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PDBsum entry 1fse

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protein ligands Protein-protein interface(s) links
Transcription PDB id
1fse
Jmol
Contents
Protein chains
67 a.a. *
70 a.a. *
50 a.a. *
Ligands
GOL ×3
SO4 ×4
Waters ×322
* Residue conservation analysis
PDB id:
1fse
Name: Transcription
Title: Crystal structure of the bacillus subtilis regulatory protei
Structure: Gere. Chain: a, b, c, d, e, f. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.05Å     R-factor:   0.214     R-free:   0.272
Authors: V.M.-A.Ducros,R.J.Lewis,C.S.Verma,E.J.Dodson,G.Leonard, J.P.Turkenburg,G.N.Murshudov,A.J.Wilkinson,J.A.Brannigan
Key ref:
V.M.Ducros et al. (2001). Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis. J Mol Biol, 306, 759-771. PubMed id: 11243786 DOI: 10.1006/jmbi.2001.4443
Date:
08-Sep-00     Release date:   21-Mar-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P11470  (GERE_BACSU) -  Spore germination protein GerE
Seq:
Struc:
74 a.a.
67 a.a.
Protein chains
Pfam   ArchSchema ?
P11470  (GERE_BACSU) -  Spore germination protein GerE
Seq:
Struc:
74 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
P11470  (GERE_BACSU) -  Spore germination protein GerE
Seq:
Struc:
74 a.a.
50 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1006/jmbi.2001.4443 J Mol Biol 306:759-771 (2001)
PubMed id: 11243786  
 
 
Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis.
V.M.Ducros, R.J.Lewis, C.S.Verma, E.J.Dodson, G.Leonard, J.P.Turkenburg, G.N.Murshudov, A.J.Wilkinson, J.A.Brannigan.
 
  ABSTRACT  
 
The small, DNA-binding protein GerE regulates gene transcription in the terminally differentiated mother-cell compartment during late stages of sporulation in Bacillus subtilis. This versatile transcription factor shares sequence homology with the LuxR/FixJ/UhpA family of activators and modulates the expression of a number of genes, in particular those encoding the components of the coat that surrounds the mature spore. GerE orchestrates the final stages of coat deposition and maturation that lead to a spore with remarkable resistance properties but that must be responsive to low levels of germination signals. As this germination process is largely passive and can occur in the absence of de novo protein synthesis, the correct assembly of germination machinery, including germinant receptors and energy storage compounds, is crucial to the survival of the cell. The crystal structure of GerE has been solved at 2.05 A resolution using multi-wavelength anomalous dispersion techniques and reveals the nature of the GerE dimer. Each monomer comprises four alpha-helices, of which the central pair forms a helix-turn-helix DNA-binding motif. Implications for DNA-binding and the structural organisation of the LuxR/FixJ/UhpA family of transcription activator domains are discussed.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Stereoview of a structural comparison of one protomer of GerE (red) with the DNA-binding domain of NarL (yellow). The structures were superposed by least-squares minimisation of the difference in 62 C^a atomic positions for residues 11 to 72 of GerE to the equivalent C^a atoms, residues 155 to 216 of NarL. The first helix of the HTH motif is to the right of the picture, with the recognition helix running horizontally from right to left towards the bottom of the Figure. The similarity of the proteins is evident, and broken by the C-terminal a-helix, which is flexible in NarL with mean B-values in the region of 70 Å2, compared to an overall value of 42 Å2.
Figure 7.
Figure 7. (a) Electrostatic surface representation, with positive and negative potential coloured blue and red, respectively. The two stereoviews correspond to the orientations presented in Figure 2(a) and (b). (b) Overall structure of a modelled DNA-protein complex.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 306, 759-771) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21460451 N.S.Pannu, W.J.Waterreus, P.Skubák, I.Sikharulidze, J.P.Abrahams, and R.A.de Graaff (2011).
Recent advances in the CRANK software suite for experimental phasing.
  Acta Crystallogr D Biol Crystallogr, 67, 331-337.  
20634237 A.V.Lin, and V.Stewart (2010).
Functional roles for the GerE-family carboxyl-terminal domains of nitrate response regulators NarL and NarP of Escherichia coli K-12.
  Microbiology, 156, 2933-2943.  
20302877 C.A.Hobbs, B.G.Bobay, R.J.Thompson, M.Perego, and J.Cavanagh (2010).
NMR solution structure and DNA-binding model of the DNA-binding domain of competence protein A.
  J Mol Biol, 398, 248-263.
PDB code: 2krf
20383001 G.M.Sheldrick (2010).
Experimental phasing with SHELXC/D/E: combining chain tracing with density modification.
  Acta Crystallogr D Biol Crystallogr, 66, 479-485.  
20529360 J.N.Weeks, C.L.Galindo, K.L.Drake, G.L.Adams, H.R.Garner, and T.A.Ficht (2010).
Brucella melitensis VjbR and C12-HSL regulons: contributions of the N-dodecanoyl homoserine lactone signaling molecule and LuxR homologue VjbR to gene expression.
  BMC Microbiol, 10, 167.  
20942908 J.Rodríguez-Moya, M.Argandoña, M.Reina-Bueno, J.J.Nieto, F.Iglesias-Guerra, M.Jebbar, and C.Vargas (2010).
Involvement of EupR, a response regulator of the NarL/FixJ family, in the control of the uptake of the compatible solutes ectoines by the halophilic bacterium Chromohalobacter salexigens.
  BMC Microbiol, 10, 256.  
20662766 M.Horiuchi, K.Nakamura, K.Kojima, Y.Nishiyama, W.Hatakeyama, T.Hisabori, and Y.Hihara (2010).
The PedR transcriptional regulator interacts with thioredoxin to connect photosynthesis with gene expression in cyanobacteria.
  Biochem J, 431, 135-140.  
20846031 N.Bhargava, P.Sharma, and N.Capalash (2010).
Quorum sensing in Acinetobacter: an emerging pathogen.
  Crit Rev Microbiol, 36, 349-360.  
20061473 P.Himes, S.J.McBryant, and L.Kroos (2010).
Two regions of Bacillus subtilis transcription factor SpoIIID allow a monomer to bind DNA.
  J Bacteriol, 192, 1596-1606.  
20606258 P.Skubák, W.J.Waterreus, and N.S.Pannu (2010).
Multivariate phase combination improves automated crystallographic model building.
  Acta Crystallogr D Biol Crystallogr, 66, 783-788.  
20378989 S.Kim, H.Hirakawa, S.Muta, and S.Kuhara (2010).
Identification and classification of a two-component system based on domain structures in bacteria and differences in domain structure between gram-positive and gram-negative bacteria.
  Biosci Biotechnol Biochem, 74, 716-720.  
21217812 S.Thao, C.S.Chen, H.Zhu, and J.C.Escalante-Semerena (2010).
Nε-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity.
  PLoS One, 5, e15123.  
20179338 T.C.Terwilliger (2010).
Rapid model building of alpha-helices in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 268-275.  
20179339 T.C.Terwilliger (2010).
Rapid model building of beta-sheets in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 276-284.  
20179340 T.C.Terwilliger (2010).
Rapid chain tracing of polypeptide backbones in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 285-294.  
19088317 A.V.Patankar, and J.E.González (2009).
An orphan LuxR homolog of Sinorhizobium meliloti affects stress adaptation and competition for nodulation.
  Appl Environ Microbiol, 75, 946-955.  
19060142 H.Takamatsu, D.Imamura, R.Kuwana, and K.Watabe (2009).
Expression of yeeK during Bacillus subtilis sporulation and localization of YeeK to the inner spore coat using fluorescence microscopy.
  J Bacteriol, 191, 1220-1229.  
19447950 I.de Bruijn, and J.M.Raaijmakers (2009).
Diversity and functional analysis of LuxR-type transcriptional regulators of cyclic lipopeptide biosynthesis in Pseudomonas fluorescens.
  Appl Environ Microbiol, 75, 4753-4761.  
19126546 R.K.Carroll, X.Liao, L.K.Morgan, E.M.Cicirelli, Y.Li, W.Sheng, X.Feng, and L.J.Kenney (2009).
Structural and Functional Analysis of the C-terminal DNA Binding Domain of the Salmonella typhimurium SPI-2 Response Regulator SsrB.
  J Biol Chem, 284, 12008-12019.  
19465773 T.C.Terwilliger, P.D.Adams, R.J.Read, A.J.McCoy, N.W.Moriarty, R.W.Grosse-Kunstleve, P.V.Afonine, P.H.Zwart, and L.W.Hung (2009).
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.
  Acta Crystallogr D Biol Crystallogr, 65, 582-601.  
18063573 E.Severi, A.Müller, J.R.Potts, A.Leech, D.Williamson, K.S.Wilson, and G.H.Thomas (2008).
Sialic acid mutarotation is catalyzed by the Escherichia coli beta-propeller protein YjhT.
  J Biol Chem, 283, 4841-4849.
PDB code: 2uvk
18395223 G.D.Malo, M.Wang, D.Wu, A.L.Stelling, P.J.Tonge, and R.M.Wachter (2008).
Crystal structure and Raman studies of dsFP483, a cyan fluorescent protein from Discosoma striata.
  J Mol Biol, 378, 871-886.
PDB code: 3cgl
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
17376086 C.E.White, and S.C.Winans (2007).
The quorum-sensing transcription factor TraR decodes its DNA binding site by direct contacts with DNA bases and by detection of DNA flexibility.
  Mol Microbiol, 64, 245-256.  
17360279 C.E.White, and S.C.Winans (2007).
Cell-cell communication in the plant pathogen Agrobacterium tumefaciens.
  Philos Trans R Soc Lond B Biol Sci, 362, 1135-1148.  
17890309 L.Wang, J.Perpich, A.Driks, and L.Kroos (2007).
One perturbation of the mother cell gene regulatory network suppresses the effects of another during sporulation of Bacillus subtilis.
  J Bacteriol, 189, 8467-8473.  
16702222 A.Müller, E.Severi, C.Mulligan, A.G.Watts, D.J.Kelly, K.S.Wilson, A.J.Wilkinson, and G.H.Thomas (2006).
Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae.
  J Biol Chem, 281, 22212-22222.
PDB codes: 2cex 2cey
17035238 K.Nakamura, and Y.Hihara (2006).
Photon flux density-dependent gene expression in Synechocystis sp. PCC 6803 is regulated by a small, redox-responsive, LuxR-type regulator.
  J Biol Chem, 281, 36758-36766.  
16831870 S.Castang, S.Reverchon, P.Gouet, and W.Nasser (2006).
Direct evidence for the modulation of the activity of the Erwinia chrysanthemi quorum-sensing regulator ExpR by acylhomoserine lactone pheromone.
  J Biol Chem, 281, 29972-29987.  
16488888 V.M.Levdikov, E.Blagova, P.Joseph, A.L.Sonenshein, and A.J.Wilkinson (2006).
The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in gram-positive bacteria.
  J Biol Chem, 281, 11366-11373.
PDB codes: 2b0l 2b18 2gx5 2hgv
15720554 C.E.White, and S.C.Winans (2005).
Identification of amino acid residues of the Agrobacterium tumefaciens quorum-sensing regulator TraR that are critical for positive control of transcription.
  Mol Microbiol, 55, 1473-1486.  
16301796 P.Skubák, S.Ness, and N.S.Pannu (2005).
Extending the resolution and phase-quality limits in automated model building with iterative refinement.
  Acta Crystallogr D Biol Crystallogr, 61, 1626-1635.  
15359276 S.Rumpel, A.Razeto, C.M.Pillar, V.Vijayan, A.Taylor, K.Giller, M.S.Gilmore, S.Becker, and M.Zweckstetter (2004).
Structure and DNA-binding properties of the cytolysin regulator CylR2 from Enterococcus faecalis.
  EMBO J, 23, 3632-3642.
PDB code: 1utx
15035041 J.Errington (2003).
Regulation of endospore formation in Bacillus subtilis.
  Nat Rev Microbiol, 1, 117-126.  
12740396 P.Pristovsek, K.Sengupta, F.Löhr, B.Schäfer, M.W.von Trebra, H.Rüterjans, and F.Bernhard (2003).
Structural analysis of the DNA-binding domain of the Erwinia amylovora RcsB protein and its interaction with the RcsAB box.
  J Biol Chem, 278, 17752-17759.
PDB code: 1p4w
12198141 A.Vannini, C.Volpari, C.Gargioli, E.Muraglia, R.Cortese, R.De Francesco, P.Neddermann, and S.D.Marco (2002).
The crystal structure of the quorum sensing protein TraR bound to its autoinducer and target DNA.
  EMBO J, 21, 4393-4401.
PDB code: 1h0m
11741866 D.L.Crater, and C.P.Moran (2002).
Two regions of GerE required for promoter activation in Bacillus subtilis.
  J Bacteriol, 184, 241-249.  
11931761 E.A.Campbell, O.Muzzin, M.Chlenov, J.L.Sun, C.A.Olson, O.Weinman, M.L.Trester-Zedlitz, and S.A.Darst (2002).
Structure of the bacterial RNA polymerase promoter specificity sigma subunit.
  Mol Cell, 9, 527-539.
PDB codes: 1ku2 1ku3 1ku7
11839496 J.L.Huffman, and R.G.Brennan (2002).
Prokaryotic transcription regulators: more than just the helix-turn-helix motif.
  Curr Opin Struct Biol, 12, 98.  
11418558 D.L.Crater, and C.P.Moran (2001).
Identification of a DNA binding region in GerE from Bacillus subtilis.
  J Bacteriol, 183, 4183-4189.  
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.