PDBsum entry 3bvp

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protein Protein-protein interface(s) links
Recombination PDB id
Protein chains
136 a.a. *
Waters ×200
* Residue conservation analysis
PDB id:
Name: Recombination
Title: Crystal structure of the n-terminal catalytic domain of tp90 integrase
Structure: Tp901-1 integrase. Chain: a, b. Fragment: n-terminal catalytic domain. Synonym: int. Engineered: yes
Source: Lactococcus phage tp901-1. Gene: int. Expressed in: escherichia coli.
2.10Å     R-factor:   0.201     R-free:   0.263
Authors: P.Yuan,G.D.Van Duyne
Key ref:
P.Yuan et al. (2008). Tetrameric structure of a serine integrase catalytic domain. Structure, 16, 1275-1286. PubMed id: 18682229 DOI: 10.1016/j.str.2008.04.018
07-Jan-08     Release date:   12-Aug-08    
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Protein chains
Pfam   ArchSchema ?
Q38184  (Q38184_9CAUD) -  INT
485 a.a.
136 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA recombination   1 term 
  Biochemical function     recombinase activity     2 terms  


DOI no: 10.1016/j.str.2008.04.018 Structure 16:1275-1286 (2008)
PubMed id: 18682229  
Tetrameric structure of a serine integrase catalytic domain.
P.Yuan, K.Gupta, G.D.Van Duyne.
The serine integrases have recently emerged as powerful new chromosome engineering tools in various organisms and show promise for therapeutic use in human cells. The serine integrases are structurally and mechanistically unrelated to the bacteriophage lambda integrase but share a similar catalytic domain with the resolvase/invertase enzymes typified by the resolvase proteins from transposons Tn3 and gammadelta. Here we report the crystal structure and solution properties of the catalytic domain from bacteriophage TP901-1 integrase. The protein is a dimer in solution but crystallizes as a tetramer that is closely related in overall architecture to structures of activated gammadelta-resolvase mutants. The ability of the integrase tetramer to explain biochemical experiments performed in the resolvase and invertase systems suggests that the TP901 integrase tetramer represents a unique intermediate on the recombination pathway that is shared within the serine recombinase superfamily.
  Selected figure(s)  
Figure 3.
Figure 3. Comparison of TP901 and Activated γδ-Resolvase Catalytic Domain Tetramers
(A and B) Orthogonal views of the TP901 integrase tetramer. Subunits are labeled I–IV as discussed in the text and the catalytic serine residues (Ser12) are drawn as red spheres. (C and D) Orthogonal views of the γδ-resolvase tetramer, as seen in the crystal structure of an activated resolvase mutant covalently bound to DNA half-sites (Protein Data Bank code 1ZR4; Li et al., 2005). The tetramer orientations are based on a superposition of E helices with the TP901 tetramer in (A) and (B). Subunit rotation has been proposed to occur about the flat interface separating the top and bottom halves of the tetramer shown in (C), as indicated.
Figure 5.
Figure 5. Dimer Interfaces within the Integrase Tetramer
(A) The I–II dimer interface, composed primarily of interactions between helix E. A carboxyl-carboxylate pair formed by strictly conserved Glu133 is enlarged.
(B) The I–IV dimer interface, formed by interactions between the base of helix E, helix A, and β5. Each of these three regions is enlarged. The middle enlarged panel also illustrates the site of cysteine crosslinking in Hin recombinase S94C mutants (corresponding to TP901 integrase Ser111). Subunits are colored as in Figure 3.
  The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 1275-1286) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20415519 R.Liesner, W.Zhang, N.Noske, and A.Ehrhardt (2010).
Critical amino acid residues within the φC31 integrase DNA-binding domain affect recombination activities in mammalian cells.
  Hum Gene Ther, 21, 1104-1118.  
19002165 A.Keravala, S.Lee, B.Thyagarajan, E.C.Olivares, V.E.Gabrovsky, L.E.Woodard, and M.P.Calos (2009).
Mutational derivatives of PhiC31 integrase with increased efficiency and specificity.
  Mol Ther, 17, 112-120.  
19515935 A.R.McEwan, P.A.Rowley, and M.C.Smith (2009).
DNA binding and synapsis by the large C-terminal domain of phiC31 integrase.
  Nucleic Acids Res, 37, 4764-4773.  
19560425 G.Dhar, J.K.Heiss, and R.C.Johnson (2009).
Mechanical constraints on Hin subunit rotation imposed by the Fis/enhancer system and DNA supercoiling during site-specific recombination.
  Mol Cell, 34, 746-759.  
19515933 G.Dhar, M.M.McLean, J.K.Heiss, and R.C.Johnson (2009).
The Hin recombinase assembles a tetrameric protein swivel that exchanges DNA strands.
  Nucleic Acids Res, 37, 4743-4756.  
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