Brand  (β version)

PDB ID: 5WN5

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Ligands
Code Name Style Show Link
MN Manganese (II) ion PoSSuM
EDO 1,2-ethanediol PoSSuM
Non-standard Residues
Code Name Show
C7R 2'-deoxy-5'-O-thiophosphonocytidine
Glycosylation
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Modification
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Structure summary

Code : 5WN5   PDBj   RCSB PDB   PDBe
Header : HYDROLASE, LYASE/DNA
Title : APE1 exonuclease substrate complex with a C/T mismatch and Mn2+
Release Data : 2018-02-28
Compound :
mol_id molecule chains
1 DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') C
mol_id molecule chains
2 DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DV3))-3') D
mol_id molecule chains
3 DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') E
mol_id molecule chains synonym
4 DNA-(apurinic or apyrimidinic site) lyase A,B APEX1, APEX nuclease,APEN,Apurinic-apyrimidinic endonuclease 1, APE-1, REF-1, Redox factor-1
ec: 3.1.-.-, 4.2.99.18
Source :
mol_id organism_scientific
1 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
2 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
3 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific organism_common expression_system
4 Homo sapiens  (taxid:9606) Human Escherichia coli BL21(DE3)  (taxid:469008)
gene: APEX1, APE, APE1, APEX, APX, HAP1, REF1
Authors : Freudenthal, B.D., Whitaker, A.M.
Keywords : HYDROLASE, LYASE-DNA complex
Exp. method : X-RAY DIFFRACTION ( 2.20 Å )
Citation :

Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.

Whitaker, A.M.,Flynn, T.S.,Freudenthal, B.D.
(2018)  Nat Commun  9 : 399 - 399

PubMed: 29374164
DOI: 10.1038/s41467-017-02175-y

Reaction

Chain : A, B
UniProt : P27695 (APEX1_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
a deoxyribonucleotide-2'-deoxyribose-5'-monophosphate-DNA + H2O = a 5'-end 2'-deoxyribose-5'-monophosphate-DNA + a 3'-end 2'- deoxyribonucleotide-DNA + H(+) - PubMed:15380100, PubMed:24079850, PubMed:8995436
left-to-right PubMed:19934257
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates. 3.1.11.2 PubMed:11832948
-
a 3'-end 2'-deoxyribonucleotide-3'-phosphoglycolate-DNA + H2O = 2-phosphoglycolate + a 3'-end 2'-deoxyribonucleotide-DNA + H(+) - PubMed:7516064
left-to-right
a 3'-end 2'-deoxyribonucleotide-8-oxoguanine-DNA + H2O = 8- oxo-dGMP + a 3'-end 2'-deoxyribonucleotide-DNA + H(+) - PubMed:15831793
left-to-right
Cofactor: Evidence: Note:
Mn(2+) ECO:0000269 | PubMed:11286553
ECO:0000269 | PubMed:19123919
ECO:0000269 | PubMed:21762700
ECO:0000269 | PubMed:24079850
ECO:0000269 | PubMed:9804799
ECO:0000269 | PubMed:11286553
ECO:0000269 | PubMed:19123919
ECO:0000269 | PubMed:21762700
ECO:0000269 | PubMed:24079850
ECO:0000269 | PubMed:9804799
Probably binds two magnesium or manganese ions per subunit.