1QUM

CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV IN COMPLEX WITH DAMAGED DNA

Summary for 1QUM

• Entry DOI: 10.2210/pdb1qum/pdb
• Related: 1QTW
• Descriptor: 5'-D(*CP*GP*TP*CP*C)-3', 5'-D(*(3DR)P*CP*GP*AP*CP*GP*A)-3', 5'-D(*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*G)-3', ... (6 entities in total)
• Functional Keywords: enzyme:dna complex, trinuclear zn cluster, dna repair enzyme, tim barrel, hydrolase-dna complex, hydrolase/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 39506.84

Authors

Hosfield, D.J.,Guan, Y.,Haas, B.J.,Cunningham, R.P.,Tainer, J.A. (deposition date: 1999-07-01, release date: 1999-08-31, Last modification date: 2024-02-14)

Primary citation

Hosfield, D.J.,Guan, Y.,Haas, B.J.,Cunningham, R.P.,Tainer, J.A.
Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis.
Cell(Cambridge,Mass.), 98:397-408, 1999

PubMed Abstract: Endonuclease IV is the archetype for a conserved apurinic/apyrimidinic (AP) endonuclease family that primes DNA repair synthesis by cleaving the DNA backbone 5' of AP sites. The crystal structures of Endonuclease IV and its AP-DNA complex at 1.02 and 1.55 A resolution reveal how an alpha8beta8 TIM barrel fold can bind dsDNA. Enzyme loops intercalate side chains at the abasic site, compress the DNA backbone, bend the DNA approximately 90 degrees, and promote double-nucleotide flipping to sequester the extrahelical AP site in an enzyme pocket that excludes undamaged nucleotides. These structures suggest three Zn2+ ions directly participate in phosphodiester bond cleavage and prompt hypotheses that double-nucleotide flipping and sharp bending by AP endonucleases provide exquisite damage specificity while aiding subsequent base excision repair pathway progression.

PubMed: 10458614
DOI: 10.1016/S0092-8674(00)81968-6

Experimental method

X-RAY DIFFRACTION (1.55 Å)