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PDBsum entry 4nrw

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protein dna_rna Protein-protein interface(s) links
Hydrolase, lyase/DNA PDB id
4nrw
Jmol
Contents
Protein chains
285 a.a.
DNA/RNA
Waters ×8
PDB id:
4nrw
Name: Hydrolase, lyase/DNA
Title: Mvnei1-g86d
Structure: Formamidopyrimidine-DNA glycosylase. Chain: a, b. Synonym: nei1 (mvnei1) DNA glycosylase, fapy-DNA glycosylas (apurinic or apyrimidinic site) lyase, ap lyase. Engineered: yes. Mutation: yes. 5'-d( Gp Tp Ap Gp Ap Cp Cp Tp Gp Gp Ap Cp G)-3'. Chain: c, e. Engineered: yes.
Source: Acanthamoeba polyphaga mimivirus. Apmv. Organism_taxid: 212035. Gene: endonuclease viii (nei) 1, mimi_l315. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes
Resolution:
2.85Å     R-factor:   0.265     R-free:   0.315
Authors: A.Prakash,S.Doublie
Key ref: A.Prakash et al. (2014). Genome and cancer single nucleotide polymorphisms of the human NEIL1 DNA glycosylase: activity, structure, and the effect of editing. DNA Repair (Amst), 14, 17-26. PubMed id: 24382305 DOI: 10.1016/j.dnarep.2013.12.003
Date:
27-Nov-13     Release date:   01-Jan-14    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5UQ00  (FPG_MIMIV) -  Probable formamidopyrimidine-DNA glycosylase
Seq:
Struc:
287 a.a.
285 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: E.C.3.2.2.23  - DNA-formamidopyrimidine glycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of DNA containing ring-opened N(7)-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimide.
   Enzyme class 2: 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.
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.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     11 terms  

 

 
DOI no: 10.1016/j.dnarep.2013.12.003 DNA Repair (Amst) 14:17-26 (2014)
PubMed id: 24382305  
 
 
Genome and cancer single nucleotide polymorphisms of the human NEIL1 DNA glycosylase: activity, structure, and the effect of editing.
A.Prakash, B.L.Carroll, J.B.Sweasy, S.S.Wallace, S.Doublié.
 
  ABSTRACT  
 
The repair of free-radical oxidative DNA damage is carried out by lesion-specific DNA glycosylases as the first step of the highly conserved base excision repair (BER) pathway. In humans, three orthologs of the prototypical endonuclease VIII (Nei), the Nei-like NEIL1-3 enzymes are involved in the repair of oxidized DNA lesions. In recent years, several genome and cancer single-nucleotide polymorphic variants of the NEIL1 glycosylase have been identified. In this study we characterized four variants of human NEIL1: S82C, G83D, P208S, and ΔE28, and tested their ability to excise pyrimidine-derived lesions such as thymine glycol (Tg), 5-hydroxyuracil (5-OHU), and dihydrouracil (DHU) and the purine-derived guanidinohydantoin (Gh), spiroiminodihydantoin 1 (Sp1), and methylated 2,6-diamino-4-hydroxy-5-formamidopyrimidine (MeFapyG). The P208S variant has near wild-type activity on all substrates tested. The S82C and ΔE28 variants exhibit decreased Tg excision compared to wild-type. G83D displays little to no activity with any of the substrates tested, with the exception of Gh and Sp1. Human NEIL1 is known to undergo editing whereby the lysine at position 242 is recoded into an arginine. The non-edited form of NEIL1 is more efficient at cleaving Tg than the R242 form, but the G83D variant does not cleave Tg regardless of the edited status of NEIL1. The corresponding G86D variant in Mimivirus Nei1 similarly lacks glycosylase activity. A structure of a G86D-DNA complex reveals a rearrangement in the β4/5 loop comprising Leu84, the highly-conserved void-filling residue, thereby providing a structural rationale for the decreased glycosylase activity of the glycine to aspartate variant.