PDBsum entry 1l5y

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protein ligands metals Protein-protein interface(s) links
Transcription regulator PDB id
Protein chains
143 a.a. *
151 a.a. *
SO4 ×4
BEF ×3
BF2 ×10
_MG ×2
Waters ×224
* Residue conservation analysis
PDB id:
Name: Transcription regulator
Title: Crystal structure of mg2+ / bef3-bound receiver domain of sinorhizobium meliloti dctd
Structure: C4-dicarboxylate transport transcriptional regula protein dctd. Chain: a, b. Fragment: receiver domain, residues 2-143. Synonym: dctdnl. Engineered: yes. Mutation: yes
Source: Sinorhizobium meliloti. Organism_taxid: 382. Gene: dctd. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.10Å     R-factor:   0.184     R-free:   0.229
Authors: S.Park,M.Meyer,A.D.Jones,H.P.Yennawar,N.H.Yennawar,B.T.Nixon
Key ref: S.Park et al. (2002). Two-component signaling in the AAA + ATPase DctD: binding Mg2+ and BeF3- selects between alternate dimeric states of the receiver domain. FASEB J, 16, 1964-1966. PubMed id: 12368235
08-Mar-02     Release date:   23-Oct-02    
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Protein chain
Pfam   ArchSchema ?
P13632  (DCTD_RHIME) -  C4-dicarboxylate transport transcriptional regulatory protein DctD
460 a.a.
143 a.a.*
Protein chain
Pfam   ArchSchema ?
P13632  (DCTD_RHIME) -  C4-dicarboxylate transport transcriptional regulatory protein DctD
460 a.a.
151 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 14 residue positions (black crosses)

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


FASEB J 16:1964-1966 (2002)
PubMed id: 12368235  
Two-component signaling in the AAA + ATPase DctD: binding Mg2+ and BeF3- selects between alternate dimeric states of the receiver domain.
S.Park, M.Meyer, A.D.Jones, H.P.Yennawar, N.H.Yennawar, B.T.Nixon.
A Crystallogral structure is described for the Mg2+-BeF3--bound receiver domain of Sinorhizobium meliloti DctD bearing amino acid substitution E121K. Differences between the apo- and ligand-bound active sites are similar to those reported for other receiver domains. However, the off and on states of the DctD receiver domain are characterized by dramatically different dimeric structures, which supports the following hypothesis of signal transduction. In the off state, the receiver domain and coiled-coil linker form a dimer that inhibits oligomerization of the AAA+ ATPase domain. In this conformation, the receiver domain cannot be phosphorylated or bind Mg2+ and BeF3-. Instead, these modifications stabilize an alternative dimeric conformation that repositions the subunits by approximately 20 A, thus replacing the a4-b5-a5 interface with an a4-b5 interface. Reoriented receiver domains permit the ATPase domain to oligomerize and stimulate open complex formation by the s54 form of RNA polymerase. NtrC, which shares 38% sequence identity with DctD, works differently. Its activated receiver domain must facilitate oligomerization of its ATPase domain. Significant differences exist in the signaling surfaces of the DctD and NtrC receiver domains that may help explain how triggering the common two-component switch can variously regulate assembly of a AAA+ ATPase domain.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20080056 R.Gao, and A.M.Stock (2010).
Molecular strategies for phosphorylation-mediated regulation of response regulator activity.
  Curr Opin Microbiol, 13, 160-167.  
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.  
18208392 B.Chen, T.A.Sysoeva, S.Chowdhury, and B.T.Nixon (2008).
Regulation and action of the bacterial enhancer-binding protein AAA+ domains.
  Biochem Soc Trans, 36, 89-93.  
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
18557815 S.A.Thomas, J.A.Brewster, and R.B.Bourret (2008).
Two variable active site residues modulate response regulator phosphoryl group stability.
  Mol Microbiol, 69, 453-465.  
17157497 M.Rappas, D.Bose, and X.Zhang (2007).
Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription.
  Curr Opin Struct Biol, 17, 110-116.  
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.  
16816192 R.Gao, A.Mukhopadhyay, F.Fang, and D.G.Lynn (2006).
Constitutive activation of two-component response regulators: characterization of VirG activation in Agrobacterium tumefaciens.
  J Bacteriol, 188, 5204-5211.  
16751184 S.De Carlo, B.Chen, T.R.Hoover, E.Kondrashkina, E.Nogales, and B.T.Nixon (2006).
The structural basis for regulated assembly and function of the transcriptional activator NtrC.
  Genes Dev, 20, 1485-1495.  
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
15255896 K.Muchová, R.J.Lewis, D.Perecko, J.A.Brannigan, J.C.Ladds, A.Leech, A.J.Wilkinson, and I.Barák (2004).
Dimer-induced signal propagation in Spo0A.
  Mol Microbiol, 53, 829-842.  
14561776 S.Y.Lee, A.De La Torre, D.Yan, S.Kustu, B.T.Nixon, and D.E.Wemmer (2003).
Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains.
  Genes Dev, 17, 2552-2563.
PDB codes: 1ny5 1ny6
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