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Catalytic Site Atlas

CSA LITERATURE entry for 1qum

E.C. namedeoxyribonuclease IV (phage-T4-induced)
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1qumThere are 84 Homologs
CSA Entries With UniProtID P0A6C1
CSA Entries With EC Number
PDBe Entry 1qum
PDBSum Entry 1qum
MACiE Entry M0011

Literature Report

IntroductionThe genetic integrity of cells depends on the concerted action of repair enzymes that recognise and excise damaged bases and mutagenic lesions from DNA. The primary defence against these genotoxic insults is the DNA base excision repair (BER) pathway. The first step of BER is initiated by many distinct DNA glycosylases that each recognise a specific class of damaged DNA nucleotide and cleave the N-C1' glycosidic bond, linking the aberrant base to the deoxyribose sugar. These damage-specific glycosyllases generate as a common product apurinic/apyrimidinic (AP or abasic) sites, which are inherently toxic and mutagenic and thus must be rapidly processed and removed. In the subsequent damage-general steps of single nucleotide BER, an AP endonuclease cleaves the DNA backbone at AP sites, providing a product that is further processed by a DNA deoxyribosephosphodiesterase, a DNA polymerase, and a DNA ligase [1]. Endo IV is an ~30kDa Zn2+ -dependent endonuclease that, unlike the Mg2+ -dependent AP endonuclease III and APE-1, resists inactivation by EDTA. The purified enzyme specifically cleaves the DNA backbone at AP sites and also removes 3'-DNA-blocking groups such as 3' phosphate, 3' phosphoglycolates, and 3' alpha,beta-unsaturated aldehydes that arise from oxidative base damage and the activity of combined glycosylase/lyase enzymes [1].
MechansimHydrolysis proceeds through a pentacoordinate transition state where the unesterified phosphate oxygen that bridges Zn2 and Zn3 remains bound to its cognate metal ions. Initial binding of Endo IV to an extrahelical AP site is constrained by the intact target P-O3' covalent bond, and in the pretransition state, the bridging hydroxide between Zn1 and Zn2 would be positioned ideally for an in-line attack on the phosphate. Glu-261, which is also a Zn2 ligand, may assist in orienting and activating the attacking nucleophile. Charge neutralisation of the phosphate group by interaction with the three Zn2+ ions likely renders the phosphorus atom susceptible to nucleophilic substitution, and the pentacoordinate transition state resulting from attack by the bridging hydroxide is stabilised by all the three metal ions. As this transition state collapses to the reaction products, the stereochemical configuration of the phosphate is inverted and the developing negative charge at O3' stabilised by interactions with Zn3 [1].

Catalytic Sites for 1qum

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription

Literature References

Hosfield DJ
Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis.
Cell 1999 98 397-408
PubMed: 10458614