Protein Family Models

This is the central domain of phage integrases. This domain is known to mediate DNA binding and binds to the major groove adjacent to the site of DNA cleavage [1]. It consists of two pairs of antiparallel helices that pack together at nearly a right angle and form a four-helix bundle. Paper describing PDB structure 1p7d. [1]. 12887904. A conformational switch controls the DNA cleavage activity of lambda integrase. Aihara H, Kwon HJ, Nunes-Duby SE, Landy A, Ellenberger T;. Mol Cell. 2003;12:187-198. Paper describing PDB structure 1z19. [2]. 15973401. A structural basis for allosteric control of DNA recombination by lambda integrase. Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy A, Ellenberger T;. Nature. 2005;435:1059-1066. Paper describing PDB structure 2oxo. [3]. 18540053. Crystallization and structure determination of the core-binding domain of bacteriophage lambda integrase. Kamadurai HB, Jain R, Foster MP;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008;64:470-473. Paper describing PDB structure 5j0n. [4]. 27223329. Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction. Laxmikanthan G, Xu C, Brilot AF, Warren D, Steele L, Seah N, Tong W, Grigorieff N, Landy A, Van Duyne GD;. Elife. 2016; [Epub ahead of print] (from Pfam)

Date:

2024-10-16

The domain found by this HMM, previously named DUF4102, is found often phage intergrases and predicted to bind arm-type integrase binding sites.

Date:

2024-08-14

Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase (Swiss:P06956) are Arg-173, His-289, Arg-292 and Tyr-324. [1]. 9082984. Flexibility in DNA recombination: structure of the lambda integrase catalytic core. Kwon HJ, Tirumalai R, Landy A, Ellenberger T;. Science 1997;276:126-131. [2]. 9288963. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Guo F, Gopaul DN, van Duyne GD;. Nature 1997;389:40-46. (from Pfam)

Date:

2024-10-16

tyrosine-type recombinase/integrase is a tyrosine based site-specific recombinase (integrase) involved in cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct

Date:

2024-04-25