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PDBsum entry 1p2f

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protein links
Transcription PDB id
1p2f
Jmol
Contents
Protein chain
217 a.a. *
Waters ×163
* Residue conservation analysis
PDB id:
1p2f
Name: Transcription
Title: Crystal structure analysis of response regulator drrb, a thermotoga maritima ompr/phob homolog
Structure: Response regulator. Chain: a. Synonym: response regulator drrb. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.80Å     R-factor:   0.198     R-free:   0.224
Authors: V.L.Robinson,T.Wu,A.M.Stock
Key ref: V.L.Robinson et al. (2003). Structural analysis of the domain interface in DrrB, a response regulator of the OmpR/PhoB subfamily. J Bacteriol, 185, 4186-4194. PubMed id: 12837793
Date:
15-Apr-03     Release date:   29-Apr-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9WXY0  (Q9WXY0_THEMA) -  Response regulator
Seq:
Struc:
220 a.a.
217 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  

 

 
J Bacteriol 185:4186-4194 (2003)
PubMed id: 12837793  
 
 
Structural analysis of the domain interface in DrrB, a response regulator of the OmpR/PhoB subfamily.
V.L.Robinson, T.Wu, A.M.Stock.
 
  ABSTRACT  
 
The N-terminal regulatory domains of bacterial response regulator proteins catalyze phosphoryl transfer and function as phosphorylation-dependent regulatory switches to control the output activities of C-terminal effector domains. Structures of numerous isolated regulatory and effector domains have been determined. However, a detailed understanding of regulatory interactions among these domains has been limited by the relative paucity of structural data for intact multidomain response regulator proteins. The first multidomain structures determined, those of transcription factor NarL and methylesterase CheB, both revealed extensive interdomain interfaces. The regulatory domains obstruct access to the functional sites of the effector domains, indicating a regulatory mechanism based on inhibition. In contrast, the recently determined structure of the OmpR/PhoB homologue DrrD revealed no significant interdomain interface, suggesting that the domains are tethered by a flexible linker and lack a fixed orientation relative to each other. To address the generality of this feature, we have determined the 1.8-A resolution crystal structure of Thermotoga maritima DrrB, providing a second structure of a multidomain response regulator of the OmpR/PhoB subfamily. The structure reveals an extensive domain interface of 751 A(2) and therefore differs greatly from that observed in DrrD. Residues that are crucial players in defining the activation state of the regulatory domain contribute to this interface, implying that conformational changes associated with phosphorylation will influence these intramolecular contacts. The DrrB and DrrD structures are suggestive of different signaling mechanisms, with intramolecular communication between N- and C-terminal domains making substantially different contributions to effector domain regulation in individual members of the OmpR/PhoB family.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
20080056 R.Gao, and A.M.Stock (2010).
Molecular strategies for phosphorylation-mediated regulation of response regulator activity.
  Curr Opin Microbiol, 13, 160-167.  
20161694 K.D.Koclega, M.Chruszcz, M.D.Zimmerman, G.Bujacz, and W.Minor (2009).
'Hot' macromolecular crystals.
  Cryst Growth Des, 10, 580.
PDB codes: 3ih2 3ih3 3ih4
19575571 R.Gao, and A.M.Stock (2009).
Biological insights from structures of two-component proteins.
  Annu Rev Microbiol, 63, 133-154.  
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.  
19371748 T.R.Mack, R.Gao, and A.M.Stock (2009).
Probing the roles of the two different dimers mediated by the receiver domain of the response regulator PhoB.
  J Mol Biol, 389, 349-364.  
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.  
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
18346116 L.Li, R.M.Alvey, R.P.Bezy, and D.M.Kehoe (2008).
Inverse transcriptional activities during complementary chromatic adaptation are controlled by the response regulator RcaC binding to red and green light-responsive promoters.
  Mol Microbiol, 68, 286-297.  
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
17576598 D.Straume, M.Kjos, I.F.Nes, and D.B.Diep (2007).
Quorum-sensing based bacteriocin production is down-regulated by N-terminally truncated species of gene activators.
  Mol Genet Genomics, 278, 283-293.  
18076326 M.T.Laub, and M.Goulian (2007).
Specificity in two-component signal transduction pathways.
  Annu Rev Genet, 41, 121-145.  
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
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
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
16823552 A.Mooney, P.G.Ward, and K.E.O'Connor (2006).
Microbial degradation of styrene: biochemistry, molecular genetics, and perspectives for biotechnological applications.
  Appl Microbiol Biotechnol, 72, 1.  
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.  
16740923 M.Y.Galperin (2006).
Structural classification of bacterial response regulators: diversity of output domains and domain combinations.
  J Bacteriol, 188, 4169-4182.  
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.  
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
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
16154079 W.R.McCleary (2005).
No phobias about PhoB activation.
  Structure, 13, 1238-1239.  
15231782 C.Bordi, M.Ansaldi, S.Gon, C.Jourlin-Castelli, C.Iobbi-Nivol, and V.Méjean (2004).
Genes regulated by TorR, the trimethylamine oxide response regulator of Shewanella oneidensis.
  J Bacteriol, 186, 4502-4509.  
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
15090529 C.J.Bent, N.W.Isaacs, T.J.Mitchell, and A.Riboldi-Tunnicliffe (2004).
Crystal structure of the response regulator 02 receiver domain, the essential YycF two-component system of Streptococcus pneumoniae in both complexed and native states.
  J Bacteriol, 186, 2872-2879.
PDB codes: 1nxo 1nxp 1nxt 1nxw
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.  
15289606 S.Y.Park, B.D.Beel, M.I.Simon, A.M.Bilwes, and B.R.Crane (2004).
In different organisms, the mode of interaction between two signaling proteins is not necessarily conserved.
  Proc Natl Acad Sci U S A, 101, 11646-11651.
PDB code: 1u0s
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.  
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.