PDBsum entry: 2gm4

Recombination, DNA

PDB-id: 2gm4

Asymmetric unit

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Protein chains

179 a.a. *

DNA/RNA

* Residue conservation analysis

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Biological unit, 60mer
- as defined in PDB file (see also PQS)

PDB id:

2gm4

Name:

Recombination, DNA

Title:

An activated, tetrameric gamma-delta resolvase: hin chimaera bound to cleaved DNA

Structure:

5'- d( Cp Ap Gp Tp Gp Tp Cp Cp Gp Ap Tp Ap Ap Tp Tp Tp Ap Tp Ap Ap A)-3'. Chain: x, z, j, i. Engineered: yes. 5'-d( Tp Tp Ap Tp Cp Gp Gp Ap Cp Ap Cp Tp G)-3'. Chain: y, k. Engineered: yes. Transposon gamma-delta resolvase.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: tnpr. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biological unit:

60mer (from PDB file)

UniProt:

Chains A, B: P03012 (TNR1_ECOLI)

Seq:

183 a.a.

Struc:

179 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

Resolution:

3.50Å

R-factor:

0.282

R-free:

0.323

Authors:

S.Kamtekar,R.S.Ho,W.Li,T.A.Steitz

Key ref:

S.Kamtekar et al. (2006). Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination.. Proc Natl Acad Sci U S A, 103, 10642-10647. [PubMed id: 16807292] [DOI: 10.1073/pnas.0604062103]

Date:

05-Apr-06

Release date:

27-Jun-06

Related entries:

1gdt
crystal structure of a site-specific recombinase, gamma-
delta resolvase complexed with a 34 bp cleavage site
1zr2
structure of a synaptic gamma-delta resolvase tetramer
covalently linked to two cleaved dnas
1zr4
structure of a synaptic gamma-delta resolvase tetramer
covalently linked to two cleaved dnas
2rsl
... plus others (see Header records)

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Key reference

DOI no: 10.1073/pnas.0604062103

Proc Natl Acad Sci U S A 103:10642-10647 (2006)

PubMed id: 16807292

Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination.

S.Kamtekar, R.S.Ho, M.J.Cocco, W.Li, S.V.Wenwieser, M.R.Boocock, N.D.Grindley, T.A.Steitz.

ABSTRACT

The structures of two mutants of the site-specific recombinase, gammadelta resolvase, that form activated tetramers have been determined. One, at 3.5-A resolution, forms a synaptic intermediate of resolvase that is covalently linked to two cleaved DNAs, whereas the other is of an unliganded structure determined at 2.1-A resolution. Comparisons of the four known tetrameric resolvase structures show that the subunits interact through the formation of a common core of four helices. The N-terminal halves of these helices superimpose well on each other, whereas the orientations of their C termini are more variable. The catalytic domains of resolvase in the unliganded structure are arranged asymmetrically, demonstrating that their positions can move substantially while preserving the four-helix core that forms the tetramer. These results suggest that the precleavage synaptic tetramer of gammadelta resolvase, whose structure is not known, may be formed by a similar four-helix core, but differ in the relative orientations of its catalytic and DNA-binding domains.

Selected figure(s)

Figure 1.
Fig. 1. Structural consequences of variable conformation within E helices. (a) The structure of the resolvase:Hin chimera (in color) superimposed by using C atoms 2–120 in all four chains on a tetramer with a different set of activating mutations (shown in white; PDB ID code 1ZR4). Differences between the structures are apparent at the C termini of the E helices and lead to different orientations for the DNA and DNA-binding domains. (b) Individual E helices (residues 102–137) superimposed by using their N-terminal C atoms (102–120) from dimeric resolvase (blue and cyan; PDB ID code 1GDT), the resolvase:Hin chimera (green and lime), and other tetrameric cleaved intermediate structures (yellow, red, magenta, and salmon, PDB ID code 1ZR4; gray and black, PDB ID code 1ZR2). The location of the C atom of residue 137 differs by up to 6 Å when only the tetrameric resolvases are considered and by 8 Å when the dimeric structure of wild-type resolvase bound to a site analog (PDB ID code 1GDT) is included as well. Figures in this paper were generated by using PYMOL (www.pymol.org).

Figure 3.
Fig. 3. Disulfide links can lock mutant resolvases into specific quaternary associations. Resolvase structures in ribbon form, with the E helix represented as a cylinder and DNA shown as a surface. The C positions of selected residues are shown as spheres. The DNA-bound dimer structure is taken from ref. 10. The resolvase mutant, M106C, can form disulfides readily in the context of a dimer but not when either cleaved-intermediate or activated apo tetramers are used as scaffolds. Conversely, of these three scaffolds, only the activated apo form appears appropriate for the formation of G96C-mediated disulfides. The cleaved complex scaffold appears compatible with the formation of four intramolecular T73C/S112C links, and the activated apo scaffold appears compatible with only two, consistent with the observation that the tertiary conformations of two of the monomers in the activated apo form resemble those of unactivated resolvase.

Figures were selected by the author.