4js4

Crystal structure of E. coli Exonuclease I in complex with a dA16 oligonucleotideCrystal structure of E. coli Exonuclease I in complex with a dA16 oligonucleotide

Structural highlights 4js4 is a 4 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3.1Å Ligands: Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function EX1_ECOLI Also functions as a DNA deoxyribophosphodiesterase that releases deoxyribose-phosphate moieties following the cleavage DNA at an apurinic/apyrimidinic (AP) site by either an AP endonuclease AP lyase. Publication Abstract from PubMed Escherichia coli Exonuclease I (ExoI) digests single-stranded DNA (ssDNA) in the 3'-5' direction in a highly processive manner. The crystal structure of ExoI, determined previously in the absence of DNA, revealed a C-shaped molecule with three domains that form a central positively charged groove. The active site is at the bottom of the groove, while an extended loop, proposed to encircle the DNA, crosses over the groove. Here, we present crystal structures of ExoI in complex with four different ssDNA substrates. The structures all have the ssDNA bound in essentially the predicted manner, with the 3'-end in the active site and the downstream end under the crossover loop. The central nucleotides of the DNA form a prominent bulge that contacts the SH3-like domain, while the nucleotides at the downstream end of the DNA form extensive interactions with an 'anchor' site. Seven of the complexes are similar to one another, but one has the ssDNA bound in a distinct conformation. The highest-resolution structure, determined at 1.95 A, reveals an Mg2+ ion bound to the scissile phosphate in a position corresponding to MgB in related two-metal nucleases. The structures provide new insights into the mechanism of processive digestion that will be discussed. Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion.,Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA, Bell CE Nucleic Acids Res. 2013 Apr 22. PMID:23609540 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Exonuclease 3D structures

spinqualitylabelsall models 4js4, resolution 3.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image