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Transcription PDB id
1lj9
Jmol
Contents
Protein chains
144 a.a. *
Waters ×289
* Residue conservation analysis
PDB id:
1lj9
Name: Transcription
Title: The crystal structure of the transcriptional regulator slya
Structure: Transcriptional regulator slya. Chain: a, b. Engineered: yes
Source: Enterococcus faecalis. Organism_taxid: 1351. Gene: ref02436. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.60Å     R-factor:   0.248     R-free:   0.275
Authors: R.Y.Wu,R.G.Zhang,P.Gornicki,A.Joachimiak,Midwest Center For Structural Genomics (Mcsg)
Key ref:
R.Y.Wu et al. (2003). Crystal structure of Enterococcus faecalis SlyA-like transcriptional factor. J Biol Chem, 278, 20240-20244. PubMed id: 12649270 DOI: 10.1074/jbc.M300292200
Date:
19-Apr-02     Release date:   21-Jan-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q82ZP8  (Q82ZP8_ENTFA) -  Transcriptional regulator, MarR family
Seq:
Struc: 		150 a.a.
144 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1074/jbc.M300292200 J Biol Chem 278:20240-20244 (2003)
PubMed id: 12649270  
 
 
Crystal structure of Enterococcus faecalis SlyA-like transcriptional factor.
R.Y.Wu, R.G.Zhang, O.Zagnitko, I.Dementieva, N.Maltzev, J.D.Watson, R.Laskowski, P.Gornicki, A.Joachimiak.
 
  ABSTRACT  
 
The crystal structure of a SlyA transcriptional regulator at 1.6 A resolution is presented, and structural relationships between members of the MarR/SlyA family are discussed. The SlyA family, which includes SlyA, Rap, Hor, and RovA proteins, is widely distributed in bacterial and archaeal genomes. Current evidence suggests that SlyA-like factors act as repressors, activators, and modulators of gene transcription. These proteins have been shown to up-regulate the expression of molecular chaperones, acid-resistance proteins, and cytolysin, and down-regulate several biosynthetic enzymes. The structure of SlyA from Enterococcus faecalis, determined as a part of an ongoing structural genomics initiative (www.mcsg.anl.gov), revealed the same winged helix DNA-binding motif that was recently found in the MarR repressor from Escherichia coli and the MexR repressor from Pseudomonas aeruginosa, a sequence homologue of MarR. Phylogenetic analysis of the MarR/SlyA family suggests that Sly is placed between the SlyA and MarR subfamilies and shows significant sequence similarity to members of both subfamilies.
 
  Selected figure(s)  
 
Figure 3.
FIG. 3. Secondary and domain structure of SlyA-Ef. A, secondary structure of SlyA-Ef. b, SlyA-Ef dimerization domain showing domain swapping. c, DNA-binding domain with winged helix motif. Drawings prepared with WebLabViewerPro. 		Figure 4.
FIG. 4. Comparison of the SlyA-Ef structure with the structures of MarR and MexR. a, superimposition of SlyA-Ef (blue) on MarR (red) subunits. b, superimposition of the SlyA-Ef (blue) and MexR (red) structures.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 20240-20244) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20676430 B.Apostolovic, M.Danial, and H.A.Klok (2010).
Coiled coils: attractive protein folding motifs for the fabrication of self-assembled, responsive and bioactive materials.
  Chem Soc Rev, 39, 3541-3575.  
20095047 C.Andrésen, S.Jalal, D.Aili, Y.Wang, S.Islam, A.Jarl, B.Liedberg, B.Wretlind, L.G.Mårtensson, and M.Sunnerhagen (2010).
Critical biophysical properties in the Pseudomonas aeruginosa efflux gene regulator MexR are targeted by mutations conferring multidrug resistance.
  Protein Sci, 19, 680-692.  
20094649 V.Duarte, and J.M.Latour (2010).
PerR vs OhrR: selective peroxide sensing in Bacillus subtilis.
  Mol Biosyst, 6, 316-323.  
20421503 Y.M.Chang, W.Y.Jeng, T.P.Ko, Y.J.Yeh, C.K.Chen, and A.H.Wang (2010).
Structural study of TcaR and its complexes with multiple antibiotics from Staphylococcus epidermidis.
  Proc Natl Acad Sci U S A, 107, 8617-8622.
PDB codes: 3kp2 3kp3 3kp4 3kp5 3kp6 3kp7
  19255465 C.E.Nichols, S.Sainsbury, J.Ren, T.S.Walter, A.Verma, D.K.Stammers, N.J.Saunders, and R.J.Owens (2009).
The structure of NMB1585, a MarR-family regulator from Neisseria meningitidis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 204-209.
PDB code: 3g3z
19114478 P.Xue, D.Corbett, M.Goldrick, C.Naylor, and I.S.Roberts (2009).
Regulation of expression of the region 3 promoter of the Escherichia coli K5 capsule gene cluster involves H-NS, SlyA, and a large 5' untranslated region.
  J Bacteriol, 191, 1838-1846.  
19509310 T.Kumarevel, T.Tanaka, T.Umehara, and S.Yokoyama (2009).
ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.
  Nucleic Acids Res, 37, 4723-4735.
PDB codes: 3gez 3gf2 3gfi 3gfj 3gfl 3gfm
17322537 E.A.Sieminska, X.Xu, A.Savchenko, and D.A.Sanders (2007).
The X-ray crystal structure of PA1607 from Pseudomonas aureginosa at 1.9 A resolution--a putative transcription factor.
  Protein Sci, 16, 543-549.
PDB code: 2f2e
17892462 J.K.Lithgow, F.Haider, I.S.Roberts, and J.Green (2007).
Alternate SlyA and H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12.
  Mol Microbiol, 66, 685-698.  
18042459 K.J.Newberry, M.Fuangthong, W.Panmanee, S.Mongkolsuk, and R.G.Brennan (2007).
Structural mechanism of organic hydroperoxide induction of the transcription regulator OhrR.
  Mol Cell, 28, 652-664.
PDB codes: 2pex 2pfb
16529980 D.W.Ellison, and V.L.Miller (2006).
Regulation of virulence by members of the MarR/SlyA family.
  Curr Opin Microbiol, 9, 153-159.  
16862595 K.H.Chin, Z.L.Tu, J.N.Li, C.C.Chou, A.H.Wang, and S.H.Chou (2006).
The crystal structure of XC1739: a putative multiple antibiotic-resistance repressor (MarR) from Xanthomonas campestris at 1.8 A resolution.
  Proteins, 65, 239-242.
PDB code: 2fa5
16452421 W.Panmanee, P.Vattanaviboon, L.B.Poole, and S.Mongkolsuk (2006).
Novel organic hydroperoxide-sensing and responding mechanisms for OhrR, a major bacterial sensor and regulator of organic hydroperoxide stress.
  J Bacteriol, 188, 1389-1395.  
16287087 Y.Qiu, V.Tereshko, Y.Kim, R.Zhang, F.Collart, M.Yousef, A.Kossiakoff, and A.Joachimiak (2006).
The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold.
  Proteins, 62, 8.
PDB code: 1r4v
16209951 M.Hong, M.Fuangthong, J.D.Helmann, and R.G.Brennan (2005).
Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family.
  Mol Cell, 20, 131-141.
PDB codes: 1z91 1z9c
15731069 M.J.Ferrándiz, K.Bishop, P.Williams, and H.Withers (2005).
HosA, a member of the SlyA family, regulates motility in enteropathogenic Escherichia coli.
  Infect Immun, 73, 1684-1694.  
15647287 R.S.De Silva, G.Kovacikova, W.Lin, R.K.Taylor, K.Skorupski, and F.J.Kull (2005).
Crystal structure of the virulence gene activator AphA from Vibrio cholerae reveals it is a novel member of the winged helix transcription factor superfamily.
  J Biol Chem, 280, 13779-13783.
PDB code: 1yg2
15813739 W.W.Navarre, T.A.Halsey, D.Walthers, J.Frye, M.McClelland, J.L.Potter, L.J.Kenney, J.S.Gunn, F.C.Fang, and S.J.Libby (2005).
Co-regulation of Salmonella enterica genes required for virulence and resistance to antimicrobial peptides by SlyA and PhoP/PhoQ.
  Mol Microbiol, 56, 492-508.  
15353566 D.Tropel, and J.R.van der Meer (2004).
Bacterial transcriptional regulators for degradation pathways of aromatic compounds.
  Microbiol Mol Biol Rev, 68, 474-500.  
15225309 G.Kovacikova, W.Lin, and K.Skorupski (2004).
Vibrio cholerae AphA uses a novel mechanism for virulence gene activation that involves interaction with the LysR-type regulator AphB at the tcpPH promoter.
  Mol Microbiol, 53, 129-142.  
  15374664 M.A.Prieto, B.Galán, B.Torres, A.Ferrández, C.Fernández, B.Miñambres, J.L.García, and E.Díaz (2004).
Aromatic metabolism versus carbon availability: the regulatory network that controls catabolism of less-preferred carbon sources in Escherichia coli.
  FEMS Microbiol Rev, 28, 503-518.  
14996792 N.R.Wyborn, M.R.Stapleton, V.A.Norte, R.E.Roberts, J.Grafton, and J.Green (2004).
Regulation of Escherichia coli hemolysin E expression by H-NS and Salmonella SlyA.
  J Bacteriol, 186, 1620-1628.  
15479795 P.Kraft, A.Oeckinghaus, D.Kümmel, G.H.Gauss, J.Gilmore, B.Wiedenheft, M.Young, and C.M.Lawrence (2004).
Crystal structure of F-93 from Sulfolobus spindle-shaped virus 1, a winged-helix DNA binding protein.
  J Virol, 78, 11544-11550.
PDB code: 1tbx
15263850 Y.Kim, I.Dementieva, M.Zhou, R.Wu, L.Lezondra, P.Quartey, G.Joachimiak, O.Korolev, H.Li, and A.Joachimiak (2004).
Automation of protein purification for structural genomics.
  J Struct Funct Genomics, 5, 111-118.  
14602920 B.Galán, A.Kolb, J.M.Sanz, J.L.García, and M.A.Prieto (2003).
Molecular determinants of the hpa regulatory system of Escherichia coli: the HpaR repressor.
  Nucleic Acids Res, 31, 6598-6609.  
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.