PDBsum entry 1ae9

DNA recombination

PDB id: 1ae9

Contents

Protein chains

172 a.a. *

Waters ×195

* Residue conservation analysis

PDB id:

1ae9

Name:

DNA recombination

Title:

Structure of the lambda integrase catalytic core

Structure:

Lambda integrase. Chain: a, b. Fragment: catalytic domain. Engineered: yes. Mutation: yes

Source:

Enterobacteria phage lambda. Organism_taxid: 10710. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Hexamer (from PQS)

Resolution:

1.90Å R-factor: 0.199 R-free: 0.232

Authors:

H.J.Kwon,R.Tirumalai,A.Landy,T.Ellenberger

Key ref:

H.J.Kwon et al. (1997). Flexibility in DNA recombination: structure of the lambda integrase catalytic core. Science, 276, 126-131. PubMed id: 9082984 DOI: 10.1126/science.276.5309.126

Date:

06-Mar-97 Release date: 19-Nov-97

Protein chains

P03700  (VINT_LAMBD) -  Integrase from Escherichia phage lambda

Seq: 356 a.a.

Struc: 172 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.- - ?????
• Enzyme class 2: E.C.3.1.-.-

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: 10.1126/science.276.5309.126

Science 276:126-131 (1997)

PubMed id: 9082984

Flexibility in DNA recombination: structure of the lambda integrase catalytic core.

H.J.Kwon, R.Tirumalai, A.Landy, T.Ellenberger.

ABSTRACT

Lambda integrase is archetypic of site-specific recombinases that catalyze intermolecular DNA rearrangements without energetic input. DNA cleavage, strand exchange, and religation steps are linked by a covalent phosphotyrosine intermediate in which Tyr342 is attached to the 3'-phosphate of the DNA cut site. The 1.9 angstrom crystal structure of the integrase catalytic domain reveals a protein fold that is conserved in organisms ranging from archaebacteria to yeast and that suggests a model for interaction with target DNA. The attacking Tyr342 nucleophile is located on a flexible loop about 20 angstroms from a basic groove that contains all the other catalytically essential residues. This bipartite active site can account for several apparently paradoxical features of integrase family recombinases, including the capacity for both cis and trans cleavage of DNA.

Selected figure(s)

Figure 3.
Fig. 3. Theoretical model of the Int catalytic core bound to a B-form half-att site. A full att site contains a pair of inverted^ core-type Int binding sites. An Int protomer at each site is responsible^ for cleaving one DNA strand via formation of a covalent 3 phospho-tyrosine^ linkage and a free 5 -hydroxyl. The two nicks are staggered by seven base pairs with a 5 overhang. For clarity, only one subunit of the Int c170 dimer that was modeled on DNA is shown. The catalytic^ Arg-His-Arg triad (cyan) of Int is docked over one of the scissile^ phosphates (shown as breaks in the DNA ribbon). The C trace of^ Int c170 (blue) is displayed with the active site loop containing the Tyr342 nucleophile shown in two alternative conformations. The orientation corresponding to cis cleavage (orange tyrosine) is a theoretical model, whereas that corresponding to trans cleavage (red tyrosine) is present in one of two Int protomers in the crystal structure. The segment of the loop that is disordered in both protomers (Lys334 to Gln341) is modeled in pink.

The above figure is reprinted by permission from the AAAs: Science (1997, 276, 126-131) copyright 1997.