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PDBsum entry 1neq

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protein links
DNA-binding protein PDB id
1neq
Jmol
Contents
Protein chain
74 a.a. *
* Residue conservation analysis
PDB id:
1neq
Name: DNA-binding protein
Title: Solution structure of the mu ner protein by multidimensional nmr
Structure: DNA-binding protein ner. Chain: a
Source: Enterobacteria phage mu. Organism_taxid: 10677
NMR struc: 1 models
Authors: G.M.Clore,T.E.Strzelecka,A.M.Gronenborn
Key ref:
T.E.Strzelecka et al. (1995). The solution structure of the Mu Ner protein reveals a helix-turn-helix DNA recognition motif. Structure, 3, 1087-1095. PubMed id: 8590003 DOI: 10.1016/S0969-2126(01)00244-1
Date:
24-Aug-95     Release date:   07-Dec-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06020  (NER_BPMU) -  Negative regulator of transcription
Seq:
Struc:
75 a.a.
74 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1016/S0969-2126(01)00244-1 Structure 3:1087-1095 (1995)
PubMed id: 8590003  
 
 
The solution structure of the Mu Ner protein reveals a helix-turn-helix DNA recognition motif.
T.E.Strzelecka, G.M.Clore, A.M.Gronenborn.
 
  ABSTRACT  
 
BACKGROUND: The Mu Ner protein is a small (74 amino acids), basic, DNA-binding protein found in phage Mu. It belongs to a class of proteins, the cro and repressor proteins, that regulate the switch from the lysogenic to the lytic state of the phage life cycle. There is no significant sequence identity between Mu Ner and the cro proteins of other phages, despite their functional similarity. In addition, there is no significant sequence identity with any other DNA-binding proteins, with the exception of Ner from the related phage D108 and the Nlp protein of Escherichia coli. As the tertiary structures of Mu Ner and these two related proteins are unknown, it is clear that a three-dimensional (3D) structure of Mu Ner is essential in order to gain insight into its mode of DNA binding. RESULTS: The 3D solution structure of Mu Ner has been solved by 3D and 4D heteronuclear magnetic resonance spectroscopy. The structure consists of five alpha helices, two of which comprise a helix-turn-helix (HTH) motif. Analysis of line broadening and disappearance of crosspeaks in a 1H-15N correlation spectrum of the Mu Ner-DNA complex suggests that residues in these two helices are most likely to be in contact with the DNA. CONCLUSIONS: Like the functionally analogous cro proteins from phages lambda and 434, the Mu Ner protein possesses a HTH DNA recognition motif. The Ner protein from phage D108 and the Nlp protein from E. coli are likely to have very similar tertiary structures due to high amino-acid-sequence identity with Mu Ner.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Overall structure of Mu Ner. (a) Backbone fold of Mu Ner, with the HTH motif shown in yellow. (b) The surface of Mu Ner color coded by electrostatic potential. Red indicates negative potentials that are less than −7 kT, and blue indicates positive potentials that are greater than 7 kT. The electrostatic potential was calculated and the images generated using the program GRASP [66]. The labeled residues in (b) indicate residues that give rise to a contiguous patch of positive electrostatic potential. Figure 3. Overall structure of Mu Ner. (a) Backbone fold of Mu Ner, with the HTH motif shown in yellow. (b) The surface of Mu Ner color coded by electrostatic potential. Red indicates negative potentials that are less than −7 kT, and blue indicates positive potentials that are greater than 7 kT. The electrostatic potential was calculated and the images generated using the program GRASP [[3]66]. The labeled residues in (b) indicate residues that give rise to a contiguous patch of positive electrostatic potential.
Figure 4.
Figure 4. Ribbon drawings of 434 cro, the 434 repressor (residues 1–69), the P22 repressor (residues 6–65), the λ repressor (residues 1–92) and Mu Ner (residues 8–66), all in the same orientation. The HTH motif is shown in yellow. Figure 4. Ribbon drawings of 434 cro, the 434 repressor (residues 1–69), the P22 repressor (residues 6–65), the λ repressor (residues 1–92) and Mu Ner (residues 8–66), all in the same orientation. The HTH motif is shown in yellow. (The figure was generated using with the program RIBBONS [[3]67].)
 
  The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 1087-1095) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
15062080 T.Newlove, J.H.Konieczka, and M.H.Cordes (2004).
Secondary structure switching in Cro protein evolution.
  Structure, 12, 569-581.
PDB code: 1rzs
12003952 K.H.O'Neill, D.M.Roche, D.J.Clarke, and B.C.Dowds (2002).
The ner gene of Photorhabdus: effects on primary-form-specific phenotypes and outer membrane protein composition.
  J Bacteriol, 184, 3096-3105.  
11272834 K.Takeda, C.Akimoto, and M.Kawamukai (2001).
Effects of the Escherichia coli sfsA gene on mal genes expression and a DNA binding activity of SfsA.
  Biosci Biotechnol Biochem, 65, 213-217.  
10931317 N.J.Saunders, A.C.Jeffries, J.F.Peden, D.W.Hood, H.Tettelin, R.Rappuoli, and E.R.Moxon (2000).
Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58.
  Mol Microbiol, 37, 207-215.  
9032054 M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.
  Curr Opin Struct Biol, 7, 76-85.  
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.