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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1nkk
Original Entry
Title:
Hydrolase
Compound:
Capsid protein p40
Mutant:
No
UniProt/Swiss-Prot:
P16753-VP40_HCMVA
EC Class:
3.4.21.97
Other CSA Entries:
Overview of all sites for 1nkk
Homologues of 1nkk
Entries for UniProt/Swiss-Prot: P16753
Entries for EC: 3.4.21.97
Other Databases:
PDB entry: 1nkk
PDBsum entry: 1nkk
UniProt/Swiss-Prot: P16753
IntEnz entry: 3.4.21.97
Literature Report:
Introduction:
Herpesviruses, such as human cytomegalovirus, are large double stranded DNA viruses that infect most species throughout the animal kingdom. They encode a protease that is essential for production of infectious virons: this enzyme catalyses the maturational processing of the herpesvirus assembly protein. Herpesvirus proteases have little sequence homology to other known proteases, and all have similar substrate specificity, prefering to cleave Ala-Ser bonds. They exist as a monomer-dimer equilibrium, with the dimer being the active species.
Mechanism:
Herpesvirus protease uses a Ser-His-His catalytic triad. Ser 132 acts as a nucleophile to attack the peptide bond, while His 63 deprotonates the attacking serine residue. The resulting tetrahedral intermediate is stabilised by an oxyanion hole consisting of the backbone NH of Arg 165 and two water molecules positioned by the guanidinium group of Arg 166. Collapse of the tetrahedral intermediate with protonation of the departing amine by His 63 generates an acyl-enzyme intermediate. This is then hydrolysed by a water molecule that is deprotonated by His 63. His 157 functions to modify the pKa of His 63, although its effect of catalysis is much smaller than that of the aspartate in the classical Ser-His-Asp serine proteases.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
2138 0
ElectrostaticTransition state
Form part of oxyanion hole to stabilise the tetrahedral intermediate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12549906 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
2246 0
ElectrostaticTransition state
Form part of oxyanion hole to stabilise the tetrahedral intermediate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12549906 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 63 63Sidechain
Acid/baseResidue
Acid/baseWater
Acid/baseSubstrate
Deprotonates Ser 132 as this residue attacks the peptide bond. Protonates the departing amine leaving group. Later deprotonates a water molecule during hydrolysis of the acyl-enzyme intermediate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 8230459 Related protein: UniProt P16046 Mutagenesis of residue
PubMed ID 8805707 Current protein Conservation of residue
PubMed ID 8805707 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
SERA 132 132Sidechain
NucleophileSubstrate
Attacks the peptide carbonyl to form an acyl-enzyme intermediate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 7929296 Current protein Chemical modification of residue
PubMed ID 8230459 Related protein: UniProt P16046 Mutagenesis of residue
PubMed ID 8805708 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12549906 Current protein Residue is covalently bound to intermediate, based on structural data
PubMed ID 8805708 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 157 157Sidechain
ElectrostaticResidue
Increases the pKa of His 63 by forming an additional hydrogen bond to it.
Evidence from paper Evidence concerns Evidence type
PubMed ID 8805707 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 11371196 Current protein Mutagenesis of residue
PubMed ID 8805707 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 165 165Backbone amide
ElectrostaticTransition state
Backbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 8805707 Current protein Conservation of residue
PubMed ID 12549906 Current protein Residue is positioned appropriately (ligand position known)
References:
1
Herpesvirus proteinase: site-directed mutagenesis used to study maturational, release, and inactivation cleavage sites of precursor and to identify a possible catalytic site serine and histidine.
A. R. Welch and L. M. McNally and M. R. Hall and W. Gibson
J Virol 67, (12) 7360-72, (1993).
8230459
2
Three-dimensional structure of human cytomegalovirus protease.
H. S. Shieh and R. G. Kurumbail and A. M. Stevens and R. A. Stegeman and E. J. Sturman and J. Y. Pak and A. J. Wittwer and M. O. Palmier and R. C. Wiegand and B. C. Holwerda and W. C. Stallings
Nature 383, (6597) 279-82, (1996).
8805708
3
Activity of two-chain recombinant human cytomegalovirus protease.
B. C. Holwerda and A. J. Wittwer and K. L. Duffin and C. Smith and M. V. Toth and L. S. Carr and R. C. Wiegand and M. L. Bryant
J Biol Chem 269, (41) 25911-5, (1994).
7929296
4
Structural and biochemical studies of inhibitor binding to human cytomegalovirus protease.
R. Khayat and R. Batra and C. Qian and T. Halmos and M. Bailey and L. Tong
Biochemistry 42, (4) 885-91, (2003).
12549906
5
Unique fold and active site in cytomegalovirus protease.
X. Qiu and J. S. Culp and A. G. DiLella and B. Hellmig and S. S. Hoog and C. A. Janson and W. W. Smith and S. S. Abdel-Meguid
Nature 383, (6597) 275-9, (1996).
8805707
6
Investigating the role of histidine 157 in the catalytic activity of human cytomegalovirus protease.
R. Khayat and R. Batra and M. J. Massariol and L. Lagacé and L. Tong
Biochemistry 40, (21) 6344-51, (2001).
11371196
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