determine the mode of HMG1 domains A and B binding to cisplatin-modified DNA.
  Biochemistry, 39, 14426-14435.  
10101970 A.Lebrun, and R.Lavery (1999).
Modeling DNA deformations induced by minor groove binding proteins.
  Biopolymers, 49, 341-353.  
10647179 C.A.Spronk, A.M.Bonvin, P.K.Radha, G.Melacini, R.Boelens, and R.Kaptein (1999).
The solution structure of Lac repressor headpiece 62 complexed to a symmetrical lac operator.
  Structure, 7, 1483-1492.
PDB code: 1cjg
10562559 C.A.Spronk, G.E.Folkers, A.M.Noordman, R.Wechselberger, N.van den Brink, R.Boelens, and R.Kaptein (1999).
Hinge-helix formation and DNA bending in various lac repressor-operator complexes.
  EMBO J, 18, 6472-6480.  
  10383986 E.Küster, T.Hilbich, M.K.Dahl, and W.Hillen (1999).
Mutations in catabolite control protein CcpA separating growth effects from catabolite repression.
  J Bacteriol, 181, 4125-4128.  
  10601226 E.Küster-Schöck, A.Wagner, U.Völker, and W.Hillen (1999).
Mutations in catabolite control protein CcpA showing glucose-independent regulation in Bacillus megaterium.
  J Bacteriol, 181, 7634-7638.  
  10197993 J.S.Hwang, J.Yang, and A.J.Pittard (1999).
Specific contacts between residues in the DNA-binding domain of the TyrR protein and bases in the operator of the tyrP gene of Escherichia coli.
  J Bacteriol, 181, 2338-2345.  
  10346814 M.Geanacopoulos, G.Vasmatzis, D.E.Lewis, S.Roy, B.Lee, and S.Adhya (1999).
GalR mutants defective in repressosome formation.
  Genes Dev, 13, 1251-1262.  
10571997 Q.Yang, N.Berton, M.C.Manning, and C.E.Catalano (1999).
Domain structure of gpNu1, a phage lambda DNA packaging protein.
  Biochemistry, 38, 14238-14247.  
10487755 Y.Fujii, T.Shimizu, M.Kusumoto, Y.Kyogoku, T.Taniguchi, and T.Hakoshima (1999).
Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences.
  EMBO J, 18, 5028-5041.
PDB code: 2irf
9489920 A.Balaeff, M.E.Churchill, and K.Schulten (1998).
Structure prediction of a complex between the chromosomal protein HMG-D and DNA.
  Proteins, 30, 113-135.  
9891796 A.J.Cozzone (1998).
Regulation of acetate metabolism by protein phosphorylation in enteric bacteria.
  Annu Rev Microbiol, 52, 127-164.  
9988473 A.Kraus, E.Küster, A.Wagner, K.Hoffmann, and W.Hillen (1998).
Identification of a co-repressor binding site in catabolite control protein CcpA.
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10066473 B.Müller-Hill (1998).
Some repressors of bacterial transcription.
  Curr Opin Microbiol, 1, 145-151.  
9646864 C.A.Bewley, A.M.Gronenborn, and G.M.Clore (1998).
Minor groove-binding architectural proteins: structure, function, and DNA recognition.
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9466254 C.I.Jørgensen, B.H.Kallipolitis, and P.Valentin-Hansen (1998).
DNA-binding characteristics of the Escherichia coli CytR regulator: a relaxed spacing requirement between operator half-sites is provided by a flexible, unstructured interdomain linker.
  Mol Microbiol, 27, 41-50.  
9628480 D.N.Arvidson, F.Lu, C.Faber, H.Zalkin, and R.G.Brennan (1998).
The structure of PurR mutant L54M shows an alternative route to DNA kinking.
  Nat Struct Biol, 5, 436-441.
PDB code: 1vpw
9770480 J.F.Leger, J.Robert, L.Bourdieu, D.Chatenay, and J.F.Marko (1998).
RecA binding to a single double-stranded DNA molecule: a possible role of DNA conformational fluctuations.
  Proc Natl Acad Sci U S A, 95, 12295-12299.  
9449341 L.Swint-Kruse, K.S.Matthews, P.E.Smith, and B.M.Pettitt (1998).
Comparison of simulated and experimentally determined dynamics for a variant of the Lacl DNA-binding domain, Nlac-P.
  Biophys J, 74, 413-421.  
  9683488 M.Kilstrup, and J.Martinussen (1998).
A transcriptional activator, homologous to the Bacillus subtilis PurR repressor, is required for expression of purine biosynthetic genes in Lactococcus lactis.
  J Bacteriol, 180, 3907-3916.  
  9683487 M.Kilstrup, S.G.Jessing, S.B.Wichmand-Jørgensen, M.Madsen, and D.Nilsson (1998).
Activation control of pur gene expression in Lactococcus lactis: proposal for a consensus activator binding sequence based on deletion analysis and site-directed mutagenesis of purC and purD promoter regions.
  J Bacteriol, 180, 3900-3906.  
  9521130 P.Oertel-Buchheit, J.Reinbolt, M.John, M.Granger-Schnarr, and M.Schnarr (1998).
A LexA mutant repressor with a relaxed inter-domain linker.
  Protein Sci, 7, 512-515.  
9518483 R.E.Dickerson (1998).
DNA bending: the prevalence of kinkiness and the virtues of normality.
  Nucleic Acids Res, 26, 1906-1926.  
10384265 S.Adhya, M.Geanacopoulos, D.E.Lewis, S.Roy, and T.Aki (1998).
Transcription regulation by repressosome and by RNA polymerase contact.
  Cold Spring Harb Symp Quant Biol, 63, 1-9.  
  9865945 U.Hars, R.Horlacher, W.Boos, W.Welte, and K.Diederichs (1998).
Crystal structure of the effector-binding domain of the trehalose-repressor of Escherichia coli, a member of the LacI family, in its complexes with inducer trehalose-6-phosphate and noninducer trehalose.
  Protein Sci, 7, 2511-2521.
PDB codes: 1byk 4xxh
9731772 Y.G.Gao, S.Y.Su, H.Robinson, S.Padmanabhan, L.Lim, B.S.McCrary, S.P.Edmondson, J.W.Shriver, and A.H.Wang (1998).
The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA.
  Nat Struct Biol, 5, 782-786.
PDB codes: 1bf4 1bnz
9822817 Y.Xia, K.Forsman, J.Jass, and B.E.Uhlin (1998).
Oligomeric interaction of the PapB transcriptional regulator with the upstream activating region of pili adhesin gene promoters in Escherichia coli.
  Mol Microbiol, 30, 513-523.  
9237992 A.Herbert, J.Alfken, Y.G.Kim, I.S.Mian, K.Nishikura, and A.Rich (1997).
A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase.
  Proc Natl Acad Sci U S A, 94, 8421-8426.  
9252590 A.Kraus, and W.Hillen (1997).
Analysis of CcpA mutations defective in carbon catabolite repression in Bacillus megaterium.
  FEMS Microbiol Lett, 153, 221-226.  
9162504 A.Travers (1997).
DNA-protein interactions: IHF--the master bender.
  Curr Biol, 7, R252-R254.  
  9171422 B.D.Nelson, C.Manoil, and B.Traxler (1997).
Insertion mutagenesis of the lac repressor and its implications for structure-function analysis.
  J Bacteriol, 179, 3721-3728.  
9215632 B.H.Kallipolitis, M.Nørregaard-Madsen, and P.Valentin-Hansen (1997).
Protein-protein communication: structural model of the repression complex formed by CytR and the global regulator CRP.
  Cell, 89, 1101-1109.  
  9393704 B.S.Shin, A.Stein, and H.Zalkin (1997).
Interaction of Bacillus subtilis purine repressor with DNA.
  J Bacteriol, 179, 7394-7402.  
9204277 D.E.Wemmer, and P.B.Dervan (1997).
Targeting the minor groove of DNA.
  Curr Opin Struct Biol, 7, 355-361.  
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.  
9360594 E.N.Baker (1997).
Iron-ic twists of fate.
  Nat Struct Biol, 4, 869-871.  
9140942 G.C.Ruben, and T.B.Roos (1997).
Conformation of Lac repressor tetramer in solution, bound and unbound to operator DNA.
  Microsc Res Tech, 36, 400-416.  
9154913 H.Backes, C.Berens, V.Helbl, S.Walter, F.X.Schmid, and W.Hillen (1997).
Combinations of the alpha-helix-turn-alpha-helix motif of TetR with respective residues from LacI or 434Cro: DNA recognition, inducer binding, and urea-dependent denaturation.
  Biochemistry, 36, 5311-5322.  
9155036 H.Pedersen, and P.Valentin-Hansen (1997).
Protein-induced fit: the CRP activator protein changes sequence-specific DNA recognition by the CytR repressor, a highly flexible LacI member.
  EMBO J, 16, 2108-2118.  
9254709 J.H.Kim, and G.H.Chambliss (1997).
Contacts between Bacillus subtilis catabolite regulatory protein CcpA and amyO target site.
  Nucleic Acids Res, 25, 3490-3496.  
  9335287 J.Nguyen, F.Francou, M.J.Virolle, and M.Guérineau (1997).
Amylase and chitinase genes in Streptomyces lividans are regulated by reg1, a pleiotropic regulatory gene.
  J Bacteriol, 179, 6383-6390.  
  9023183 J.S.Hwang, J.Yang, and A.J.Pittard (1997).
Critical base pairs and amino acid residues for protein-DNA interaction between the TyrR protein and tyrP operator of Escherichia coli.
  J Bacteriol, 179, 1051-1058.  
9303004 K.Swaminathan, P.Flynn, R.J.Reece, and R.Marmorstein (1997).
Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster.
  Nat Struct Biol, 4, 751-759.
PDB code: 1zme
9062120 L.P.Gardner, K.A.Mookhtiar, and J.E.Coleman (1997).
Initiation, elongation, and processivity of carboxyl-terminal mutants of T7 RNA polymerase.
  Biochemistry, 36, 2908-2918.  
9032054 M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.
  Curr Opin Struct Biol, 7, 76-85.  
  9372184 M.Lopata, D.Schlieper, B.von Wilcken-Bergmann, and B.Müller-Hill (1997).
A lethal mutant of the catabolite gene activator protein CAP of Escherichia coli.
  Biol Chem, 378, 1153-1162.  
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.  
9207039 R.Bravieri, T.Shiyanova, T.H.Chen, D.Overdier, and X.Liao (1997).
Different DNA contact schemes are used by two winged helix proteins to recognize a DNA binding sequence.
  Nucleic Acids Res, 25, 2888-2896.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
9309218 R.Tyrrell, K.H.Verschueren, E.J.Dodson, G.N.Murshudov, C.Addy, and A.J.Wilkinson (1997).
The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with a surprising subunit arrangement.
  Structure, 5, 1017-1032.
PDB code: 1al3
9321414 S.Alberti (1997).
The origin of the genetic code and protein synthesis.
  J Mol Evol, 45, 352-358.  
9405381 S.Schumacher, R.T.Clubb, M.Cai, K.Mizuuchi, G.M.Clore, and A.M.Gronenborn (1997).
Solution structure of the Mu end DNA-binding ibeta subdomain of phage Mu transposase: modular DNA recognition by two tethered domains.
  EMBO J, 16, 7532-7541.
PDB codes: 2ezk 2ezl
9032076 T.Ellenberger, and A.Landy (1997).
A good turn for DNA: the structure of integration host factor bound to DNA.
  Structure, 5, 153-157.  
9335337 T.M.Hall, J.A.Porter, K.E.Young, E.V.Koonin, P.A.Beachy, and D.J.Leahy (1997).
Crystal structure of a Hedgehog autoprocessing domain: homology between Hedgehog and self-splicing proteins.
  Cell, 91, 85-97.
PDB code: 1at0
8901866 C.A.Spronk, M.Slijper, J.H.van Boom, R.Kaptein, and R.Boelens (1996).
Formation of the hinge helix in the lac repressor is induced upon binding to the lac operator.
  Nat Struct Biol, 3, 916-919.  
8619994 D.D.Dalma-Weiszhausz, and M.Brenowitz (1996).
Interactions between RNA polymerase and the positive and negative regulators of transcription at the Escherichia coli gal operon.
  Biochemistry, 35, 3735-3745.  
8861200 F.A.Quiocho, and P.S.Ledvina (1996).
Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation of common themes.
  Mol Microbiol, 20, 17-25.  
8807872 H.C.Nelson, and T.H.Bestor (1996).
Base eversion and shuffling by DNA methyltransferases.
  Chem Biol, 3, 419-423.  
8599752 J.H.Miller (1996).
Structure of a paradigm.
  Nat Struct Biol, 3, 310-312.  
  8599943 M.Suckow, M.Lopata, A.Seydel, B.Kisters-Woike, B.von Wilcken-Bergmann, and B.Müller-Hill (1996).
Mutant bZip-DNA complexes with four quasi-identical protein-DNA interfaces.
  EMBO J, 15, 598-606.  
8723315 P.G.Artz, K.G.Valentine, S.J.Opella, and P.Lu (1996).
Lac repressor-operator interaction: N-terminal peptide backbone 1H and 15N chemical shifts upon complex formation with DNA.
  J Mol Recognit, 9, 13-22.  
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
8805532 R.T.Sauer (1996).
Lac repressor at last.
  Structure, 4, 219-222.  
7552720 A.A.Travers (1995).
Reading the minor groove.
  Nat Struct Biol, 2, 615-618.  
8749361 A.M.Stock, and S.L.Mowbray (1995).
Bacterial chemotaxis: a field in motion.
  Curr Opin Struct Biol, 5, 744-751.  
8591032 A.Nagadoi, S.Morikawa, H.Nakamura, M.Enari, K.Kobayashi, H.Yamamoto, G.Sampei, K.Mizobuchi, M.A.Schumacher, and R.G.Brennan (1995).
Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain.
  Structure, 3, 1217-1224.
PDB codes: 1pru 1prv
8521494 D.G.Vassylyev, T.Kashiwagi, Y.Mikami, M.Ariyoshi, S.Iwai, E.Ohtsuka, and K.Morikawa (1995).
Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.
  Cell, 83, 773-782.
PDB code: 1vas
7667096 H.C.van Leeuwen, M.J.Strating, M.Cox, R.Kaptein, and P.C.van der Vliet (1995).
Mutation of the Oct-1 POU-specific recognition helix leads to altered DNA binding and influences enhancement of adenovirus DNA replication.
  Nucleic Acids Res, 23, 3189-3197.  
7606780 K.M.Reinisch, L.Chen, G.L.Verdine, and W.N.Lipscomb (1995).
The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.
  Cell, 82, 143-153.
PDB code: 1dct
7761451 L.Chen, and A.D.Frankel (1995).
A peptide interaction in the major groove of RNA resembles protein interactions in the minor groove of DNA.
  Proc Natl Acad Sci U S A, 92, 5077-5081.  
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
8521493 M.H.Werner, M.Clore, C.L.Fisher, R.J.Fisher, L.Trinh, J.Shiloach, and A.M.Gronenborn (1995).
The solution structure of the human ETS1-DNA complex reveals a novel mode of binding and true side chain intercalation.
  Cell, 83, 761-771.
PDB codes: 1stt 1stw
7610037 M.Suzuki, and N.Yagi (1995).
Stereochemical basis of DNA bending by transcription factors.
  Nucleic Acids Res, 23, 2083-2091.  
7638212 M.Weng, P.L.Nagy, and H.Zalkin (1995).
Identification of the Bacillus subtilis pur operon repressor.
  Proc Natl Acad Sci U S A, 92, 7455-7459.  
7568230 N.Schiering, X.Tao, H.Zeng, J.R.Murphy, G.A.Petsko, and D.Ringe (1995).
Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae.
  Proc Natl Acad Sci U S A, 92, 9843-9850.
PDB code: 1dpr
  7730272 O.Egeter, and R.Brückner (1995).
Characterization of a genetic locus essential for maltose-maltotriose utilization in Staphylococcus xylosus.
  J Bacteriol, 177, 2408-2415.  
7719857 R.T.Sauer (1995).
Minor groove DNA-recognition by alpha-helices.
  Nat Struct Biol, 2, 7-9.  
7628011 W.Yang, and T.A.Steitz (1995).
Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.
  Cell, 82, 193-207.
PDB code: 1gdt
7784203 X.Zhang, and P.A.Gottlieb (1995).
Modified nucleotides reveal the indirect role of the central base pairs in stabilizing the lac repressor-operator complex.
  Nucleic Acids Res, 23, 1502-1511.  
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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