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Catalytic Site Atlas

CSA LITERATURE entry for 1a2t

E.C. namemicrococcal nuclease
SpeciesStaphylococcus aureus (Bacteria)
E.C. Number (IntEnz) 3.1.31.1
CSA Homologues of 1a2tThere are 130 Homologs
CSA Entries With UniProtID P00644
CSA Entries With EC Number 3.1.31.1
PDBe Entry 1a2t
PDBSum Entry 1a2t
MACiE Entry M0165

Literature Report

IntroductionStaphyloccal nuclease is a Ca2+ activated phosphodiesterase which catalyses the hydrolysis of both DND and RNA at the 5' position of the phophodiester bond to yield a 3'-mononucleotides and polynucleotides.
MechansimThe hydrolysis proceeds via direct nucleophilic attack on phosphate with formation of a five-coordinate, trigonal bipyramidal transition state or meta-stable intermediate followed by breakdown to from the product.
The attacking nucleophile is a water molecule coordinated to the Ca2+ ion. Ca2+ facilitates the generation of hydroxide ion to allow its nucleophilic attack on the phosphate group. It also stabilises the transition state. Arg35 and Arg87 stabilise the transition state via bidentate hydrogen bonding. Arg87 is also the general acid that protonates the 5'-hydroxyl leaving group.

Catalytic Sites for 1a2t

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgA35117macie:sideChainIt stabilises the negatively charged transition state via bidentate hydrogen bonding.
ArgA87169macie:sideChainIt stabilises the transition state via bidentate hydrogen bonding and acts as an acid to protonate the 5'-hydroxyl leaving group.

Literature References

Notes:
Weber DJ
NMR docking of a substrate into the X-ray structure of staphylococcal nuclease.
Proteins 1992 13 275-287
PubMed: 1518799
Pourmotabbed T
Kinetic and conformational effects of lysine substitutions for arginines 35 and 87 in the active site of staphylococcal nuclease.
Biochemistry 1990 29 3677-3683
PubMed: 2111164
Hale SP
Mechanism of the reaction catalyzed by staphylococcal nuclease: identification of the rate-determining step.
Biochemistry 1993 32 7479-7487
PubMed: 8338846
Libson AM
Crystal structures of the binary Ca2+ and pdTp complexes and the ternary complex of the Asp21-->Glu mutant of staphylococcal nuclease. Implications for catalysis and ligand binding.
Biochemistry 1994 33 8007-8016
PubMed: 8025105
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