6zpb | pdb_00006zpb

Cyanophage S-2L HD phosphohydrolase (DatZ) bound to dA and two catalytic Co2+ ions

spinqualitylabelsall models 6zpb, resolution 1.72Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6zpb is a 1 chain structure with sequence from Cyanobacteria phage s-2l. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: 3D1, CO Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Bacteriophages have long been known to use modified bases in their DNA to prevent cleavage by the host's restriction endonucleases. Among them, cyanophage S-2L is unique because its genome has all its adenines (A) systematically replaced by 2-aminoadenines (Z). Here, we identify a member of the PrimPol family as the sole possible polymerase of S-2L and we find it can incorporate both A and Z in front of a T. Its crystal structure at 1.5 A resolution confirms that there is no structural element in the active site that could lead to the rejection of A in front of T. To resolve this contradiction, we show that a nearby gene is a triphosphohydolase specific of dATP (DatZ), that leaves intact all other dNTPs, including dZTP. This explains the absence of A in S-2L genome. Crystal structures of DatZ with various ligands, including one at sub-angstrom resolution, allow to describe its mechanism as a typical two-metal-ion mechanism and to set the stage for its engineering. How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA.,Czernecki D, Legrand P, Tekpinar M, Rosario S, Kaminski PA, Delarue M Nat Commun. 2021 Apr 23;12(1):2420. doi: 10.1038/s41467-021-22626-x. PMID:33893297 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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