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PDBsum entry 4iem

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase, lyase/DNA PDB id
4iem
Jmol
Contents
Protein chain
278 a.a.
DNA/RNA
Metals
_NA ×9
_MG ×7
Waters ×272
PDB id:
4iem
Name: Hydrolase, lyase/DNA
Title: Human apurinic/apyrimidinic endonuclease (ape1) with product mg2+
Structure: DNA-(apurinic or apyrimidinic site) lyase. Chain: a, b, c, d. Synonym: apex nuclease, apen, apurinic-apyrimidinic endonuc ap endonuclease 1, ape-1, ref-1, redox factor-1, DNA-(apuri apyrimidinic site) lyase, mitochondrial. Engineered: yes. DNA (5'-d( Gp Cp Tp Ap C)-3'). Chain: e, h, k, n. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ape, ape1, apex, apex1, apx, hap1, ref1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic DNA. Organism_taxid: 32630.
Resolution:
2.39Å     R-factor:   0.210     R-free:   0.246
Authors: S.E.Tsutakawa,C.D.Mol,A.S.Arvai,J.A.Tainer
Key ref: S.E.Tsutakawa et al. (2013). Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. J Biol Chem, 288, 8445-8455. PubMed id: 23355472 DOI: 10.1074/jbc.M112.422774
Date:
13-Dec-12     Release date:   23-Jan-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P27695  (APEX1_HUMAN) -  DNA-(apurinic or apyrimidinic site) lyase
Seq:
Struc:
318 a.a.
278 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 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.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   12 terms 
  Biological process     cellular response to cAMP   35 terms 
  Biochemical function     protein binding     27 terms  

 

 
DOI no: 10.1074/jbc.M112.422774 J Biol Chem 288:8445-8455 (2013)
PubMed id: 23355472  
 
 
Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes.
S.E.Tsutakawa, D.S.Shin, C.D.Mol, T.Izumi, A.S.Arvai, A.K.Mantha, B.Szczesny, I.N.Ivanov, D.J.Hosfield, B.Maiti, M.E.Pique, K.A.Frankel, K.Hitomi, R.P.Cunningham, S.Mitra, J.A.Tainer.
 
  ABSTRACT  
 
No abstract given.