PDBsum entry 2ezk

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protein links
DNA-binding protein PDB id
Protein chain
93 a.a. *
* Residue conservation analysis
PDB id:
Name: DNA-binding protein
Title: Solution nmr structure of the ibeta subdomain of the mu end DNA binding domain of phage mu transposase, regularized mean structure
Structure: Transposase. Chain: a. Fragment: ibeta subdomain, residues 77 - 174
Source: Enterobacteria phage mu. Organism_taxid: 10677
NMR struc: 1 models
Authors: G.M.Clore,R.T.Clubb,S.Schumaker,A.M.Gronenborn
Key ref:
S.Schumacher et al. (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. PubMed id: 9405381 DOI: 10.1093/emboj/16.24.7532
04-Oct-97     Release date:   14-Jan-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P07636  (TRA_BPMU) -  DDE-recombinase A
663 a.a.
93 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: 10.1093/emboj/16.24.7532 EMBO J 16:7532-7541 (1997)
PubMed id: 9405381  
Solution structure of the Mu end DNA-binding ibeta subdomain of phage Mu transposase: modular DNA recognition by two tethered domains.
S.Schumacher, R.T.Clubb, M.Cai, K.Mizuuchi, G.M.Clore, A.M.Gronenborn.
The phage Mu transposase (MuA) binds to the ends of the Mu genome during the assembly of higher order nucleoprotein complexes. We investigate the structure and function of the MuA end-binding domain (Ibetagamma). The three-dimensional solution structure of the Ibeta subdomain (residues 77-174) has been determined using multidimensional NMR spectroscopy. It comprises five alpha-helices, including a helix-turn-helix (HTH) DNA-binding motif formed by helices 3 and 4, and can be subdivided into two interacting structural elements. The structure has an elongated disc-like appearance from which protrudes the recognition helix of the HTH motif. The topology of helices 2-4 is very similar to that of helices 1-3 of the previously determined solution structure of the MuA Igamma subdomain and to that of the homeodomain family of HTH DNA-binding proteins. We show that each of the two subdomains binds to one half of the 22 bp recognition sequence, Ibeta to the more conserved Mu end distal half (beta subsite) and Igamma to the Mu end proximal half (gamma subsite) of the consensus Mu end-binding site. The complete Ibetagamma domain binds the recognition sequence with a 100- to 1000-fold higher affinity than the two subdomains independently, indicating a cooperative effect. Our results show that the Mu end DNA-binding domain of MuA has a modular organization, with each module acting on a specific part of the 22 bp binding site. Based on the present binding data and the structures of the Ibeta and Igamma subdomains, a model for the interaction of the complete Ibetagamma domain with DNA is proposed.
  Selected figure(s)  
Figure 1.
Figure 1 (A) Schematic diagram of the domain structure of MuA transposase. Domains identified by partial proteolysis (Nagayama et al., 1987) are labeled I -III and marked with residue numbers at the beginning and end of each domain. The constructs used in this study comprising subdomains I (residues 77 -174) or I (residues 174 -247) are shown below as bars. (B) Sequence of I (residues 77 -174), with the location of the five helices determined by NMR indicated.
Figure 4.
Figure 4 (A and B) Two views of a ribbon diagram representation of the restrained regularized mean structure of MuA I (residues 77 -168). Helix 4 (marked in green) is the recognition helix of the HTH DNA-binding motif. (C) Comparison of the MuA I (blue) and I (yellow) subdomains. Helices 2 -4 of I have been superimposed on helices 1 -3 of I with a C atomic r.m.s. difference of 1.9 for 37 residues. The figure was generated using the program MOLMOL (Konradi et al., 1996).
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1997, 16, 7532-7541) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23135398 S.P.Montaño, Y.Z.Pigli, and P.A.Rice (2012).
The Mu transpososome structure sheds light on DDE recombinase evolution.
  Nature, 491, 413-417.
PDB code: 4fcy
20615441 I.V.Nesmelova, and P.B.Hackett (2010).
DDE transposases: Structural similarity and diversity.
  Adv Drug Deliv Rev, 62, 1187-1195.  
17098894 M.Han, M.Yagura, and T.Itoh (2007).
Specific interaction between the initiator protein (Rep) and origin of plasmid ColE2-P9.
  J Bacteriol, 189, 1061-1071.  
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.  
15103153 J.M.Richardson, L.Zhang, S.Marcos, D.J.Finnegan, M.M.Harding, P.Taylor, and M.D.Walkinshaw (2004).
Expression, purification and preliminary crystallographic studies of a single-point mutant of Mos1 mariner transposase.
  Acta Crystallogr D Biol Crystallogr, 60, 962-964.  
14981152 P.Rousseau, E.Gueguen, G.Duval-Valentin, and M.Chandler (2004).
The helix-turn-helix motif of bacterial insertion sequence IS911 transposase is required for DNA binding.
  Nucleic Acids Res, 32, 1335-1344.  
15225314 S.Ohta, E.Yoshimura, and E.Ohtsubo (2004).
Involvement of two domains with helix-turn-helix and zinc finger motifs in the binding of IS1 transposase to terminal inverted repeats.
  Mol Microbiol, 53, 193-202.  
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.  
14661976 I.Goldhaber-Gordon, M.H.Early, and T.A.Baker (2003).
MuA transposase separates DNA sequence recognition from catalysis.
  Biochemistry, 42, 14633-14642.  
12535534 K.Yanagihara, and K.Mizuuchi (2003).
Progressive structural transitions within Mu transpositional complexes.
  Mol Cell, 11, 215-224.  
12169640 B.J.Stewart, S.J.Wardle, and D.B.Haniford (2002).
IHF-independent assembly of the Tn10 strand transfer transpososome: implications for inhibition of disintegration.
  EMBO J, 21, 4380-4390.  
12145217 C.Loot, C.Turlan, P.Rousseau, B.Ton-Hoang, and M.Chandler (2002).
A target specificity switch in IS911 transposition: the role of the OrfA protein.
  EMBO J, 21, 4172-4182.  
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.  
10884228 D.R.Davies, I.Y.Goryshin, W.S.Reznikoff, and I.Rayment (2000).
Three-dimensional structure of the Tn5 synaptic complex transposition intermediate.
  Science, 289, 77-85.
PDB codes: 1f3i 1muh
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
10545119 J.Iwahara, and R.T.Clubb (1999).
Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID).
  EMBO J, 18, 6084-6094.
PDB code: 1c20
9867814 L.A.Mahnke Braam, I.Y.Goryshin, and W.S.Reznikoff (1999).
A mechanism for Tn5 inhibition. carboxyl-terminal dimerization.
  J Biol Chem, 274, 86-92.  
10547692 L.Haren, B.Ton-Hoang, and M.Chandler (1999).
Integrating DNA: transposases and retroviral integrases.
  Annu Rev Microbiol, 53, 245-281.  
10541558 T.L.Williams, E.L.Jackson, A.Carritte, and T.A.Baker (1999).
Organization and dynamics of the Mu transpososome: recombination by communication between two active sites.
  Genes Dev, 13, 2725-2737.  
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.  
9783751 M.Cai, Y.Huang, R.Zheng, S.Q.Wei, R.Ghirlando, M.S.Lee, R.Craigie, A.M.Gronenborn, and G.M.Clore (1998).
Solution structure of the cellular factor BAF responsible for protecting retroviral DNA from autointegration.
  Nat Struct Biol, 5, 903-909.
PDB codes: 2ezx 2ezy 2ezz
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.  
9671813 S.Y.Namgoong, S.Sankaralingam, and R.M.Harshey (1998).
Altering the DNA-binding specificity of Mu transposase in vitro.
  Nucleic Acids Res, 26, 3521-3527.  
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.