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PDBsum entry 1tns

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protein links
DNA-binding protein PDB id
1tns
Jmol
Contents
Protein chain
76 a.a. *
* Residue conservation analysis
PDB id:
1tns
Name: DNA-binding protein
Title: A novel class of winged helix-turn-helix protein: the DNA- binding domain of mu transposase
Structure: Mu-transposase. Chain: a. Engineered: yes
Source: Enterobacteria phage mu. Organism_taxid: 10677
NMR struc: 1 models
Authors: G.M.Clore,R.T.Clubb,J.G.Omichinski,A.M.Gronenborn
Key ref:
R.T.Clubb et al. (1994). A novel class of winged helix-turn-helix protein: the DNA-binding domain of Mu transposase. Structure, 2, 1041-1048. PubMed id: 7881904 DOI: 10.1016/S0969-2126(94)00107-3
Date:
10-Oct-94     Release date:   14-Feb-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07636  (TRA_BPMU) -  DDE-recombinase A
Seq:
Struc:
 
Seq:
Struc:
663 a.a.
76 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     DNA binding     1 term  

 

 
DOI no: 10.1016/S0969-2126(94)00107-3 Structure 2:1041-1048 (1994)
PubMed id: 7881904  
 
 
A novel class of winged helix-turn-helix protein: the DNA-binding domain of Mu transposase.
R.T.Clubb, J.G.Omichinski, H.Savilahti, K.Mizuuchi, A.M.Gronenborn, G.M.Clore.
 
  ABSTRACT  
 
BACKGROUND: Mu transposase (MuA) is a multidomain protein encoded by the bacteriophage Mu genome. It is responsible for translocation of the Mu genome, which is the largest and most efficient transposon known. While the various domains of MuA have been delineated by means of biochemical methods, no data have been obtained to date relating to its tertiary structure. RESULTS: We have solved the three-dimensional solution structure of the DNA-binding domain (residues 1-76; MuA76) of MuA by multidimensional heteronuclear NMR spectroscopy. The structure consists of a three-membered alpha-helical bundle buttressed by a three-stranded antiparallel beta-sheet. Helices H1 and H2 and the seven-residue turn connecting them comprise a helix-turn-helix (HTH) motif. In addition, there is a long nine-residue flexible loop or wing connecting strands B2 and B3 of the sheet. NMR studies of MuA76 complexed with a consensus DNA site from the internal activation region of the Mu genome indicate that the wing and the second helix of the HTH motif are significantly perturbed upon DNA binding. CONCLUSIONS: While the general appearance of the DNA-binding domain of MuA76 is similar to that of other winged HTH proteins, the connectivity of the secondary structure elements is permuted. Hence, the fold of MuA76 represents a novel class of winged HTH DNA-binding domain.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Ribbon drawing of the average solution structure of MuA^76 . The helices of the helix–turn–helix (HTH) motif are shown in red, the flexible loop (W1) and turn of the HTH motif (T) in orange, and the remainder of the protein in blue. The ribbon diagram was made with the program RIBBONS [55]. Figure 3. Ribbon drawing of the average solution structure of MuA^76 . The helices of the helix–turn–helix (HTH) motif are shown in red, the flexible loop (W1) and turn of the HTH motif (T) in orange, and the remainder of the protein in blue. The ribbon diagram was made with the program RIBBONS [[3]55].
Figure 5.
Figure 5. Schematic (left) and ribbon (right) drawings illustrating the topological differences between the two known classes of α/β–type helix–turn–helix binding domains, typified by the catabolite gene activator protein (CAP) and the hepatocyte nuclear factor (HNF)–3/fork head protein, and MuA^76 . In the schematic topological diagrams the recognition helix of the HTH motif is hatched. H, B and W stand for helix, strand and wing, respectively. W1, in the case of CAP, is shown in parentheses as the wing is much shorter than in the other two proteins. The ribbon drawings were made with the program Molscript [56]. Figure 5. Schematic (left) and ribbon (right) drawings illustrating the topological differences between the two known classes of α/β–type helix–turn–helix binding domains, typified by the catabolite gene activator protein (CAP) and the hepatocyte nuclear factor (HNF)–3/fork head protein, and MuA^76 . In the schematic topological diagrams the recognition helix of the HTH motif is hatched. H, B and W stand for helix, strand and wing, respectively. W1, in the case of CAP, is shown in parentheses as the wing is much shorter than in the other two proteins. The ribbon drawings were made with the program Molscript [[3]56].
 
  The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 1041-1048) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20615441 I.V.Nesmelova, and P.B.Hackett (2010).
DDE transposases: Structural similarity and diversity.
  Adv Drug Deliv Rev, 62, 1187-1195.  
16472303 A.J.Molina-Henares, T.Krell, M.Eugenia Guazzaroni, A.Segura, and J.L.Ramos (2006).
Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors.
  FEMS Microbiol Rev, 30, 157-186.  
15774720 J.F.Yuan, D.R.Beniac, G.Chaconas, and F.P.Ottensmeyer (2005).
3D reconstruction of the Mu transposase and the Type 1 transpososome: a structural framework for Mu DNA transposition.
  Genes Dev, 19, 840-852.  
16079126 L.Elantak, M.Ansaldi, F.Guerlesquin, V.Méjean, and X.Morelli (2005).
Structural and genetic analyses reveal a key role in prophage excision for the TorI response regulator inhibitor.
  J Biol Chem, 280, 36802-36808.
PDB code: 1z4h
14978306 P.Gutiérrez, M.J.Osborne, N.Siddiqui, J.F.Trempe, C.Arrowsmith, and K.Gehring (2004).
Structure of the archaeal translation initiation factor aIF2 beta from Methanobacterium thermoautotrophicum: implications for translation initiation.
  Protein Sci, 13, 659-667.
PDB code: 1nee
15469518 Z.Nagy, M.Szabó, M.Chandler, and F.Olasz (2004).
Analysis of the N-terminal DNA binding domain of the IS30 transposase.
  Mol Microbiol, 54, 478-488.  
12496275 J.J.Rasimas, A.E.Pegg, and M.G.Fried (2003).
DNA-binding mechanism of O6-alkylguanine-DNA alkyltransferase. Effects of protein and DNA alkylation on complex stability.
  J Biol Chem, 278, 7973-7980.  
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.  
11877432 R.G.Zhang, Y.Kim, T.Skarina, S.Beasley, R.Laskowski, C.Arrowsmith, A.Edwards, A.Joachimiak, and A.Savchenko (2002).
Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.
  J Biol Chem, 277, 19183-19190.
PDB code: 1mkm
12049735 T.de Beer, J.Fang, M.Ortega, Q.Yang, L.Maes, C.Duffy, N.Berton, J.Sippy, M.Overduin, M.Feiss, and C.E.Catalano (2002).
Insights into specific DNA recognition during the assembly of a viral genome packaging machine.
  Mol Cell, 9, 981-991.
PDB code: 1j9i
11532151 R.C.Langdon, T.Burr, S.Pagan-Westphal, and A.Hochschild (2001).
A chimeric activator of transcription that uses two DNA-binding domains to make simultaneous contact with pairs of recognition sites.
  Mol Microbiol, 41, 885-896.  
10606635 J.E.Wibley, A.E.Pegg, and P.C.Moody (2000).
Crystal structure of the human O(6)-alkylguanine-DNA alkyltransferase.
  Nucleic Acids Res, 28, 393-401.
PDB code: 1qnt
11060014 L.H.Hung, G.Chaconas, and G.S.Shaw (2000).
The solution structure of the C-terminal domain of the Mu B transposition protein.
  EMBO J, 19, 5625-5634.
PDB code: 1f6v
10397799 S.Adinolfi, C.Bagni, M.A.Castiglione Morelli, F.Fraternali, G.Musco, and A.Pastore (1999).
Novel RNA-binding motif: the KH module.
  Biopolymers, 51, 153-164.  
10387082 U.Ilangovan, J.M.Wojciak, K.M.Connolly, and R.T.Clubb (1999).
NMR structure and functional studies of the Mu repressor DNA-binding domain.
  Biochemistry, 38, 8367-8376.
PDB code: 1qpm
9813045 E.Krementsova, M.J.Giffin, D.Pincus, and T.A.Baker (1998).
Mutational analysis of the Mu transposase. Contributions of two distinct regions of domain II to recombination.
  J Biol Chem, 273, 31358-31365.  
9730821 K.Goodtzova, S.Kanugula, S.Edara, and A.E.Pegg (1998).
Investigation of the role of tyrosine-114 in the activity of human O6-alkylguanine-DNA alkyltranferase.
  Biochemistry, 37, 12489-12495.  
9649447 S.Y.Namgoong, and R.M.Harshey (1998).
The same two monomers within a MuA tetramer provide the DDE domains for the strand cleavage and strand transfer steps of transposition.
  EMBO J, 17, 3775-3785.  
9237992 A.Herbert, J.Alfken, Y.G.Kim, I.S.Mian, K.Nishikura, and A.Rich (1997).
A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase.
  Proc Natl Acad Sci U S A, 94, 8421-8426.  
9016718 E.Martínez-Hackert, and A.M.Stock (1997).
The DNA-binding domain of OmpR: crystal structures of a winged helix transcription factor.
  Structure, 5, 109-124.
PDB code: 1opc
9083114 R.M.Xu, C.Koch, Y.Liu, J.R.Horton, D.Knapp, K.Nasmyth, and X.Cheng (1997).
Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis.
  Structure, 5, 349-358.
PDB code: 1bm8
9405381 S.Schumacher, R.T.Clubb, M.Cai, K.Mizuuchi, G.M.Clore, and A.M.Gronenborn (1997).
Solution structure of the Mu end DNA-binding ibeta subdomain of phage Mu transposase: modular DNA recognition by two tethered domains.
  EMBO J, 16, 7532-7541.
PDB codes: 2ezk 2ezl
8612276 G.Musco, G.Stier, C.Joseph, M.A.Castiglione Morelli, M.Nilges, T.J.Gibson, and A.Pastore (1996).
Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome.
  Cell, 85, 237-245.
PDB codes: 1vig 1vih
  8849877 J.L.Vogel, V.Geuskens, L.Desmet, N.P.Higgins, and A.Toussaint (1996).
C-terminal deletions can suppress temperature-sensitive mutations and change dominance in the phage Mu repressor.
  Genetics, 142, 661-672.  
  8598195 L.W.Donaldson, J.M.Petersen, B.J.Graves, and L.P.McIntosh (1996).
Solution structure of the ETS domain from murine Ets-1: a winged helix-turn-helix DNA binding motif.
  EMBO J, 15, 125-134.
PDB codes: 1etc 1etd
8577730 R.T.Clubb, M.Mizuuchi, J.R.Huth, J.G.Omichinski, H.Savilahti, K.Mizuuchi, G.M.Clore, and A.M.Gronenborn (1996).
The wing of the enhancer-binding domain of Mu phage transposase is flexible and is essential for efficient transposition.
  Proc Natl Acad Sci U S A, 93, 1146-1150.  
8982450 W.M.Huang (1996).
Bacterial diversity based on type II DNA topoisomerase genes.
  Annu Rev Genet, 30, 79.  
7552753 A.P.Eijkelenboom, R.A.Lutzke, R.Boelens, R.H.Plasterk, R.Kaptein, and K.Hård (1995).
The DNA-binding domain of HIV-1 integrase has an SH3-like fold.
  Nat Struct Biol, 2, 807-810.  
7479039 K.Kim, and R.M.Harshey (1995).
Mutational analysis of the att DNA-binding domain of phage Mu transposase.
  Nucleic Acids Res, 23, 3937-3943.  
8521467 M.Mizuuchi, T.A.Baker, and K.Mizuuchi (1995).
Assembly of phage Mu transpososomes: cooperative transitions assisted by protein and DNA scaffolds.
  Cell, 83, 375-385.  
8547306 P.I.Ulycznyj, K.A.Salmon, H.Douillard, and M.S.DuBow (1995).
Characterization of the Pseudomonas aeruginosa transposable bacteriophage D3112 A and B genes.
  Biochim Biophys Acta, 1264, 249-253.  
7628012 P.Rice, and K.Mizuuchi (1995).
Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration.
  Cell, 82, 209-220.
PDB codes: 1bcm 1bco
8590003 T.E.Strzelecka, G.M.Clore, and A.M.Gronenborn (1995).
The solution structure of the Mu Ner protein reveals a helix-turn-helix DNA recognition motif.
  Structure, 3, 1087-1095.
PDB codes: 1neq 1ner
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.