PDBsum entry 1zh2

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protein metals Protein-protein interface(s) links
Transcription PDB id
Protein chains
120 a.a. *
_CA ×2
Waters ×158
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Crystal structure of the calcium-bound receiver domain of kdp potassium transport system response regulator kdpe
Structure: Kdp operon transcriptional regulatory protein kdpe. Chain: a, b. Fragment: n-terminal receiver domain (residues 1-121). Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: kdpe. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.00Å     R-factor:   0.198     R-free:   0.242
Authors: A.Toro-Roman,T.Wu,A.M.Stock
Key ref:
A.Toro-Roman et al. (2005). A common dimerization interface in bacterial response regulators KdpE and TorR. Protein Sci, 14, 3077-3088. PubMed id: 16322582 DOI: 10.1110/ps.051722805
22-Apr-05     Release date:   13-Dec-05    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P21866  (KDPE_ECOLI) -  KDP operon transcriptional regulatory protein KdpE
225 a.a.
120 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     two-component signal transduction system (phosphorelay)   1 term 


DOI no: 10.1110/ps.051722805 Protein Sci 14:3077-3088 (2005)
PubMed id: 16322582  
A common dimerization interface in bacterial response regulators KdpE and TorR.
A.Toro-Roman, T.Wu, A.M.Stock.
Bacterial response regulators are key regulatory proteins that function as the final elements of so-called two-component signaling systems. The activities of response regulators in vivo are modulated by phosphorylation that results from interactions between the response regulator and its cognate histidine protein kinase. The level of response regulator phosphorylation, which is regulated by intra-or extracellular signals sensed by the histidine protein kinase, ultimately determines the output response that is initiated or carried out by the response regulator. We have recently hypothesized that in the OmpR/PhoB subfamily of response regulator transcription factors, this activation involves a common mechanism of dimerization using a set of highly conserved residues in the alpha4-beta5-alpha5 face. Here we report the X-ray crystal structures of the regulatory domains of response regulators TorR (1.8 A), Ca(2+)-bound KdpE (2.0 A), and Mg(2+)/BeF(3)(-)-bound KdpE (2.2 A), both members of the OmpR/ PhoB subfamily from Escherichia coli. Both regulatory domains form symmetric dimers in the asymmetric unit that involve the alpha4-beta5-alpha5 face. As observed previously in other OmpR/PhoB response regulators, the dimer interfaces are mediated by highly conserved residues within this subfamily. These results provide further evidence that most all response regulators of the OmpR/ PhoB subfamily share a common mechanism of activation by dimerization.
  Selected figure(s)  
Figure 1.
Figure 1. (A,B) Ribbon diagrams of the regulatory domains of KdpE[N]-BeF[3]^- (gold) and TorR[N] (protomers A and B, teal). The two proteins form symmetric dimers mediated by the 4- 5- 5 faces. In KdpE[N]-BeF[3]^- the side chains of Asp53, Ser79, and Tyr98 (gray and red), and BeF[3]^- (magenta and salmon) are shown as stick models, and the Mg2+ ion (orange) is shown in sphere representation. BeF[3]^- is noncovalently bound to the site of phosphorylation, Asp52, and serves as one of the ligands for the catalytic Mg2+. Ser79 and Tyr98 are conserved residues involved in the "switch" mechanism of activation associated with phosphorylation of the conserved Asp52. The equivalent residues Asp53, Thr80, and Tyr99 are shown for TorR[N]. (C) Alignment of KdpE[N]-Ca2+ (protomer B, green) vs. KdpE[N]-BeF[3]^- (protomer B, gold) showing the conserved residues involved in propagation of the activation signal from the active site aspartate to the 4- 5- 5 face. The side chains of Asp52, Ser79, and Tyr98 (oxygens in red), and BeF[3]^- (magenta and salmon) are shown in stick representation, with the Mg2+ (orange) and Ca^2+ (green) ions shown as spheres. The 4- 4 loops are further stabilized into a fixed conformation by interacting with Tyr98. Minimal differences are seen between the two structures. (D) Alignment of the four protomers found in the asymmetric unit of the TorR[N] crystals. Side chains of Asp53, Thr80, and Tyr99 (oxygens in red) are shown as sticks. Two dimers are formed between protomers A-B and C-D. Protomers A and D (teal) have the switch residues Thr80 and Tyr99 in an inward active conformation, while in protomers B and C (brown) they adopt an outward conformation associated with the inactive state. The conformation of the 4- 4 loops in protomers B and C differs from that of protomers A and D because side chains of residues in these loops are used for crystal contacts.
Figure 3.
Figure 3. Conserved intermolecular interactions of KdpE[N]-BeF[3]^- (A,B) and TorR[N] (C,D) at the dimer interface. KdpE[N]-BeF[3]^- protomers are distinguished by the colors gold and green, and TorR[N], by the colors teal and brown. Hydrophobic and electrostatic interactions are represented by sphere and stick models, respectively. (A,C) In both KdpE[N]-BeF[3]^- and TorR[N], the 4 and 5 helices are packed together through a conserved hydrophobic patch formed in KdpE[N]-BeF[3]^- by Ile88 ( 4), Leu91 ( 4), Ala110 ( 5), and Val114 ( 5). Analogous conserved interactions are seen in TorR[N] except for an additional nonconserved hydrophobic residue in KdpE[N]-BeF[3]^- (Val114) that further extends the hydrophobic patch down the path of the helices. (B,D) The interface of these dimers is further stabilized by a network of inter- and intramolecular salt bridges formed in KdpE[N]-BeF[3]- by Glu107 ( 5) and Arg111 ( 5), Asp97 ( 5) and Arg111 ( 5), Asp96 ( 4- 5 loop) and Arg118 ( 5), Asp92 ( 4) and Arg113 ( 5), and Ala95 ( 4- 5 loop)/Leu91 ( 4) and Arg117 ( 5). In TorR[N] the interactions are formed between Glu108 ( 5) and Arg88 ( 4), Glu108 ( 5) and Arg112 ( 5), Asp98 ( 5) and Arg112 ( 5), Asp97 ( 4- 5 loop) and Arg119 ( 5), and Ala96 ( 4- 5 loop)/Leu92 ( 4) and Asn115 ( 5). On the right side of the TorR[N] interface the Glu108-Arg88 interaction is bridged by the side-chain oxygen of Tyr99, which is found in an outward conformation in protomers B and C (see Fig. 1D Go-). The side chains of Glu93 and Lys114 are involved in crystal contacts, and thus do not form the analogous salt bridge seen in KdpE[N]-BeF[3]^-.
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2005, 14, 3077-3088) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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
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.  
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.  
19246239 U.Jenal, and M.Y.Galperin (2009).
Single domain response regulators: molecular switches with emerging roles in cell organization and dynamics.
  Curr Opin Microbiol, 12, 152-160.  
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.  
17376070 G.Churchward (2007).
The two faces of Janus: virulence gene regulation by CovR/S in group A streptococci.
  Mol Microbiol, 64, 34-41.  
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
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
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
16788170 A.A.Gusa, J.Gao, V.Stringer, G.Churchward, and J.R.Scott (2006).
Phosphorylation of the group A Streptococcal CovR response regulator causes dimerization and promoter-specific recruitment by RNA polymerase.
  J Bacteriol, 188, 4620-4626.  
17050920 A.M.Stock, and J.Guhaniyogi (2006).
A new perspective on response regulator activation.
  J Bacteriol, 188, 7328-7330.  
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.