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PDBsum entry 1lyr

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protein dna_rna links
Lyase/DNA PDB id
1lyr
Jmol
Contents
Protein chain
279 a.a.
DNA/RNA
Theoretical model
PDB id:
1lyr
Name: Lyase/DNA
Title: Theoretical model of bovine ap lyase, bap1
Structure: DNA-(apurinic or apyrimidinic site) lyase. Chain: a. Synonym: ap lyase, bap1, ap endonuclease 1, apex nuclease, apen. 5'-d( Gp Cp Gp Tp Cp Cp (3Dr) p Cp Gp Ap Cp Gp Ap Cp G)-3'. Chain: x. Engineered: yes. 5'-d( Gp Tp Cp Gp Tp Cp Gp Gp Gp Gp Ap Cp Gp C)-
Source: Bos taurus. Bovine. Synthetic: yes. Synthetic: yes
Authors: R.Khurshid,A.Salim,A.Abbasi
Key ref: R.Khurshid et al. (2005). Three-dimensional structure prediction of bovine AP lyase, BAP1: prediction of interaction with DNA and alterations as a result of Arg176-->Ala, Asp282-->Ala, and His308-->Asn mutations. Biochem Biophys Res Commun, 326, 711-717. PubMed id: 15607727 DOI: 10.1016/j.bbrc.2004.11.103
Date:
08-Jun-02     Release date:   26-Jun-02    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23196  (APEX1_BOVIN) -  DNA-(apurinic or apyrimidinic site) lyase
Seq:
Struc:
318 a.a.
279 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.4.2.99.18  - DNA-(apurinic or apyrimidinic site) lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.

 

 
DOI no: 10.1016/j.bbrc.2004.11.103 Biochem Biophys Res Commun 326:711-717 (2005)
PubMed id: 15607727  
 
 
Three-dimensional structure prediction of bovine AP lyase, BAP1: prediction of interaction with DNA and alterations as a result of Arg176-->Ala, Asp282-->Ala, and His308-->Asn mutations.
R.Khurshid, A.Salim, A.Abbasi.
 
  ABSTRACT  
 
BAP1 is an apurinic/apyrimidinic lyase (AP lyase) that plays an important role in the repair of DNA damage. The present study deals with the prediction of the 3D structure of bovine AP lyase based on its sequence homology with human AP lyase. The predicted 3D model of bovine AP1 shows remarkable similarity with human endonuclease in the overall 3D fold. However, significant differences in the model and the X-ray structure were located at some of the important sites. We have analyzed the active center of the enzyme and other sites that are involved in DNA repair. A number of amino acids bind the bases located in the major/minor grooves of DNA. An insertion of Arg176 in the major groove and Met270 in the minor groove caps the DNA bound enzyme's active site, stabilizing the extra helical AP site conformation and effectively locking the protein onto the AP-DNA. Three BAP1 mutants were also modeled and analyzed as regards the changes in the structure. Substitution of Arg176-->Ala leads to the loss of DNA binding whereas mutation of Asp282-->Ala and His308-->Asn leads to a decrease in the enzymatic activity.