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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1oba
Original Entry
Title:
Hydrolase
Compound:
Endolysin
Mutant:
No
UniProt/Swiss-Prot:
P15057-LYCA_BPCP1
EC Class:
3.2.1.17
Other CSA Entries:
Overview of all sites for 1oba
Homologues of 1oba
Entries for UniProt/Swiss-Prot: P15057
Entries for EC: 3.2.1.17
Other Databases:
PDB entry: 1oba
PDBsum entry: 1oba
UniProt/Swiss-Prot: P15057
IntEnz entry: 3.2.1.17
Literature Report:
Introduction:
Cpl-1 lysin from Bacteriophage cp-1 catalyses the hydrolysis of the
1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of prokaryote cell walls. On binding to choline, the enzymes geometry changes, its specificity increases, and catalytic activity is increased. Cpl-1 is used against bacteria such as Streptococcus pneumoniae (which causes pneumonia), as it kills the bacteria by breaking down its cell wall.
Mechanism:
1. Asp 10 acts as a general base, activating a water molecule for nucleophilic attack at the carbon atom of the glycosidic bond.
2. As the glycosidic bond cleaves, protonated Glu 94 acts as a general acid by protonating the leaving group oxygen atom.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 10 10Sidechain
Acid/baseWater
Asp 10 acts as a general base by deprotonating a water molecule, activating it for nucleophilic attack on the carbon atom of the glycosidic bond.
Evidence from paper Evidence concerns Evidence type
PubMed ID 14527392 Current protein Mutagenesis of residue
PubMed ID 14527392 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 92 92Sidechain
Acid/baseResidue
Asp 92 allows protons to move freely between itself and Glu 94, thus ensuring regeneration of the protonated state of Glu 94.
Evidence from paper Evidence concerns Evidence type
PubMed ID 14527392 Current protein Mutagenesis of residue
PubMed ID 14527392 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 94 94Sidechain
Acid/baseSubstrate
The protonated form of Glu 94 acts as a general acid, by protonating the leaving group oxygen atom as the glycosidic bond is broken.
Evidence from paper Evidence concerns Evidence type
PubMed ID 14527392 Current protein Structural similarity to homologue of known mechanism
PubMed ID 14527392 Current protein Mutagenesis of residue
PubMed ID 14527392 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 14527392 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 182 182Sidechain
Acid/baseResidue
Low barrier hydrogen bonds allow the free transfer of protons between Asp 182 and Asp 10, ensuring the regeneration of the deprotonated state of Asp 10.
Evidence from paper Evidence concerns Evidence type
PubMed ID 14527392 Current protein Mutagenesis of residue
PubMed ID 14527392 Current protein Residue is positioned appropriately (ligand position known)
Notes:

References:
1
Structural basis for selective recognition of pneumococcal cell wall by modular endolysin from phage Cp-1.
J. A. Hermoso and B. Monterroso and A. Albert and B. Galán and O. Ahrazem and P. García and M. Martínez-Ripoll and J. L. García and M. Menéndez
Structure 11, (10) 1239-49, (2003).
14527392
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