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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1a2t
Original Entry
Title:
Nuclease
Compound:
Staphylococcal nuclease
Mutant:
Yes
UniProt/Swiss-Prot:
P00644-NUC_STAAU
EC Class:
3.1.31.1
Other CSA Entries:
Overview of all sites for 1a2t
Homologues of 1a2t
Entries for UniProt/Swiss-Prot: P00644
Entries for EC: 3.1.31.1
Other Databases:
PDB entry: 1a2t
PDBsum entry: 1a2t
UniProt/Swiss-Prot: P00644
IntEnz entry: 3.1.31.1
Literature Report:
Introduction:
Staphyloccal 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.
Mechanism:
The 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.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
UA 142 224
ElectrostaticWater
ElectrostaticTransition state
It generates hydroxide ions from water molecule bound, to promote the nucleophilic attack on the phosphate. Its positive charges stabilise the negatively charged transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 1518799 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 1518799 Current protein Ligand is essential for catalysis
PubMed ID 1518799 Current protein Chemical modification of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 35 117Sidechain
ElectrostaticTransition state
It stabilises the negatively charged transition state via bidentate hydrogen bonding.
Evidence from paper Evidence concerns Evidence type
PubMed ID 2111164 Current protein Mutagenesis of residue
PubMed ID 1518799 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 87 169Sidechain
ElectrostaticTransition state
Acid/baseSubstrate
It stabilises the transition state via bidentate hydrogen bonding and acts as an acid to protonate the 5'-hydroxyl leaving group.
Evidence from paper Evidence concerns Evidence type
PubMed ID 1518799 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 2111164 Current protein Mutagenesis of residue
References:
1
NMR docking of a substrate into the X-ray structure of staphylococcal nuclease.
D. J. Weber and A. G. Gittis and G. P. Mullen and C. Abeygunawardana and E. E. Lattman and A. S. Mildvan
Proteins 13, (4) 275-87, (1992).
1518799
2
Kinetic and conformational effects of lysine substitutions for arginines 35 and 87 in the active site of staphylococcal nuclease.
T. Pourmotabbed and M. Dell'Acqua and J. A. Gerlt and S. M. Stanczyk and P. H. Bolton
Biochemistry 29, (15) 3677-83, (1990).
2111164
3
Mechanism of the reaction catalyzed by staphylococcal nuclease: identification of the rate-determining step.
S. P. Hale and L. B. Poole and J. A. Gerlt
Biochemistry 32, (29) 7479-87, (1993).
8338846
4
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.
A. M. Libson and A. G. Gittis and E. E. Lattman
Biochemistry 33, (26) 8007-16, (1994).
8025105
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