PDBsum entry 2ezh

DNA binding protein

PDB id: 2ezh

Contents

Protein chain

65 a.a. *

* Residue conservation analysis

PDB id:

2ezh

Name:

DNA binding protein

Title:

Solution nmr structure of the igamma subdomain of the mu end DNA binding domain of mu phage transposase, minimized average structure

Structure:

Transposase. Chain: a. Fragment: igamma subdomain, residues 174 - 247. Other_details: mua of phage mu transposase

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:

R.T.Clubb et al. (1997). Solution structure of the I gamma subdomain of the Mu end DNA-binding domain of phage Mu transposase. J Mol Biol, 273, 19-25. PubMed id: 9367742 DOI: 10.1006/jmbi.1997.1312

Date:

25-Jul-97 Release date: 03-Dec-97

Protein chain

P07636  (TNPA_BPMU) -  DDE-recombinase A from Escherichia phage Mu

Seq: 663 a.a.

Struc: 65 a.a.

Enzyme reactions

• Enzyme class 2: E.C.3.1.22.- - ?????
• Enzyme class 3: E.C.6.5.1.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1006/jmbi.1997.1312

J Mol Biol 273:19-25 (1997)

PubMed id: 9367742

Solution structure of the I gamma subdomain of the Mu end DNA-binding domain of phage Mu transposase.

R.T.Clubb, S.Schumacher, K.Mizuuchi, A.M.Gronenborn, G.M.Clore.

ABSTRACT

The MuA transposase of phase Mu is a large modular protein that plays a central role in transposition. We show that the Mu end DNA-binding domain, I beta gamma, which is responsible for binding the DNA attachment sites at each end of the Mu genome, comprises two subdomains, I beta and I gamma, that are structurally autonomous and do not interact with each other in the absence of DNA. The solution structure of the I gamma subdomain has been determined by multidimensional NMR spectroscopy. The structure of I gamma comprises a four helix bundle and, despite the absence of any significant sequence identity, the topology of the first three helices is very similar to that of the homeodomain family of helix-turn-helix DNA-binding proteins. The helix-turn-helix motif of I gamma, however, differs from that of the homeodomains in so far as the loop is longer and the second helix is shorter, reminiscent of that in the POU-specific domain.

Selected figure(s)

Figure 1.
Figure 1. a, A drawing of the domain organization of MuA transposase, and of the various fragments studied by NMR. b, Sequence of Ig (residues 174 to 247) with the location of the four helices determined by NMR indicated. MuA deletion variants were constructed using PCR methodology. Plasmid pMK609 (Mizuuchi & Mizuuchi, 1989), which contains DNA encoding the MuA transposase, was targeted for deletion. Appropri- ate restriction sites were engineered into the PCR pri- mers allowing selectively amplified DNAs to be ligated into the phage T7 RNA polymerase expression plasmid pET3c (Novagen). The expression plasmids were then transferred to E. coli strain BL21(DE3) for protein expression. Three deletion constructs of the MuA trans- posase were constructed and comprise residues 77 to 247 (Ibg), residues 77 to 174 (Ib), and residues 174 to 247 (Ig) of MuA transposase.

Figure 4.
Figure 4. Comparison of the Ig domain (a) with the Oct-1 POU homeodomain (b). The two structures can be super- imposed with a C a atomic rms difference of 2 Å for 41 residues (residues 179 to 194, 199 to 212 and 223 to 233 of Ig and residues 107 to 122, 126 to 139 and 147 to 157 of the Oct-1 POU homeodomain) comprising principally helices 1, 2 and 3. Helices 1, 2 and 3 of Ig comprise residues 182 to 192, 200 to 214 and 221 to 231, respectively, while in the recognition helix of the POU homedomain these three helices extend from residues 110 to 122, 128 to 137 and 142 to 160, respect- ively. The HTH motif is shown in yellow, and the other helices in red. The coordinates of the Oct-1 POU homeodomain are taken from Klemm et al. (1994). The Figure was generated with the program MOLMOL (Konradi et al., 1996).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 273, 19-25) copyright 1997.

Figures were selected by an automated process.