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PDBsum entry 1je8

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protein dna_rna ligands Protein-protein interface(s) links
Transcription/DNA PDB id
1je8
Jmol
Contents
Protein chains
66 a.a. *
DNA/RNA
Ligands
SO4 ×8
Waters ×330
* Residue conservation analysis
PDB id:
1je8
Name: Transcription/DNA
Title: Two-component response regulator narl/DNA complex: DNA bending found in a high affinity site
Structure: 5'- d( Cp Gp Tp Ap Cp Cp Cp Ap Tp Tp Ap Ap Tp Gp Gp Gp Tp Ap Cp G)-3'. Chain: c, d, g, h. Engineered: yes. Other_details: e. Coli nirb -74 half site palindrome. Nitrate/nitrite response regulator protein narl. Chain: a, b, e, f. Fragment: DNA binding domain (147-216).
Source: Synthetic: yes. Other_details: DNA was synthesized using solid phase phosphoramidite chemistry.. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.12Å     R-factor:   0.228     R-free:   0.273
Authors: A.E.Maris,M.R.Sawaya,M.Kaczor-Grzeskowiak,M.R.Jarvis, S.M.D.Bearson,M.L.Kopka,I.Schroder,R.P.Gunsalus, R.E.Dickerson
Key ref:
A.E.Maris et al. (2002). Dimerization allows DNA target site recognition by the NarL response regulator. Nat Struct Biol, 9, 771-778. PubMed id: 12352954 DOI: 10.1038/nsb845
Date:
15-Jun-01     Release date:   27-Sep-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AF28  (NARL_ECOLI) -  Nitrate/nitrite response regulator protein NarL
Seq:
Struc:
216 a.a.
66 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1038/nsb845 Nat Struct Biol 9:771-778 (2002)
PubMed id: 12352954  
 
 
Dimerization allows DNA target site recognition by the NarL response regulator.
A.E.Maris, M.R.Sawaya, M.Kaczor-Grzeskowiak, M.R.Jarvis, S.M.Bearson, M.L.Kopka, I.Schröder, R.P.Gunsalus, R.E.Dickerson.
 
  ABSTRACT  
 
Two-component signal transduction systems are modular phosphorelay regulatory pathways common in prokaryotes. In the co-crystal structure of the Escherichia coli NarL signal output domain bound to DNA, we observe how the NarL family of two-component response regulators can bind DNA. DNA recognition is accompanied by the formation of a new dimerization interface, which could occur only in the full-length protein via a large intramolecular domain rearrangement. The DNA is recognized by the concerted effects of solvation, van der Waals forces and inherent DNA deformability, rather than determined primarily by major groove hydrogen bonding. These subtle forces permit a small DNA-binding domain to perturb the DNA helix, leading to major DNA curvature and a transition from B- to A-form DNA at the binding site, where valine on the recognition helix interacts unexpectedly with the polar major groove floor.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. NarLC -DNA structure and DNA contacts. a, The NarLC dimer bends the DNA helix 42 by gradual curvature. Below the unexpected dimerization interface (Val 204, Val 208 and His 211 shown in white), the DNA minor groove narrows to 3 . Residues contacting the major groove floor are shown (yellow) at site of the B- to A-form transition, where the minor groove widens to 10 . b, DNA contacts of one NarLC protomer. Vertical lines represent base pairs; and horizontal lines, the DNA backbone. Base numbering is shown in each phosphate circle, with bases involved in the B-to-A transition in purple lettering. Hydrogen bond donors (open bar) and acceptors (open circle) on the major groove floor are indicated. Contacts are color-coded by type of interaction: van der Waals in blue (<3.8 ), hydrogen bonds in green (<3.4 ) and water-mediated hydrogen bonds in pink. Pink and green stripes indicate both types of interactions. Residues with side chains contacting the major groove floor are pink. The remaining residues (black) contact DNA via their main chain or contact the DNA backbone.
Figure 3.
Figure 3. Stereo views of major groove recognition. a, View from the minor groove, looking at contacts on the major groove floor. The van der Waals radii (gray cages) are shown for the methyl carbon atoms of Val 189, which distorts the CG base pair. N4 of the distorted cytosine shares a hydrogen-bonded water (red sphere) with the main chain carbonyl of Ser 185. Lys 192 hydrogen bonds (dashed white lines) to the attractive negative major groove edges of two consecutive guanines. b, 2F[O] - F[c] Electron density contoured at 1.4 of the recognition helix in the major groove. Val 189 excludes waters at the binding site, whereas extensive solvent is visible to the right. c, Lys 192 partially replaces the DNA hydration structure in the binding site. For simplicity, the DNA backbone is removed, and only one shared water (red sphere) and residues 186 -194 of the recognition helix are shown. Both Lys 192 and the water shown bridge successive bases via hydrogen bonds (dashed lines).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 771-778) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20634237 A.V.Lin, and V.Stewart (2010).
Functional roles for the GerE-family carboxyl-terminal domains of nitrate response regulators NarL and NarP of Escherichia coli K-12.
  Microbiology, 156, 2933-2943.  
20048056 B.Humair, B.Wackwitz, and D.Haas (2010).
GacA-controlled activation of promoters for small RNA genes in Pseudomonas fluorescens.
  Appl Environ Microbiol, 76, 1497-1506.  
20302877 C.A.Hobbs, B.G.Bobay, R.J.Thompson, M.Perego, and J.Cavanagh (2010).
NMR solution structure and DNA-binding model of the DNA-binding domain of competence protein A.
  J Mol Biol, 398, 248-263.
PDB code: 2krf
20589823 F.Kudo, A.Motegi, K.Mizoue, and T.Eguchi (2010).
Cloning and characterization of the biosynthetic gene cluster of 16-membered macrolide antibiotic FD-891: involvement of a dual functional cytochrome P450 monooxygenase catalyzing epoxidation and hydroxylation.
  Chembiochem, 11, 1574-1582.  
19926656 H.Zhao, A.Volkov, V.H.Veldore, J.A.Hoch, and K.I.Varughese (2010).
Crystal structure of the transcriptional repressor PagR of Bacillus anthracis.
  Microbiology, 156, 385-391.
PDB code: 2zkz
20545866 K.Zakikhany, C.R.Harrington, M.Nimtz, J.C.Hinton, and U.Römling (2010).
Unphosphorylated CsgD controls biofilm formation in Salmonella enterica serovar Typhimurium.
  Mol Microbiol, 77, 771-786.  
20846031 N.Bhargava, P.Sharma, and N.Capalash (2010).
Quorum sensing in Acinetobacter: an emerging pathogen.
  Crit Rev Microbiol, 36, 349-360.  
20662776 Q.Chen, K.B.Decker, P.E.Boucher, D.Hinton, and S.Stibitz (2010).
Novel architectural features of Bordetella pertussis fimbrial subunit promoters and their activation by the global virulence regulator BvgA.
  Mol Microbiol, 77, 1326-1340.  
20080056 R.Gao, and A.M.Stock (2010).
Molecular strategies for phosphorylation-mediated regulation of response regulator activity.
  Curr Opin Microbiol, 13, 160-167.  
19695263 N.De, M.V.Navarro, R.V.Raghavan, and H.Sondermann (2009).
Determinants for the activation and autoinhibition of the diguanylate cyclase response regulator WspR.
  J Mol Biol, 393, 619-633.
PDB codes: 3i5a 3i5b 3i5c
19126546 R.K.Carroll, X.Liao, L.K.Morgan, E.M.Cicirelli, Y.Li, W.Sheng, X.Feng, and L.J.Kenney (2009).
Structural and Functional Analysis of the C-terminal DNA Binding Domain of the Salmonella typhimurium SPI-2 Response Regulator SsrB.
  J Biol Chem, 284, 12008-12019.  
19648251 S.Chauhan, and J.S.Tyagi (2009).
Powerful induction of divergent tgs1-Rv3131 genes in Mycobacterium tuberculosis is mediated by DevR interaction with a high-affinity site and an adjacent cryptic low-affinity site.
  J Bacteriol, 191, 6075-6081.  
19234126 S.E.Osborne, D.Walthers, A.M.Tomljenovic, D.T.Mulder, U.Silphaduang, N.Duong, M.J.Lowden, M.E.Wickham, R.F.Waller, L.J.Kenney, and B.K.Coombes (2009).
Pathogenic adaptation of intracellular bacteria by rewiring a cis-regulatory input function.
  Proc Natl Acad Sci U S A, 106, 3982-3987.  
19324807 S.Puthiyaveetil, and J.F.Allen (2009).
Chloroplast two-component systems: evolution of the link between photosynthesis and gene expression.
  Proc Biol Sci, 276, 2133-2145.  
19734658 T.Ohsawa, K.Tsukahara, and M.Ogura (2009).
Bacillus subtilis response regulator DegU is a direct activator of pgsB transcription involved in gamma-poly-glutamic acid synthesis.
  Biosci Biotechnol Biochem, 73, 2096-2102.  
18187507 A.Sola-Landa, A.Rodríguez-García, A.K.Apel, and J.F.Martín (2008).
Target genes and structure of the direct repeats in the DNA-binding sequences of the response regulator PhoP in Streptomyces coelicolor.
  Nucleic Acids Res, 36, 1358-1368.  
17938953 D.J.Lee, S.Kim, Y.M.Ha, and J.Kim (2008).
Phosphorylation of Arabidopsis response regulator 7 (ARR7) at the putative phospho-accepting site is required for ARR7 to act as a negative regulator of cytokinin signaling.
  Planta, 227, 577-587.  
18353359 G.Wisedchaisri, M.Wu, D.R.Sherman, and W.G.Hol (2008).
Crystal structures of the response regulator DosR from Mycobacterium tuberculosis suggest a helix rearrangement mechanism for phosphorylation activation.
  J Mol Biol, 378, 227-242.
PDB codes: 3c3w 3c57
18466918 I.Lozada-Chávez, V.E.Angarica, J.Collado-Vides, and B.Contreras-Moreira (2008).
The role of DNA-binding specificity in the evolution of bacterial regulatory networks.
  J Mol Biol, 379, 627-643.  
  19841668 J.Kim (2008).
Phosphorylation of A-Type ARR to function as negative regulator of cytokinin signal transduction.
  Plant Signal Behav, 3, 348-350.  
18197985 K.Tsukahara, and M.Ogura (2008).
Promoter selectivity of the Bacillus subtilis response regulator DegU, a positive regulator of the fla/che operon and sacB.
  BMC Microbiol, 8, 8.  
18662309 M.de Been, M.J.Bart, T.Abee, R.J.Siezen, and C.Francke (2008).
The identification of response regulator-specific binding sites reveals new roles of two-component systems in Bacillus cereus and closely related low-GC Gram-positives.
  Environ Microbiol, 10, 2796-2809.  
18631241 R.Gao, Y.Tao, and A.M.Stock (2008).
System-level mapping of Escherichia coli response regulator dimerization with FRET hybrids.
  Mol Microbiol, 69, 1358-1372.  
18359816 S.Chauhan, and J.S.Tyagi (2008).
Cooperative binding of phosphorylated DevR to upstream sites is necessary and sufficient for activation of the Rv3134c-devRS operon in Mycobacterium tuberculosis: implication in the induction of DevR target genes.
  J Bacteriol, 190, 4301-4312.  
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.  
17965164 V.Stewart, and P.J.Bledsoe (2008).
Substitutions at auxiliary operator O3 enhance repression by nitrate-responsive regulator NarL at synthetic lac control regions in Escherichia coli K-12.
  J Bacteriol, 190, 428-433.  
17376086 C.E.White, and S.C.Winans (2007).
The quorum-sensing transcription factor TraR decodes its DNA binding site by direct contacts with DNA bases and by detection of DNA flexibility.
  Mol Microbiol, 64, 245-256.  
17360279 C.E.White, and S.C.Winans (2007).
Cell-cell communication in the plant pathogen Agrobacterium tumefaciens.
  Philos Trans R Soc Lond B Biol Sci, 362, 1135-1148.  
17313674 D.A.Ravcheev, A.V.Gerasimova, A.A.Mironov, and M.S.Gelfand (2007).
Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae).
  BMC Genomics, 8, 54.  
17630976 D.Walthers, R.K.Carroll, W.W.Navarre, S.J.Libby, F.C.Fang, and L.J.Kenney (2007).
The response regulator SsrB activates expression of diverse Salmonella pathogenicity island 2 promoters and counters silencing by the nucleoid-associated protein H-NS.
  Mol Microbiol, 65, 477-493.  
17491010 E.Hong, H.M.Lee, H.Ko, D.U.Kim, B.Y.Jeon, J.Jung, J.Shin, S.A.Lee, Y.Kim, Y.H.Jeon, C.Cheong, H.S.Cho, and W.Lee (2007).
Structure of an atypical orphan response regulator protein supports a new phosphorylation-independent regulatory mechanism.
  J Biol Chem, 282, 20667-20675.
PDB codes: 2hqn 2hqo 2hqr
17697997 P.Wassmann, C.Chan, R.Paul, A.Beck, H.Heerklotz, U.Jenal, and T.Schirmer (2007).
Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition.
  Structure, 15, 915-927.
PDB code: 2v0n
16816188 D.R.Yoder-Himes, and L.Kroos (2006).
Regulation of the Myxococcus xanthus C-signal-dependent Omega4400 promoter by the essential developmental protein FruA.
  J Bacteriol, 188, 5167-5176.  
16816181 M.Merighi, D.R.Majerczak, M.Zianni, K.Tessanne, and D.L.Coplin (2006).
Molecular characterization of Pantoea stewartii subsp. stewartii HrpY, a conserved response regulator of the Hrp type III secretion system, and its interaction with the hrpS promoter.
  J Bacteriol, 188, 5089-5100.  
16621822 N.Wang, S.E.Lu, A.R.Records, and D.C.Gross (2006).
Characterization of the transcriptional activators SalA and SyrF, Which are required for syringomycin and syringopeptin production by Pseudomonas syringae pv. syringae.
  J Bacteriol, 188, 3290-3298.  
16624907 P.Goymer, S.G.Kahn, J.G.Malone, S.M.Gehrig, A.J.Spiers, and P.B.Rainey (2006).
Adaptive divergence in experimental populations of Pseudomonas fluorescens. II. Role of the GGDEF regulator WspR in evolution and development of the wrinkly spreader phenotype.
  Genetics, 173, 515-526.  
16238621 A.M.Jones, P.E.Boucher, C.L.Williams, S.Stibitz, and P.A.Cotter (2005).
Role of BvgA phosphorylation and DNA binding affinity in control of Bvg-mediated phenotypic phase transition in Bordetella pertussis.
  Mol Microbiol, 58, 700-713.  
15728117 A.V.Favorov, M.S.Gelfand, A.V.Gerasimova, D.A.Ravcheev, A.A.Mironov, and V.J.Makeev (2005).
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
  Bioinformatics, 21, 2240-2245.  
15995204 E.B.Goh, P.J.Bledsoe, L.L.Chen, P.Gyaneshwar, V.Stewart, and M.M.Igo (2005).
Hierarchical control of anaerobic gene expression in Escherichia coli K-12: the nitrate-responsive NarX-NarL regulatory system represses synthesis of the fumarate-responsive DcuS-DcuR regulatory system.
  J Bacteriol, 187, 4890-4899.  
16159764 J.L.Rowe, G.L.Starnes, and P.T.Chivers (2005).
Complex transcriptional control links NikABCDE-dependent nickel transport with hydrogenase expression in Escherichia coli.
  J Bacteriol, 187, 6317-6323.  
16154086 M.Milani, L.Leoni, G.Rampioni, E.Zennaro, P.Ascenzi, and M.Bolognesi (2005).
An active-like structure in the unphosphorylated StyR response regulator suggests a phosphorylation- dependent allosteric activation mechanism.
  Structure, 13, 1289-1297.
PDB codes: 1yio 1zn2
15063844 A.Barnard, A.Wolfe, and S.Busby (2004).
Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes.
  Curr Opin Microbiol, 7, 102-108.  
14973043 C.Casper-Lindley, and F.H.Yildiz (2004).
VpsT is a transcriptional regulator required for expression of vps biosynthesis genes and the development of rugose colonial morphology in Vibrio cholerae O1 El Tor.
  J Bacteriol, 186, 1574-1578.  
15569936 C.Chan, R.Paul, D.Samoray, N.C.Amiot, B.Giese, U.Jenal, and T.Schirmer (2004).
Structural basis of activity and allosteric control of diguanylate cyclase.
  Proc Natl Acad Sci U S A, 101, 17084-17089.
PDB code: 1w25
15225315 D.F.Browning, J.A.Cole, and S.J.Busby (2004).
Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter.
  Mol Microbiol, 53, 203-215.  
15341725 J.P.Morth, V.Feng, L.J.Perry, D.I.Svergun, and P.A.Tucker (2004).
The crystal and solution structure of a putative transcriptional antiterminator from Mycobacterium tuberculosis.
  Structure, 12, 1595-1605.
PDB codes: 1s8n 1sd5
15255890 K.M.Pappas, C.L.Weingart, and S.C.Winans (2004).
Chemical communication in proteobacteria: biochemical and structural studies of signal synthases and receptors required for intercellular signalling.
  Mol Microbiol, 53, 755-769.  
15247225 L.E.Cybulski, G.del Solar, P.O.Craig, M.Espinosa, and D.de Mendoza (2004).
Bacillus subtilis DesR functions as a phosphorylation-activated switch to control membrane lipid fluidity.
  J Biol Chem, 279, 39340-39347.  
14729670 M.Kumaraswami, M.M.Howe, and H.W.Park (2004).
Crystal structure of the Mor protein of bacteriophage Mu, a member of the Mor/C family of transcription activators.
  J Biol Chem, 279, 16581-16590.
PDB code: 1rr7
15016354 P.Auffinger, L.Bielecki, and E.Westhof (2004).
Anion binding to nucleic acids.
  Structure, 12, 379-388.  
15491370 X.Feng, D.Walthers, R.Oropeza, and L.J.Kenney (2004).
The response regulator SsrB activates transcription and binds to a region overlapping OmpR binding sites at Salmonella pathogenicity island 2.
  Mol Microbiol, 54, 823-835.  
14627811 C.Laguri, M.K.Phillips-Jones, and M.P.Williamson (2003).
Solution structure and DNA binding of the effector domain from the global regulator PrrA (RegA) from Rhodobacter sphaeroides: insights into DNA binding specificity.
  Nucleic Acids Res, 31, 6778-6787.
PDB code: 1umq
12898671 C.S.Yeh, F.M.Chen, J.Y.Wang, T.L.Cheng, M.J.Hwang, and W.S.Tzou (2003).
Directional shape complementarity at the protein-DNA interface.
  J Mol Recognit, 16, 213-222.  
12614149 J.H.Zhang, G.Xiao, R.P.Gunsalus, and W.L.Hubbell (2003).
Phosphorylation triggers domain separation in the DNA binding response regulator NarL.
  Biochemistry, 42, 2552-2559.  
12644479 V.Stewart, and P.J.Bledsoe (2003).
Synthetic lac operator substitutions for studying the nitrate- and nitrite-responsive NarX-NarL and NarQ-NarP two-component regulatory systems of Escherichia coli K-12.
  J Bacteriol, 185, 2104-2111.  
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.