3OWV

Structural insights into catalytic and substrate binding mechanisms of the strategic EndA nuclease from Streptococcus pneumoniae

Summary for 3OWV

• Entry DOI: 10.2210/pdb3owv/pdb
• Related: 1G8T 1OUP 1ZM8 3ISM
• Descriptor: DNA-entry nuclease, MAGNESIUM ION, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: sequence nonspecific endonuclease, hydrolase
• Biological source: Streptococcus pneumoniae
• Cellular location: Cell membrane; Single-pass membrane protein: P0A3S3
• Total number of polymer chains: 2
• Total formula weight: 53785.26

Authors

Moon, A.F.,Midon, M.,Meiss, G.,Pingoud, A.M.,London, R.E.,Pedersen, L.C. (deposition date: 2010-09-20, release date: 2010-12-22, Last modification date: 2024-04-03)

Primary citation

Moon, A.F.,Midon, M.,Meiss, G.,Pingoud, A.,London, R.E.,Pedersen, L.C.
Structural insights into catalytic and substrate binding mechanisms of the strategic EndA nuclease from Streptococcus pneumoniae.
Nucleic Acids Res., 39:2943-2953, 2011

PubMed Abstract: EndA is a sequence non-specific endonuclease that serves as a virulence factor during Streptococcus pneumoniae infection. Expression of EndA provides a strategy for evasion of the host's neutrophil extracellular traps, digesting the DNA scaffold structure and allowing further invasion by S. pneumoniae. To define mechanisms of catalysis and substrate binding, we solved the structure of EndA at 1.75 Å resolution. The EndA structure reveals a DRGH (Asp-Arg-Gly-His) motif-containing ββα-metal finger catalytic core augmented by an interesting 'finger-loop' interruption of the active site α-helix. Subsequently, we delineated DNA binding versus catalytic functionality using structure-based alanine substitution mutagenesis. Three mutants, H154A, Q186A and Q192A, exhibited decreased nuclease activity that appears to be independent of substrate binding. Glu205 was found to be crucial for catalysis, while residues Arg127/Lys128 and Arg209/Lys210 contribute to substrate binding. The results presented here provide the molecular foundation for development of specific antibiotic inhibitors for EndA.

PubMed: 21113026
DOI: 10.1093/nar/gkq1152

Experimental method

X-RAY DIFFRACTION (1.75 Å)