PDBsum entry 1zy2

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protein metals Protein-protein interface(s) links
Transcription PDB id
Protein chains
140 a.a. *
125 a.a. *
Waters ×1
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Crystal structure of the phosphorylated receiver domain of the transcription regulator ntrc1 from aquifex aeolicus
Structure: Transcriptional regulator ntrc1. Chain: a, b. Synonym: ntrc. Engineered: yes
Source: Aquifex aeolicus. Organism_taxid: 63363. Gene: ntrc1. Expressed in: escherichia coli. Expression_system_taxid: 562. Plasmid.
Biol. unit: Dimer (from PQS)
3.03Å     R-factor:   0.251     R-free:   0.283
Authors: M.Doucleff,B.Chen,A.E.Maris,D.E.Wemmer,E.Kondrashkina, B.T.Nixon
Key ref:
M.Doucleff et al. (2005). Negative regulation of AAA + ATPase assembly by two component receiver domains: a transcription activation mechanism that is conserved in mesophilic and extremely hyperthermophilic bacteria. J Mol Biol, 353, 242-255. PubMed id: 16169010 DOI: 10.1016/j.jmb.2005.08.003
09-Jun-05     Release date:   16-Aug-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O67198  (O67198_AQUAE) -  Transcriptional regulator (NtrC family)
439 a.a.
140 a.a.*
Protein chain
Pfam   ArchSchema ?
O67198  (O67198_AQUAE) -  Transcriptional regulator (NtrC family)
439 a.a.
125 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

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


DOI no: 10.1016/j.jmb.2005.08.003 J Mol Biol 353:242-255 (2005)
PubMed id: 16169010  
Negative regulation of AAA + ATPase assembly by two component receiver domains: a transcription activation mechanism that is conserved in mesophilic and extremely hyperthermophilic bacteria.
M.Doucleff, B.Chen, A.E.Maris, D.E.Wemmer, E.Kondrashkina, B.T.Nixon.
Only a few transcriptional regulatory proteins have been characterized in extremely hyperthermophilic organisms, and most function as repressors. Structural features of the NtrC1 protein from the hyperthermophilic bacterium Aquifex aeolicus suggested that this protein functions similarly to the sigma(54)-polymerase activator DctD of Sinorhizobium meliloti. Here, we demonstrate that NtrC1 is an enzyme that hydrolyzes ATP to activate initiation of transcription by sigma(54)-holoenzyme. New structural data, including small-angle solution scattering data and the crystal structure of the phosphorylated receiver domain, show that NtrC1 uses a signal transduction mechanism very similar to that of DctD to control assembly of its AAA+ ATPase domain. As for DctD, the off-state of NtrC1 depends upon a tight dimer of the receiver domain to repress oligomerization of an intrinsically competent ATPase domain. Activation of NtrC1 stabilizes an alternative dimer configuration of the receiver domain that is very similar to the on-state dimers of the DctD and FixJ receiver domains. This alternative dimer appears to relieve repression of the ATPase domain by disrupting the off-state dimerization interface along the helical linker region between receiver and ATPase domains. Bacterial enhancer binding proteins typically have two linker sequences, one between N-terminal regulatory and central ATPase domains, and one between the central ATPase and C-terminal DNA binding domains. Sequence analyses reveal an intriguing correlation between the negative regulation mechanism of NtrC1 and DctD, and a structured N-terminal linker and unstructured C-terminal one; conversely, the very different, positive mechanism present in NtrC protein occurs in the context of an unstructured N-terminal linker and a structured C-terminal one. In both cases, the structured linkers significantly contribute to the stability of the off-state dimer conformation. These analyses also raise the possibility that a structured linker between N-terminal regulatory and central output domains is used frequently in regulatory proteins from hyperthermophilic organisms.
  Selected figure(s)  
Figure 6.
Figure 6. Sequence alignment and secondary structure prediction (H, helical; E, extended; -, random coil) for the linker regions of DctD, NtrC1, and NtrC. The top sequence shows the extended a-helix 5 and predicted coiled coils (bold residues) for linker L[1] of DctD and NtrC1, whereas in NtrC this region is unstructured. The bottom alignment shows the structured linker L[2] between the ATPase and the DNA-binding domains (in the NMR structure that defines regions of NtrC, the underlined residues of the last helix were substituted with alanine).
Figure 7.
Figure 7. Different roles of linkers L[1] and L[2] in regulatory proteins. (a) Models for the transition from off to on-states following phosphorylation are shown for NtrC (top) and DctD or NtrC1 (bottom). In activated NtrC the DNA-binding domain is hidden underneath the hexamer ring. For DctD and NtrC1, no information is available to define the position of DNA-binding domains. Models were built using published structures: for NtrC fragments R (off-state PDB 1KRW, on-state 1KRX) and L[2]-D (PDB entry 1NTC); and for NtrC1 and DctD fragment R of NtrC1 (this work), and fragments R-L[1]-C (1NY5) and L[1]-C (1NY6) of NtrC1, and R-L[1] of DctD (off 1L5Y, on 1L5Z). (b) Stereo-pair oriented as in Figure 4(b) showing the structural alignment of the phospho-NtrC1 R-L[1] homodimer (red), the Click to view the MathML source- [0?wchp=dGLzVlz-zSkzS] -bound DctD R-L[1] homodimer (blue), and the phospho-FixJ R homodimer (green). For clarity, the phosphoryl group (sticks) is shown only for the NtrC1 fragment, and the L[1] linker segments are labeled. Only the bottom subunits were used to superimpose the structures to emphasize the similar juxtapositions of the second subunits in the dimer configurations (see Materials and Methods). (c) Surface representations of the homodimer interface of a single subunit of the phospho-NtrC1 R-L[1] crystal structure (left) compared with the Click to view the MathML source- [0?wchp=dGLzVlz-zSkzS] -bound DctD R-L[1] crystal structure (right). Coloring indicates charge, and labeling of key residues of the TGXGXHydX[3]HydX[2]Hyd motif focuses attention on the upward opening of the b4-a4 loop that exposes the hydrophobic clefts for insertion of the hydrophobic knobs from the apposing subunit.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 353, 242-255) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265790 M.Bush, T.Ghosh, N.Tucker, X.Zhang, and R.Dixon (2011).
Transcriptional regulation by the dedicated nitric oxide sensor, NorR: a route towards NO detoxification.
  Biochem Soc Trans, 39, 289-293.  
21070941 B.Chen, T.A.Sysoeva, S.Chowdhury, L.Guo, S.De Carlo, J.A.Hanson, H.Yang, and B.T.Nixon (2010).
Engagement of arginine finger to ATP triggers large conformational changes in NtrC1 AAA+ ATPase for remodeling bacterial RNA polymerase.
  Structure, 18, 1420-1430.
PDB code: 3m0e
20226685 H.J.Sterling, J.D.Batchelor, D.E.Wemmer, and E.R.Williams (2010).
Effects of buffer loading for electrospray ionization mass spectrometry of a noncovalent protein complex that requires high concentrations of essential salts.
  J Am Soc Mass Spectrom, 21, 1045-1049.  
20624215 M.Bush, T.Ghosh, N.Tucker, X.Zhang, and R.Dixon (2010).
Nitric oxide-responsive interdomain regulation targets the σ54-interaction surface in the enhancer binding protein NorR.
  Mol Microbiol, 77, 1278-1288.  
20080056 R.Gao, and A.M.Stock (2010).
Molecular strategies for phosphorylation-mediated regulation of response regulator activity.
  Curr Opin Microbiol, 13, 160-167.  
19699748 J.D.Batchelor, H.J.Sterling, E.Hong, E.R.Williams, and D.E.Wemmer (2009).
Receiver domains control the active-state stoichiometry of Aquifex aeolicus sigma54 activator NtrC4, as revealed by electrospray ionization mass spectrometry.
  J Mol Biol, 393, 634-643.  
19372156 J.Peña-Sánchez, S.Poggio, U.Flores-Pérez, A.Osorio, C.Domenzain, G.Dreyfus, and L.Camarena (2009).
Identification of the binding site of the {sigma}54 hetero-oligomeric FleQ/FleT activator in the flagellar promoters of Rhodobacter sphaeroides.
  Microbiology, 155, 1669-1679.  
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
19575571 R.Gao, and A.M.Stock (2009).
Biological insights from structures of two-component proteins.
  Annu Rev Microbiol, 63, 133-154.  
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
17437715 B.Chen, M.Doucleff, D.E.Wemmer, S.De Carlo, H.H.Huang, E.Nogales, T.R.Hoover, E.Kondrashkina, L.Guo, and B.T.Nixon (2007).
ATP ground- and transition states of bacterial enhancer binding AAA+ ATPases support complex formation with their target protein, sigma54.
  Structure, 15, 429-440.  
18075577 J.Kuriyan, and D.Eisenberg (2007).
The origin of protein interactions and allostery in colocalization.
  Nature, 450, 983-990.  
17573816 J.S.Fraser, J.P.Merlie, N.Echols, S.R.Weisfield, T.Mignot, D.E.Wemmer, D.R.Zusman, and T.Alber (2007).
An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS.
  Mol Microbiol, 65, 319-332.
PDB codes: 2gkg 2i6f 2nt3 2nt4
17590233 M.N.Burtnick, J.S.Downey, P.J.Brett, J.A.Boylan, J.G.Frye, T.R.Hoover, and F.C.Gherardini (2007).
Insights into the complex regulation of rpoS in Borrelia burgdorferi.
  Mol Microbiol, 65, 277-293.  
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.  
18023171 P.A.Tucker, and L.Sallai (2007).
The AAA+ superfamily--a myriad of motions.
  Curr Opin Struct Biol, 17, 641-652.  
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.  
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.  
16321925 D.E.Wemmer, and D.Kern (2005).
Beryllofluoride binding mimics phosphorylation of aspartate in response regulators.
  J Bacteriol, 187, 8229-8230.  
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.