3p4h

Structures of archaeal members of the LigD 3'-phosphoesterase DNA repair enzyme superfamily

spinqualitylabelsall models 3p4h, resolution 1.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3p4h is a 1 chain structure with sequence from Candidatus Korarchaeum cryptofilum OPF8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.1Å Ligands: MN, PEG, PO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function B1L4V6_KORCO Publication Abstract from PubMed LigD 3'-phosphoesterase (PE) is a component of the bacterial NHEJ apparatus that performs 3'-end-healing reactions at DNA breaks. The tertiary structure, active site and substrate specificity of bacterial PE are unique vis-a-vis other end-healing enzymes. PE homologs are present in archaea, but their properties are uncharted. Here, we demonstrate the end-healing activities of two archaeal PEs-Candidatus Korarchaeum cryptofilum PE (CkoPE; 117 amino acids) and Methanosarcina barkeri PE (MbaPE; 151 amino acids)-and we report their atomic structures at 1.1 and 2.1 A, respectively. Archaeal PEs are minimized versions of bacterial PE, consisting of an eight-stranded beta barrel and a 3(10) helix. Their active sites are located in a crescent-shaped groove on the barrel's outer surface, wherein two histidines and an aspartate coordinate manganese in an octahedral complex that includes two waters and a phosphate anion. The phosphate is in turn coordinated by arginine and histidine side chains. The conservation of active site architecture in bacterial and archaeal PEs, and the concordant effects of active site mutations, underscore a common catalytic mechanism, entailing transition state stabilization by manganese and the phosphate-binding arginine and histidine. Our results fortify the proposal that PEs comprise a DNA repair superfamily distributed widely among taxa. Structures and activities of archaeal members of the LigD 3'-phosphoesterase DNA repair enzyme superfamily.,Smith P, Nair PA, Das U, Zhu H, Shuman S Nucleic Acids Res. 2011 Jan 5. PMID:21208981 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also DNA ligase 3D structures

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