scholarly journals Mechanistic consequences of replacing the active-site nucleophile Glu-358 in Agrobacterium sp. β-glucosidase with a cysteine residue

1998 ◽  
Vol 330 (1) ◽  
pp. 203-209 ◽  
Author(s):  
L. Sherry LAWSON ◽  
J. R. Antony WARREN ◽  
G. Stephen WITHERS
Keyword(s):  
Rate Constant ◽  
Active Site ◽  
Cysteine Residue ◽  
Kinetic Evaluation ◽  
Glycosidic Bonds ◽  
Proposal A ◽  
Leaving Group ◽  
Hydrolysis Of ◽  
Enzyme Intermediate

Retaining glycosidases achieve the hydrolysis of glycosidic bonds through the assistance of two key active-site carboxyls. One carboxyl functions as a nucleophile/leaving group, and the other acts as the acid-base catalyst. It has been suggested that a cysteine residue could fulfil the role of the active site nucleophile [Hardy and Poteete (1991) Biochemistry 30, 9457-9463]. To test the validity of this proposal, a kinetic evaluation was conducted on the active-site nucleophile cysteine mutant (Glu-358 → Cys) of the retaining β-glucosidase from Agrobacterium sp. The Glu-358 → Cys mutant was able to complete the first step (glycosylation) of the enzymic mechanism, forming a covalent glycosyl-enzyme intermediate, but the rate constant for this step was decreased to 1/106 of that of the native enzyme. The subsequent hydrolysis (deglycosylation) step was also severely affected by the replacement of Glu-358 with a cysteine residue, with the rate constant being depressed to 1/107 or less. Thus Cys-358 functions inefficiently in both the capacity of catalytic nucleophile and leaving group. On the basis of these results it seems unlikely that the role of the active-site nucleophile in retaining glycosidases could successfully be filled by a cysteine residue.

scholarly journals KPC-2 β-lactamase Enables Carbapenem Antibiotic Resistance Through Fast Deacylation of the Covalent Intermediate

2020 ◽  
pp. jbc.RA120.015050
Author(s):  
Shrenik C Mehta ◽  
Ian M Furey ◽  
Orville A Pemberton ◽  
David M Boragine ◽  
Yu Chen ◽  
...  
Keyword(s):  
Active Site ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
The Common ◽  
Covalent Intermediate ◽  
Hydrolysis Of ◽  
Carbapenem Antibiotic ◽  
Enzyme Intermediate

Serine active-site β-lactamases hydrolyze β-lactam antibiotics through formation of a covalent acyl-enzyme intermediate followed by deacylation via an activated water molecule. Carbapenem antibiotics are poorly hydrolyzed by most β-lactamases due to slow hydrolysis of the acyl-enzyme intermediate. However, the emergence of the KPC-2 carbapenemase has resulted in widespread resistance to these drugs, suggesting it operates more efficiently. Here, we investigated the unusual features of KPC-2 that enable this resistance. We show that KPC-2 has a 20,000-fold increased deacylation rate compared to the common TEM-1 β-lactamase. Further, kinetic analysis of active site alanine mutants indicates that carbapenem hydrolysis is a concerted effort involving multiple residues. Substitution of Asn170 greatly decreases the deacylation rate, but this residue is conserved in both KPC-2 and non-carbapenemase β-lactamases, suggesting it promotes carbapenem hydrolysis only in the context of KPC-2. X-ray structure determination of the N170A enzyme in complex with hydrolyzed imipenem suggests Asn170 may prevent the inactivation of the deacylating water by the 6α-hydroxyethyl substituent of carbapenems. In addition, the Thr235 residue, which interacts with the C3 carboxylate of carbapenems, also contributes strongly to the deacylation reaction. In contrast, mutation of the Arg220 and Thr237 residues decreases the acylation rate and, paradoxically, improves binding affinity for carbapenems. Thus, the role of these residues may be ground state destabilization of the enzyme-substrate complex or, alternatively, to ensure proper alignment of the substrate with key catalytic residues to facilitate acylation. These findings suggest modifications of the carbapenem scaffold to avoid hydrolysis by KPC-2 β-lactamase.

Role of a cysteine residue in the active site of ERK and the MAPKK family

2007 ◽  
Vol 353 (3) ◽  
pp. 633-637 ◽  
Author(s):  
Makoto Ohori ◽  
Takayoshi Kinoshita ◽  
Seiji Yoshimura ◽  
Masaichi Warizaya ◽  
Hidenori Nakajima ◽  
...  
Keyword(s):  
Active Site ◽  
Cysteine Residue

scholarly journals Understanding the Role of Histidine in the GHSxG Acyltransferase Active Site Motif: Evidence for Histidine Stabilization of the Malonyl-Enzyme Intermediate

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e109421 ◽  
Author(s):  
Sean Poust ◽  
Isu Yoon ◽  
Paul D. Adams ◽  
Leonard Katz ◽  
Christopher J. Petzold ◽  
...  
Keyword(s):  
Active Site ◽  
Active Site Motif ◽  
Enzyme Intermediate

Anchimeric assistance in hexosaminidases

2002 ◽  
Vol 80 (8) ◽  
pp. 1064-1074 ◽  
Author(s):  
Brian L Mark ◽  
Michael NG James
Keyword(s):  
Oxygen Atom ◽  
Active Site ◽  
Sequence Similarity ◽  
Carbonyl Oxygen ◽  
Carbonyl Oxygen Atom ◽  
Carboxyl Groups ◽  
Displacement Mechanism ◽  
Glycosidic Bonds ◽  
Anchimeric Assistance ◽  
Hydrolysis Of

Configuration retaining glycosidases catalyse the hydrolysis of glycosidic bonds via a double displacement mechanism, typically involving two key active site carboxyl groups (Glu or Asp). One of the enzymic carboxyl groups functions as a general acid–base catalyst, the other acts as a nucleophile. Alternatively, configuration-retaining hexosaminidases from the sequence-related glycosidase families 18, 20, and 56 lack a suitably positioned enzymic nucleophile; instead, they use the carbonyl oxygen atom of the neighbouring C2-acetamido group of the substrate. The carbonyl oxygen atom of the 2-acetamido group provides anchimeric assistance to the enzyme catalyzed reaction by acting as an intramolecular nucleophile, attacking the anomeric center and forming a cyclized oxazolinium ion intermediate that is stereochemically equivalent to the glycosyl–enzyme intermediate formed in the "normal" double displacement mechanism. Although there is little sequence similarity between families 18, 20, and 56 hexosaminidases, X-ray crystallographic studies demonstrate that they have evolved similar catalytic domains and active site architectures that are designed to distort the bound substrate so that the C2-acetamido group can become appropriately positioned to participate in catalysis. The substrate distortion allows for a substrate-assisted catalytic reaction that displays all the general characteristics of the classic double-displacement mechanism including the formation of a covalent intermediate.Key words: glycoside hydrolase, hexosaminidase, glycosidase, substrate-assisted catalysis, anchimeric assistance.

scholarly journals The action of cytoplasmic aldehyde dehydrogenase on methyl p-nitrophenyl carbonate and p-nitrophenyl dimethylcarbamate

1989 ◽  
Vol 257 (2) ◽  
pp. 579-584 ◽  
Author(s):  
T M Kitson
Keyword(s):  
Aldehyde Dehydrogenase ◽  
Chloral Hydrate ◽  
Slow Release ◽  
Cysteine Residue ◽  
Single Type ◽  
Rate Of Hydrolysis ◽  
Rate Limiting ◽  
Hydrolysis Of ◽  
Enzyme Intermediate ◽  
Esterase Activities

Cytoplasmic aldehyde dehydrogenase catalyses the hydrolysis of methyl p-nitrophenyl (PNP) carbonate at an appreciable rate that is markedly stimualted by NAD+ or NADH. The nuleotides accelerate the rate-limiting hydrolysis of the acyl-enzyme intermediate while slowing the observed burst of p-nitrophenoxide production. With PNP dimethylcarbamate the enzyme catalyses the slow release of approx. 1 molecule of p-nitrophenoxide per tetrameric enzyme molecule; during the reaction the enzyme becomes effectively inactivated, as the rate of hydrolysis of the acyl-enzyme is virtually zero. The presence of NAD+, NADH, propionaldehyde, chloral hydrate, diethylstilboestrol or disulfiram slows the reaction of enzyme with PNP dimethylcarbamate. The reaction appears to be dependent on a group of pKa 7.6, possibly a cysteine residue. The effect of PNP dimethylcarbamate on the dehydrogenase activity of the enzyme is consistent with there being a single type of active site for the enzyme's dehydrogenase and esterase activities. Steric and electronic factors that govern reaction of the enzyme with PNP substrates are discussed.

scholarly journals Probing the Role of Cysteine Residues in Glucosamine-1-Phosphate Acetyltransferase Activity of the Bifunctional GlmU Protein fromEscherichia coli: Site-Directed Mutagenesis and Characterization of the Mutant Enzymes

1998 ◽  
Vol 180 (18) ◽  
pp. 4799-4803 ◽  
Author(s):  
Frédérique Pompeo ◽  
Jean van Heijenoort ◽  
Dominique Mengin-Lecreulx
Keyword(s):  
Active Site ◽  
Cysteine Residue ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Acetyl Coa ◽  
Mutant Proteins ◽  
Acetyltransferase Activity ◽  
Phosphate Acetyltransferase ◽  
High Level

ABSTRACT The glucosamine-1-phosphate acetyltransferase activity but not the uridyltransferase activity of the bifunctional GlmU enzyme fromEscherichia coli was lost when GlmU was stored in the absence of β-mercaptoethanol or incubated with thiol-specific reagents. The enzyme was protected from inactivation in the presence of its substrate acetyl coenzyme A (acetyl-CoA), suggesting the presence of an essential cysteine residue in or near the active site of the acetyltransferase domain. To ascertain the role of cysteines in the structure and function of the enzyme, site-directed mutagenesis was performed to change each of the four cysteines to alanine, and plasmids were constructed for high-level overproduction and one-step purification of histidine-tagged proteins. Whereas the kinetic parameters of the bifunctional enzyme appeared unaffected by the C296A and C385A mutations, 1,350- and 8-fold decreases of acetyltransferase activity resulted from the C307A and C324A mutations, respectively. TheKm values for acetyl-CoA and GlcN-1-P of mutant proteins were not modified, suggesting that none of the cysteines was involved in substrate binding. The uridyltransferase activities of wild-type and mutant GlmU proteins were similar. From these studies, the two cysteines Cys307 and Cys324 appeared important for acetyltransferase activity and seemed to be located in or near the active site.

The polysulphate binding domain of human proacrosin/acrosin is involved in both the enzyme activation and spermatozoa-zona pellucida interaction

Zygote ◽  
1998 ◽  
Vol 6 (1) ◽  
pp. 75-83 ◽  
Author(s):  
R. D. Moreno ◽  
M. S. Sepúlveda ◽  
A. de Ioannes ◽  
C. Barros
Keyword(s):  
Zona Pellucida ◽  
Active Site ◽  
Enzyme Activation ◽  
Binding Domain ◽  
Present Evidence ◽  
Sperm Binding ◽  
Mammalian Sperm ◽  
Hydrolysis Of

SummaryMammalian acrosin is a protease present as a zymogen in the acrosome of a non-reacted mammalian sperm, and in vitro is able to carry out limited hydrolysis of homologous and heterologous zonae pellucidae. On the other hand, sulphated polymers and zona pellcida glycoproteins bind to acrosin on a domain different from the active site, named the polysulphate binding domain (PSBD). Thus it is believed that acrosome-reacted spermatozoa bind to glycan chains of the zona pellucida through PSBD participating as secondary binding receptor. The aim of the present work was to study the role of PSBD during both human gamete interaction and acrosin activation. In this work we present evidence that the anti-human acrosin monoclonal antibody C5F10 is directed to an epitope located on or near the PSBD on human proacrosin/acrosin. Moreover, we show that this antibody is able to inhibit both proacrosin activation induced by fucoidan and the sperm binding to the zona pellucida. Our results suggest that the same PSBD is involved in both sperm secondary binding, during zona pellucida penetration, and proacrosin activation.

scholarly journals Evolutionary Expansion of the Amidohydrolase Superfamily in Bacteria in Response to the Synthetic Compounds Molinate and Diuron

2015 ◽  
Vol 81 (7) ◽  
pp. 2612-2624 ◽  
Author(s):  
Elena Sugrue ◽  
Nicholas J. Fraser ◽  
Davis H. Hopkins ◽  
Paul D. Carr ◽  
Jeevan L. Khurana ◽  
...  
Keyword(s):  
Active Site ◽  
Metal Ion ◽  
Active Sites ◽  
Evolutionary Transition ◽  
Functional Changes ◽  
Metal Ion Analysis ◽  
Amidohydrolase Superfamily ◽  
Kinetics Of ◽  
Hydrolysis Of

ABSTRACTThe amidohydrolase superfamily has remarkable functional diversity, with considerable structural and functional annotation of known sequences. In microbes, the recent evolution of several members of this family to catalyze the breakdown of environmental xenobiotics is not well understood. An evolutionary transition from binuclear to mononuclear metal ion coordination at the active sites of these enzymes could produce large functional changes such as those observed in nature, but there are few clear examples available to support this hypothesis. To investigate the role of binuclear-mononuclear active-site transitions in the evolution of new function in this superfamily, we have characterized two recently evolved enzymes that catalyze the hydrolysis of the synthetic herbicides molinate (MolA) and phenylurea (PuhB). In this work, the crystal structures, mutagenesis, metal ion analysis, and enzyme kinetics of both MolA and PuhB establish that these enzymes utilize a mononuclear active site. However, bioinformatics and structural comparisons reveal that the closest putative ancestor of these enzymes had a binuclear active site, indicating that a binuclear-mononuclear transition has occurred. These proteins may represent examples of evolution modifying the characteristics of existing catalysts to satisfy new requirements, specifically, metal ion rearrangement leading to large leaps in activity that would not otherwise be possible.

scholarly journals The Role of the Ω-Loop in Regulation of the Catalytic Activity of TEM-Type β-Lactamases

Biomolecules ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 854 ◽  
Author(s):  
Alexey Egorov ◽  
Maya Rubtsova ◽  
Vitaly Grigorenko ◽  
Igor Uporov ◽  
Alexander Veselovsky
Keyword(s):  
Active Site ◽  
Bacterial Resistance ◽  
Structural Flexibility ◽  
Allosteric Inhibitors ◽  
Penicillin Binding Proteins ◽  
Global Challenge ◽  
Class A ◽  
Lactam Ring ◽  
Hydrolysis Of

Bacterial resistance to β-lactams, the most commonly used class of antibiotics, poses a global challenge. This resistance is caused by the production of bacterial enzymes that are termed β-lactamases (βLs). The evolution of serine-class A β-lactamases from penicillin-binding proteins (PBPs) is related to the formation of the Ω-loop at the entrance to the enzyme’s active site. In this loop, the Glu166 residue plays a key role in the two-step catalytic cycle of hydrolysis. This residue in TEM–type β-lactamases, together with Asn170, is involved in the formation of a hydrogen bonding network with a water molecule, leading to the deacylation of the acyl–enzyme complex and the hydrolysis of the β-lactam ring of the antibiotic. The activity exhibited by the Ω-loop is attributed to the positioning of its N-terminal residues near the catalytically important residues of the active site. The structure of the Ω-loop of TEM-type β-lactamases is characterized by low mutability, a stable topology, and structural flexibility. All of the revealed features of the Ω-loop, as well as the mechanisms related to its involvement in catalysis, make it a potential target for novel allosteric inhibitors of β-lactamases.

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