Substrate Assisted Catalytic Mechanism of O GlcNAc Transferase
Discovered by Quantum Mechanics/Molecular Mechanics
Investigation

J 2012

Substrate Assisted Catalytic Mechanism of O GlcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation

TVAROŠKA, Igor, Stanislav KOZMON, Michaela WIMMEROVÁ and Jaroslav KOČA

Basic information

Original name

Substrate Assisted Catalytic Mechanism of O GlcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation

Authors

TVAROŠKA, Igor (703 Slovakia, guarantor, belonging to the institution), Stanislav KOZMON (703 Slovakia, belonging to the institution), Michaela WIMMEROVÁ (203 Czech Republic, belonging to the institution) and Jaroslav KOČA (203 Czech Republic, belonging to the institution)

Edition

J. Am. Chem. Soc. Washington, American Chemical Society, 2012, 0002-7863

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 10.677

RIV identification code

RIV/00216224:14740/12:00064660

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1021/ja307040m

UT WoS

000308830600067

Keywords in English

Glycosyltransferases reaction mechanism qm/mm

Abstract

V originále

In higher eukaryotes, a variety of proteins are post-translationally modified by adding O-linked N-acetylglucosamine (GlcNAc) residue to serine or threonine residues. Misregulation of O-GlcNAcylation is linked to a wide variety of diseases, such as diabetes, cancer, and neurodegenerative diseases, including Alzheimer's disease. GlcNAc transfer is catalyzed by an inverting glycosyltransferase O-GlcNAc transferase (uridine diphospho-N-acetylglucosamine:polypeptide beta-N-acetylaminyltransferase, OGT) that belongs to the GT-B superfamily. The catalytic mechanism of this metal-independent glycosyltransferase is of primary importance and is investigated here using QM(DFT)/MM methods. The structural model of the reaction site used in this paper is based on the crystal structures of OGT. The entire enzyme substrate system was partitioned into two different subsystems: the QM subsystem containing 198 atoms, and the MM region containing 11 326 atoms. The catalytic mechanism was monitored by means of three two-dimensional potential energy maps calculated as a function of three predefined reaction coordinates at different levels of theory. These potential energy surfaces revealed the existence of a concerted S(N)2-like mechanism, in which a nucleophilic attack by O-ser, facilitated by proton transfer to the catalytic base, and the dissociation of the leaving group occur almost simultaneously. The transition state for the proposed reaction mechanism at the MPW1K level was located at C1-O-Ser = 1.92 angstrom and C1-O1 = 3.11 angstrom. The activation energy for this passage was estimated to be similar to 20 kcal mol(-1). These calculations also identified, for the first time for glycosyltransferases, the substrate-assisted mechanism in which the N-acetamino group of the donor participates in the catalytic mechanism.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

ME08008, research and development project

Name: Návrh antibakteriálních a antivirových léků na bázi cukrů a glykomimetik

Investor: Ministry of Education, Youth and Sports of the CR, Design of Carbohydrates and Glycomimetics as Antibacterial and Antiviral Drugs, Research and Development Programme KONTAKT (ME)

2SGA2747, interní kód MU

Name: Saccharide - protein dispersion interactions involved in the bacterial recognition processes (Acronym: SaProDI)

Investor: South-Moravian Region, Incoming grants

286154, interní kód MU

Name: SYLICA - Synergies of Life and Material Sciences to Create a New Future (Acronym: SYLICA)

Investor: European Union, Capacities

Citovat

TVAROŠKA, Igor, Stanislav KOZMON, Michaela WIMMEROVÁ and Jaroslav KOČA. Substrate Assisted Catalytic Mechanism of O GlcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation. J. Am. Chem. Soc. Washington: American Chemical Society, 2012, vol. 134, No 37, p. 15563-15571. ISSN 0002-7863. Available from: https://dx.doi.org/10.1021/ja307040m.

@article{1094624,
   author = {Tvaroška, Igor and Kozmon, Stanislav and Wimmerová, Michaela and Koča, Jaroslav},
   article_location = {Washington},
   article_number = {37},
   doi = {http://dx.doi.org/10.1021/ja307040m},
   keywords = {Glycosyltransferases reaction mechanism qm/mm},
   language = {eng},
   issn = {0002-7863},
   journal = {J. Am. Chem. Soc.},
   title = {Substrate Assisted Catalytic Mechanism of O GlcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation},
   url = {http://pubs.acs.org/doi/abs/10.1021/ja307040m},
   volume = {134},
   year = {2012}
}

TY  - JOUR
ID  - 1094624
AU  - Tvaroška, Igor - Kozmon, Stanislav - Wimmerová, Michaela - Koča, Jaroslav
PY  - 2012
TI  - Substrate Assisted Catalytic Mechanism of O GlcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation
JF  - J. Am. Chem. Soc.
VL  - 134
IS  - 37
SP  - 15563-15571
EP  - 15563-15571
PB  - American Chemical Society
SN  - 00027863
KW  - Glycosyltransferases reaction mechanism qm/mm
UR  - http://pubs.acs.org/doi/abs/10.1021/ja307040m
L2  - http://pubs.acs.org/doi/abs/10.1021/ja307040m
N2  - In higher eukaryotes, a variety of proteins are post-translationally modified by adding O-linked N-acetylglucosamine (GlcNAc) residue to serine or threonine residues. Misregulation of O-GlcNAcylation is linked to a wide variety of diseases, such as diabetes, cancer, and neurodegenerative diseases, including Alzheimer's disease. GlcNAc transfer is catalyzed by an inverting glycosyltransferase O-GlcNAc transferase (uridine diphospho-N-acetylglucosamine:polypeptide beta-N-acetylaminyltransferase, OGT) that belongs to the GT-B superfamily. The catalytic mechanism of this metal-independent glycosyltransferase is of primary importance and is investigated here using QM(DFT)/MM methods. The structural model of the reaction site used in this paper is based on the crystal structures of OGT. The entire enzyme substrate system was partitioned into two different subsystems: the QM subsystem containing 198 atoms, and the MM region containing 11 326 atoms. The catalytic mechanism was monitored by means of three two-dimensional potential energy maps calculated as a function of three predefined reaction coordinates at different levels of theory. These potential energy surfaces revealed the existence of a concerted S(N)2-like mechanism, in which a nucleophilic attack by O-ser, facilitated by proton transfer to the catalytic base, and the dissociation of the leaving group occur almost simultaneously. The transition state for the proposed reaction mechanism at the MPW1K level was located at C1-O-Ser = 1.92 angstrom and C1-O1 = 3.11 angstrom. The activation energy for this passage was estimated to be similar to 20 kcal mol(-1). These calculations also identified, for the first time for glycosyltransferases, the substrate-assisted mechanism in which the N-acetamino group of the donor participates in the catalytic mechanism.
ER  -

TVAROŠKA, Igor, Stanislav KOZMON, Michaela WIMMEROVÁ and Jaroslav KOČA. Substrate Assisted Catalytic Mechanism of O GlcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation. \textit{J. Am. Chem. Soc.}. Washington: American Chemical Society, 2012, vol.~134, No~37, p.~15563-15571. ISSN~0002-7863. Available from: https://dx.doi.org/10.1021/ja307040m.

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