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PDBsum entry 1kgs

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DNA binding protein PDB id
1kgs
Jmol
Contents
Protein chain
219 a.a. *
Ligands
SCN ×6
Waters ×206
* Residue conservation analysis
PDB id:
1kgs
Name: DNA binding protein
Title: Crystal structure at 1.50 a of an ompr/phob homolog from the maritima
Structure: DNA binding response regulator d. Chain: a. Synonym: drrd. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: drrd. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.50Å     R-factor:   0.181     R-free:   0.210
Authors: D.R.Buckler,Y.Zhou,A.M.Stock
Key ref:
D.R.Buckler et al. (2002). Evidence of intradomain and interdomain flexibility in an OmpR/PhoB homolog from Thermotoga maritima. Structure, 10, 153-164. PubMed id: 11839301 DOI: 10.1016/S0969-2126(01)00706-7
Date:
28-Nov-01     Release date:   05-Dec-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9WYN0  (Q9WYN0_THEMA) -  Response regulator
Seq:
Struc:
225 a.a.
219 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     intracellular signal transduction   4 terms 
  Biochemical function     two-component response regulator activity     3 terms  

 

 
DOI no: 10.1016/S0969-2126(01)00706-7 Structure 10:153-164 (2002)
PubMed id: 11839301  
 
 
Evidence of intradomain and interdomain flexibility in an OmpR/PhoB homolog from Thermotoga maritima.
D.R.Buckler, Y.Zhou, A.M.Stock.
 
  ABSTRACT  
 
Two-component systems, the predominant signal transduction strategy used by prokaryotes, involve phosphorelay from a sensor histidine kinase (HK) to an intracellular response regulator protein (RR) that typically acts as a transcription regulator. RRs are modular proteins, usually composed of a conserved regulatory domain, which functions as a phosphorylation-activated switch, and an attached DNA binding effector domain. The crystal structure of a Thermotoga maritima transcription factor, DrrD, has been determined at 1.5 A resolution, providing the first structural information for a full-length member of the OmpR/PhoB subfamily of RRs. A small interdomain interface occurs between alpha 5 of the regulatory domain and an antiparallel sheet of the effector domain. The lack of an extensive interface in the unphosphorylated protein distinguishes DrrD from other structurally characterized multidomain RRs and suggests a different mode of interdomain regulation.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of Full-Length DrrD(A) A ribbon representation of the DrrD structure highlighting residues at the interdomain interface (ball and stick rendering) and six thiocyanate ions (CPK rendering). For the stick and CPK renderings, carbon is in green, nitrogen is in blue, oxygen is in red, and sulfur is in yellow. Secondary structural elements are labeled a1-5 and b1-5 for the regulatory domain and H1-3 and S1-7 for the effector domain. The recognition helix, H3, in the effector domain is in gold. Two regions through which electron density was not observed, the interdomain linker and the loop connecting H2 and H3, are indicated by dashed lines.(B) Stereo Ca trace rendered in the same orientation as in (A).This figure and the protein models shown in Figure 3, Figure 4, Figure 5, Figure 6 and Figure 7 were generated using Ribbons [65] Version 3.14.
 
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 153-164) copyright 2002.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21347487 J.Perry, K.Koteva, and G.Wright (2011).
Receptor domains of two-component signal transduction systems.
  Mol Biosyst, 7, 1388-1398.  
20081031 A.A.Wise, F.Fang, Y.H.Lin, F.He, D.G.Lynn, and A.N.Binns (2010).
The receiver domain of hybrid histidine kinase VirA: an enhancing factor for vir gene expression in Agrobacterium tumefaciens.
  J Bacteriol, 192, 1534-1542.  
20702407 C.M.Barbieri, T.R.Mack, V.L.Robinson, M.T.Miller, and A.M.Stock (2010).
Regulation of response regulator autophosphorylation through interdomain contacts.
  J Biol Chem, 285, 32325-32335.
PDB codes: 3nhz 3nnn 3nns
20226724 M.Y.Galperin (2010).
Diversity of structure and function of response regulator output domains.
  Curr Opin Microbiol, 13, 150-159.  
20211578 R.B.Bourret (2010).
Receiver domain structure and function in response regulator proteins.
  Curr Opin Microbiol, 13, 142-149.  
20080056 R.Gao, and A.M.Stock (2010).
Molecular strategies for phosphorylation-mediated regulation of response regulator activity.
  Curr Opin Microbiol, 13, 160-167.  
19445950 E.S.Groban, E.J.Clarke, H.M.Salis, S.M.Miller, and C.A.Voigt (2009).
Kinetic buffering of cross talk between bacterial two-component sensors.
  J Mol Biol, 390, 380-393.  
19575571 R.Gao, and A.M.Stock (2009).
Biological insights from structures of two-component proteins.
  Annu Rev Microbiol, 63, 133-154.  
19820095 S.Gupta, A.Pathak, A.Sinha, and D.Sarkar (2009).
Mycobacterium tuberculosis PhoP recognizes two adjacent direct-repeat sequences to form head-to-head dimers.
  J Bacteriol, 191, 7466-7476.  
19117956 S.S.Gupta, B.N.Borin, T.L.Cover, and A.M.Krezel (2009).
Structural Analysis of the DNA-binding Domain of the Helicobacter pylori Response Regulator ArsR.
  J Biol Chem, 284, 6536-6545.  
18065544 A.Sinha, S.Gupta, S.Bhutani, A.Pathak, and D.Sarkar (2008).
PhoP-PhoP interaction at adjacent PhoP binding sites is influenced by protein phosphorylation.
  J Bacteriol, 190, 1317-1328.  
18328252 C.M.Barbieri, and A.M.Stock (2008).
Universally applicable methods for monitoring response regulator aspartate phosphorylation both in vitro and in vivo using Phos-tag-based reagents.
  Anal Biochem, 376, 73-82.  
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
18923554 R.A.Daly, and C.P.Lostroh (2008).
Genetic analysis of the Salmonella transcription factor HilA.
  Can J Microbiol, 54, 854-860.  
17242520 C.H.Trinh, Y.Liu, S.E.Phillips, and M.K.Phillips-Jones (2007).
Structure of the response regulator VicR DNA-binding domain.
  Acta Crystallogr D Biol Crystallogr, 63, 266-269.
PDB code: 2hwv
17376070 G.Churchward (2007).
The two faces of Janus: virulence gene regulation by CovR/S in group A streptococci.
  Mol Microbiol, 64, 34-41.  
17942407 J.King-Scott, E.Nowak, E.Mylonas, S.Panjikar, M.Roessle, D.I.Svergun, and P.A.Tucker (2007).
The structure of a full-length response regulator from Mycobacterium tuberculosis in a stabilized three-dimensional domain-swapped, activated state.
  J Biol Chem, 282, 37717-37729.
PDB code: 2oqr
17477873 M.R.Duplessis, K.G.Karol, E.T.Adman, L.Y.Choi, M.A.Jacobs, and R.A.Cattolico (2007).
Chloroplast His-to-Asp signal transduction: a potential mechanism for plastid gene regulation in Heterosigma akashiwo (Raphidophyceae).
  BMC Evol Biol, 7, 70.  
17511470 N.Friedland, T.R.Mack, M.Yu, L.W.Hung, T.C.Terwilliger, G.S.Waldo, and A.M.Stock (2007).
Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activation.
  Biochemistry, 46, 6733-6743.
PDB code: 2gwr
17545283 P.Bachhawat, and A.M.Stock (2007).
Crystal structures of the receiver domain of the response regulator PhoP from Escherichia coli in the absence and presence of the phosphoryl analog beryllofluoride.
  J Bacteriol, 189, 5987-5995.
PDB codes: 2pkx 2pl1
17182055 R.Arribas-Bosacoma, S.K.Kim, C.Ferrer-Orta, A.G.Blanco, P.J.Pereira, F.X.Gomis-Rüth, B.L.Wanner, M.Coll, and M.Solà (2007).
The X-ray crystal structures of two constitutively active mutants of the Escherichia coli PhoB receiver domain give insights into activation.
  J Mol Biol, 366, 626-641.
PDB codes: 2jb9 2jba
17433693 R.Gao, T.R.Mack, and A.M.Stock (2007).
Bacterial response regulators: versatile regulatory strategies from common domains.
  Trends Biochem Sci, 32, 225-234.  
18052041 S.Wang, J.Engohang-Ndong, and I.Smith (2007).
Structure of the DNA-binding domain of the response regulator PhoP from Mycobacterium tuberculosis.
  Biochemistry, 46, 14751-14761.
PDB code: 2pmu
17322531 T.Gao, X.Zhang, N.B.Ivleva, S.S.Golden, and A.LiWang (2007).
NMR structure of the pseudo-receiver domain of CikA.
  Protein Sci, 16, 465-475.
PDB code: 2j48
16784239 C.Laguri, R.A.Stenzel, T.J.Donohue, M.K.Phillips-Jones, and M.P.Williamson (2006).
Activation of the global gene regulator PrrA (RegA) from Rhodobacter sphaeroides.
  Biochemistry, 45, 7872-7881.  
16929106 M.Solà, D.L.Drew, A.G.Blanco, F.X.Gomis-Rüth, and M.Coll (2006).
The cofactor-induced pre-active conformation in PhoB.
  Acta Crystallogr D Biol Crystallogr, 62, 1046-1057.
PDB code: 2iyn
16322582 A.Toro-Roman, T.Wu, and A.M.Stock (2005).
A common dimerization interface in bacterial response regulators KdpE and TorR.
  Protein Sci, 14, 3077-3088.
PDB codes: 1zgz 1zh2 1zh4
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
16154092 P.Bachhawat, G.V.Swapna, G.T.Montelione, and A.M.Stock (2005).
Mechanism of activation for transcription factor PhoB suggested by different modes of dimerization in the inactive and active states.
  Structure, 13, 1353-1363.
PDB code: 1zes
14563853 A.C.Harrod, X.Yang, M.Junker, and L.Reitzer (2004).
Evidence for a second interaction between the regulatory amino-terminal and central output domains of the response regulator NtrC (nitrogen regulator I) in Escherichia coli.
  J Biol Chem, 279, 2350-2359.  
15028686 H.Geng, S.Nakano, and M.M.Nakano (2004).
Transcriptional activation by Bacillus subtilis ResD: tandem binding to target elements and phosphorylation-dependent and -independent transcriptional activation.
  J Bacteriol, 186, 2028-2037.  
14731287 J.G.Smith, J.A.Latiolais, G.P.Guanga, J.D.Pennington, R.E.Silversmith, and R.B.Bourret (2004).
A search for amino acid substitutions that universally activate response regulators.
  Mol Microbiol, 51, 887-901.  
15162497 Q.Xu, R.Schwarzenbacher, D.McMullan, F.von Delft, L.S.Brinen, J.M.Canaves, X.Dai, A.M.Deacon, M.A.Elsliger, S.Eshagi, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, S.A.Lesley, I.Levin, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, K.Quijano, A.Robb, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, X.Wang, B.West, G.Wolf, K.O.Hodgson, J.Wooley, and I.A.Wilson (2004).
Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution.
  Proteins, 56, 171-175.
PDB code: 1o1x
14973033 Y.Chen, W.R.Abdel-Fattah, and F.M.Hulett (2004).
Residues required for Bacillus subtilis PhoP DNA binding or RNA polymerase interaction: alanine scanning of PhoP effector domain transactivation loop and alpha helix 3.
  J Bacteriol, 186, 1493-1502.  
12486062 C.Birck, Y.Chen, F.M.Hulett, and J.P.Samama (2003).
The crystal structure of the phosphorylation domain in PhoP reveals a functional tandem association mediated by an asymmetric interface.
  J Bacteriol, 185, 254-261.
PDB code: 1mvo
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.  
12675798 K.Saito, E.Ito, K.Hosono, K.Nakamura, K.Imai, T.Iizuka, Y.Shiro, and H.Nakamura (2003).
The uncoupling of oxygen sensing, phosphorylation signalling and transcriptional activation in oxygen sensor FixL and FixJ mutants.
  Mol Microbiol, 48, 373-383.  
14579323 L.N.Kinch, Y.Qi, T.J.Hubbard, and N.V.Grishin (2003).
CASP5 target classification.
  Proteins, 53, 340-351.  
12837793 V.L.Robinson, T.Wu, and A.M.Stock (2003).
Structural analysis of the domain interface in DrrB, a response regulator of the OmpR/PhoB subfamily.
  J Bacteriol, 185, 4186-4194.
PDB code: 1p2f
12352954 A.E.Maris, M.R.Sawaya, M.Kaczor-Grzeskowiak, M.R.Jarvis, S.M.Bearson, M.L.Kopka, I.Schröder, R.P.Gunsalus, and R.E.Dickerson (2002).
Dimerization allows DNA target site recognition by the NarL response regulator.
  Nat Struct Biol, 9, 771-778.
PDB code: 1je8
12077136 K.Mattison, R.Oropeza, and L.J.Kenney (2002).
The linker region plays an important role in the interdomain communication of the response regulator OmpR.
  J Biol Chem, 277, 32714-32721.  
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.