title: Analysis of proton wires in the enzyme active site suggests a mechanism of c-di-GMP hydrolysis by the EAL domain phosphodiesterases.
abstract: We report for the first time a hydrolysis mechanism of the cyclic dimeric guanosine monophosphate (c-di-GMP) by the EAL domain phosphodiesterases as revealed by molecular simulations. A model system for the enzyme-substrate complex was prepared on the base of the crystal structure of the EAL domain from the BlrP1 protein complexed with c-di-GMP. The nucleophilic hydroxide generated from the bridging water molecule appeared in a favorable position for attack on the phosphorus atom of c-di-GMP. The most difficult task was to find a pathway for a proton transfer to the O3' atom of c-di-GMP to promote the O3'P bond cleavage. We show that the hydrogen bond network extended over the chain of water molecules in the enzyme active site and the Glu359 and Asp303 side chains provides the relevant proton wires. The suggested mechanism is consistent with the structural, mutagenesis, and kinetic experimental studies on the EAL domain phosphodiesterases. Proteins 2016; 84:1670-1680. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow, 119991, Russia.|N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow, 119334, Russia.
authors.forename: Bella L
authors.initials: BL
authors.lastname: Grigorenko
authors.affiliation: Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow, 119991, Russia.
authors.forename: Marina A
authors.initials: MA
authors.lastname: Knyazeva
authors.affiliation: Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow, 119991, Russia. anemukhin@yahoo.com.|N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow, 119334, Russia. anemukhin@yahoo.com.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Nemukhin
mesh_terms: D019943:Amino Acid Substitution; D001224:Aspartic Acid / Q000737:chemistry* / Q000378:metabolism; D020134:Catalytic Domain; D006152:Cyclic GMP / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000737:chemistry* / Q000201:enzymology; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D018698:Glutamic Acid / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D006868:Hydrolysis; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D010727:Phosphoric Diester Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D010758:Phosphorus / Q000737:chemistry; D017433:Protein Structure, Secondary; D011522:Protons; D011789:Quantum Theory; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D029968:Escherichia coli Proteins; D011522:Protons; D014867:Water; D010758:Phosphorus; D001224:Aspartic Acid; D018698:Glutamic Acid; C062025:bis(3',5')-cyclic diguanylic acid; D010727:Phosphoric Diester Hydrolases; C510176:bluF protein, E coli; D006152:Cyclic GMP
keywords: EAL domain; QM/MM; c-di-GMP; hydrolysis reaction; molecular simulations; phosphodiesterases; proton wires