PDBsum entry 2q7u

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Hydrolase PDB id
Protein chains
268 a.a. *
Waters ×45
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the f plasmid trai relaxase domain with the scissile thymidine base and imidodiphosphate
Structure: Protein trai. Chain: a, b. Fragment: relaxase domain (unp residues 1-300). Synonym: DNA helicase i. Engineered: yes. Mutation: yes
Source: Escherichia coli. Strain: trai. Gene: trai. Expressed in: escherichia coli.
3.00Å     R-factor:   0.214     R-free:   0.312
Authors: S.A.Lujan,M.R.Redinbo
Key ref:
S.A.Lujan et al. (2007). Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase. Proc Natl Acad Sci U S A, 104, 12282-12287. PubMed id: 17630285 DOI: 10.1073/pnas.0702760104
07-Jun-07     Release date:   20-May-08    
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Protein chains
Pfam   ArchSchema ?
P14565  (TRAI1_ECOLI) -  Multifunctional conjugation protein TraI
1756 a.a.
268 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 2: E.C.  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
+ H(2)O
Bound ligand (Het Group name = TMP)
matches with 56.00% similarity
Bound ligand (Het Group name = PON)
matches with 66.00% similarity
   Enzyme class 3: E.C.  - Dna topoisomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
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.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site


DOI no: 10.1073/pnas.0702760104 Proc Natl Acad Sci U S A 104:12282-12287 (2007)
PubMed id: 17630285  
Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase.
S.A.Lujan, L.M.Guogas, H.Ragonese, S.W.Matson, M.R.Redinbo.
Conjugative transfer of plasmid DNA via close cell-cell junctions is the main route by which antibiotic resistance genes spread between bacterial strains. Relaxases are essential for conjugative transfer and act by cleaving DNA strands and forming covalent phosphotyrosine linkages. Based on data indicating that multityrosine relaxase enzymes can accommodate two phosphotyrosine intermediates within their divalent metal-containing active sites, we hypothesized that bisphosphonates would inhibit relaxase activity and conjugative DNA transfer. We identified bisphosphonates that are nanomolar inhibitors of the F plasmid conjugative relaxase in vitro. Furthermore, we used cell-based assays to demonstrate that these compounds are highly effective at preventing DNA transfer and at selectively killing cells harboring conjugative plasmids. Two potent inhibitors, clodronate and etidronate, are already clinically approved to treat bone loss. Thus, the inhibition of conjugative relaxases is a potentially novel antimicrobial approach, one that selectively targets bacteria capable of transferring antibiotic resistance and generating multidrug resistant strains.
  Selected figure(s)  
Figure 1.
F TraI N300 Y16F bound to the scissile thymidine and a two-path model of F-like bacterial conjugation. (A) N300 Y16F active site with a metal ion (blue sphere) chelated by three histidines and the −1 Thy 3′-hydroxyl. Y16F occludes a fifth octahedral coordination site. (B) Cleavage by the first tyrosine forms a covalent phosphotyrosine intermediate (red circle) on the T (red) strand. Transfer with CPR diverges from simple transfer when the 3′-hydroxyl left by initial cleavage becomes a substrate for replication (blue strand). The newly created oriT requires a second cleavage event and second phosphotyrosine (purple circle).
Figure 3.
Bisphosphonates examined for relaxase inhibition. Chemicals examined for inhibition of TraI activity and F conjugation and for toxicity versus E. coli strains. Boxed chemicals were potent in vitro TraI inhibitors. In cell testing showed that PNP and PBENP were most effective at decreasing F^+ population, CLODRO and ETIDRO were most effective at decreasing transconjugant population, and PCP and PCNCP were effective at both.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21109533 L.Dostál, S.Shao, and J.F.Schildbach (2011).
Tracking F plasmid TraI relaxase processing reactions provides insight into F plasmid transfer.
  Nucleic Acids Res, 39, 2658-2670.  
21439279 R.P.Nash, F.C.Niblock, and M.R.Redinbo (2011).
Tyrosine partners coordinate DNA nicking by the Salmonella typhimurium plasmid pCU1 relaxase enzyme.
  FEBS Lett, 585, 1216-1222.  
20061574 M.Lucas, B.González-Pérez, M.Cabezas, G.Moncalian, G.Rivas, and la Cruz (2010).
Relaxase DNA binding and cleavage are two distinguishable steps in conjugative DNA processing that involve different sequence elements of the nic site.
  J Biol Chem, 285, 8918-8926.  
20448025 R.P.Nash, S.Habibi, Y.Cheng, S.A.Lujan, and M.R.Redinbo (2010).
The mechanism and control of DNA transfer by the conjugative relaxase of resistance plasmid pCU1.
  Nucleic Acids Res, 38, 5929-5943.
PDB codes: 3l57 3l6t
20860457 T.Dandekar, and G.Dandekar (2010).
Pharmacogenomic strategies against microbial resistance: from bright to bleak to innovative.
  Pharmacogenomics, 11, 1193-1196.  
19203375 D.Pérez-Mendoza, and la Cruz (2009).
Escherichia coli genes affecting recipient ability in plasmid conjugation: are there any?
  BMC Genomics, 10, 71.  
19416011 G.Vedantam (2009).
Antimicrobial resistance in Bacteroides spp.: occurrence and dissemination.
  Future Microbiol, 4, 413-423.  
19527679 S.Xia, and J.D.Robertus (2009).
Effect of divalent ions on the minimal relaxase domain of MobA.
  Arch Biochem Biophys, 488, 42-47.  
19818715 V.Petrova, S.Chitteni-Pattu, J.C.Drees, R.B.Inman, and M.M.Cox (2009).
An SOS inhibitor that binds to free RecA protein: the PsiB protein.
  Mol Cell, 36, 121-130.  
18625335 J.J.Williams, and P.J.Hergenrother (2008).
Exposing plasmids as the Achilles' heel of drug-resistant bacteria.
  Curr Opin Chem Biol, 12, 389-399.  
18280814 J.Zaneveld, P.J.Turnbaugh, C.Lozupone, R.E.Ley, M.Hamady, J.I.Gordon, and R.Knight (2008).
Host-bacterial coevolution and the search for new drug targets.
  Curr Opin Chem Biol, 12, 109-114.  
18378719 K.Miller, A.J.O'Neill, M.H.Wilcox, E.Ingham, and I.Chopra (2008).
Delayed development of linezolid resistance in Staphylococcus aureus following exposure to low levels of antimicrobial agents.
  Antimicrob Agents Chemother, 52, 1940-1944.  
18366330 R.G.Potts, S.A.Lujan, and M.R.Redinbo (2008).
Winning the asymmetric war: new strategies for combating antibacterial resistance.
  Future Microbiol, 3, 119-123.  
18778732 R.Scharbaai-Vázquez, A.L.González-Caraballo, and L.J.Torres-Bauzá (2008).
Four different integrative recombination events involved in the mobilization of the gonococcal 5.2 kb beta-lactamase plasmid pSJ5.2 in Escherichia coli.
  Plasmid, 60, 200-211.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.