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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 39 3310-20 (2011)
Cited: 10 times
EuropePMC logo PMID: 21208981

Abstract

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-à-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 Å, respectively. Archaeal PEs are minimized versions of bacterial PE, consisting of an eight-stranded β 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.

Articles - 3p43 mentioned but not cited (2)

  1. An integrated linkage, chromosome, and genome map for the yellow fever mosquito Aedes aegypti. Timoshevskiy VA, Severson DW, Debruyn BS, Black WC, Sharakhov IV, Sharakhova MV. PLoS Negl Trop Dis 7 e2052 (2013)
  2. 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 39 3310-3320 (2011)


Articles citing this publication (8)

  1. Ribonucleolytic resection is required for repair of strand displaced nonhomologous end-joining intermediates. Bartlett EJ, Brissett NC, Doherty AJ. Proc Natl Acad Sci U S A 110 E1984-91 (2013)
  2. Rewriting the rules for end joining via enzymatic splicing of DNA 3'-PO4 and 5'-OH ends. Das U, Chakravarty AK, Remus BS, Shuman S. Proc Natl Acad Sci U S A 110 20437-20442 (2013)
  3. Characterization of Mycobacterium smegmatis PolD2 and PolD1 as RNA/DNA polymerases homologous to the POL domain of bacterial DNA ligase D. Zhu H, Bhattarai H, Yan HG, Shuman S, Glickman MS. Biochemistry 51 10147-10158 (2012)
  4. Molecular basis for DNA strand displacement by NHEJ repair polymerases. Bartlett EJ, Brissett NC, Plocinski P, Carlberg T, Doherty AJ. Nucleic Acids Res 44 2173-2186 (2016)
  5. Template-dependent polymerization across discontinuous templates by the heterodimeric primase from the hyperthermophilic archaeon Sulfolobus solfataricus. Hu J, Guo L, Wu K, Liu B, Lang S, Huang L. Nucleic Acids Res 40 3470-3483 (2012)
  6. Solution structure and DNA-binding properties of the phosphoesterase domain of DNA ligase D. Natarajan A, Dutta K, Temel DB, Nair PA, Shuman S, Ghose R. Nucleic Acids Res 40 2076-2088 (2012)
  7. Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea. Pergolizzi G, Wagner GK, Bowater RP. Biosci Rep 36 00391 (2016)
  8. Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family. Das U, Smith P, Shuman S. Nucleic Acids Res 40 828-836 (2012)


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