1
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Fernandez P, Richard JP. Adenylate Kinase-Catalyzed Reactions of AMP in Pieces: Specificity for Catalysis at the Nucleoside Activator and Dianion Catalytic Sites. Biochemistry 2022; 61:2766-2775. [PMID: 36413937 PMCID: PMC9731266 DOI: 10.1021/acs.biochem.2c00531] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The pressure to optimize the enzymatic rate acceleration for adenylate kinase (AK)-catalyzed phosphoryl transfer has led to the evolution of an induced-fit mechanism, where the binding energy from interactions between the protein and substrate adenosyl group is utilized to drive a protein conformational change that activates the enzyme for catalysis. The adenine group of adenosine contributes 11.8 kcal mol-1 to the total ≥14.7 kcal mol-1 adenosine stabilization of the transition state for AK-catalyzed phosphoryl transfer to AMP. The relative third-order rate constants for activation of adenylate kinase, by the C-5 truncated adenosine 1-(β-d-erythrofuranosyl)adenine (EA), for catalysis of phosphoryl transfer from ATP to phosphite dianion (HP, kcat/KHPKAct = 260 M-2 s-1), fluorophosphate (47 M-2 s-1), and phosphate (9.6 M-2 s-1), show that substitution of -F for -H and of -OH for -H at HP results, respectively, in decreases in the reactivity of AK for catalysis of phosphoryl transfer due to polar and steric effects of the -F and -OH substituents. The addition of a 5'-CH2OH to the EA activator results in a 3.0 kcal mol-1 destabilization of the transition state for AK-activated phosphoryl transfer to HP due to a steric effect. This is smaller than the 8.3 kcal mol-1 steric effect of the 5'-CH2OH substituent at OMP on HP-activated OMPDC-catalyzed decarboxylation of 1-(β-d-erythrofuranosyl)orotate. The 2'-OH ribosyl substituent shows significant interactions with the transition states for AK-catalyzed phosphoryl transfer from ATP to AMP and for adenosine-activated AK-catalyzed phosphoryl transfer from ATP to HP.
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Affiliation(s)
- Patrick
L. Fernandez
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York14260−3000, United States
| | - John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York14260−3000, United States
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2
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Reyes AC, Amyes TL, Richard JP. Primary Deuterium Kinetic Isotope Effects: A Probe for the Origin of the Rate Acceleration for Hydride Transfer Catalyzed by Glycerol-3-Phosphate Dehydrogenase. Biochemistry 2018; 57:4338-4348. [PMID: 29927590 PMCID: PMC6091503 DOI: 10.1021/acs.biochem.8b00536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Large
primary deuterium kinetic isotope effects (1° DKIEs)
on enzyme-catalyzed hydride transfer may be observed when the transferred
hydride tunnels through the energy barrier. The following 1°
DKIEs on kcat/Km and relative reaction driving force are reported for wild-type and
mutant glycerol-3-phosphate dehydrogenase (GPDH)-catalyzed reactions
of NADL (L = H, D): wild-type GPDH, ΔΔG⧧ = 0 kcal/mol, 1° DKIE = 1.5;
N270A, 5.6 kcal/mol, 3.1; R269A, 9.1 kcal/mol, 2.8; R269A + 1.0 M
guanidine, 2.4 kcal/mol, 2.7; R269A/N270A, 11.5 kcal/mol, 2.4. Similar
1° DKIEs were observed on kcat. The
narrow range of 1° DKIEs (2.4–3.1) observed for a 9.1
kcal/mol change in reaction driving force provides strong evidence
that these are intrinsic 1° DKIEs on rate-determining hydride
transfer. Evidence is presented that the intrinsic DKIE on wild-type
GPDH-catalyzed reduction of DHAP lies in this range. A similar range
of 1° DKIEs (2.4–2.9) on (kcat/KGA, M–1 s–1) was reported for dianion-activated hydride transfer from NADL to
glycolaldehyde (GA) [Reyes, A. C.; Amyes, T. L.; Richard, J.
P. J. Am. Chem. Soc.2016, 138, 14526–14529].
These 1° DKIEs are much smaller than those observed for enzyme-catalyzed
hydrogen transfer that occurs mainly by quantum mechanical tunneling.
These results support the conclusion that the rate acceleration for
GPDH-catalyzed reactions is due to the stabilization of the transition
state for hydride transfer by interactions with the protein catalyst.
The small 1° DKIEs reported for mutant GPDH-catalyzed and for
wild-type dianion-activated reactions are inconsistent with a model
where the dianion binding energy is utilized in the stabilization
of a tunneling ready state.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
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3
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Richard JP, Amyes TL, Reyes AC. Orotidine 5'-Monophosphate Decarboxylase: Probing the Limits of the Possible for Enzyme Catalysis. Acc Chem Res 2018; 51:960-969. [PMID: 29595949 PMCID: PMC6016548 DOI: 10.1021/acs.accounts.8b00059] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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The mystery associated with catalysis by what were once regarded
as protein black boxes, diminished with the X-ray crystallographic
determination of the three-dimensional structures of enzyme–substrate
complexes. The report that several high-resolution X-ray crystal structures
of orotidine 5′-monophosphate decarboxylase (OMPDC) failed
to provide a consensus mechanism for enzyme-catalyzed decarboxylation
of OMP to form uridine 5′-monophosphate, therefore, provoked
a flurry of controversy. This controversy was fueled by the enormous
1023-fold rate acceleration for this enzyme, which had
“jolted many biochemists’ assumptions about
the catalytic potential of enzymes.” Our studies on
the mechanism of action of OMPDC provide strong evidence that catalysis
by this enzyme is not fundamentally different from less proficient
catalysts, while highlighting important architectural elements that
enable a peak level of performance. Many enzymes undergo substrate-induced
protein conformational changes that trap their substrates in solvent
occluded protein cages, but the conformational change induced by ligand
binding to OMPDC is incredibly complex, as required to enable the
development of 22 kcal/mol of stabilizing binding interactions with
the phosphodianion and ribosyl substrate fragments of OMP. The binding
energy from these fragments is utilized to activate OMPDC for catalysis
of decarboxylation at the orotate fragment of OMP, through the creation
of a tight, catalytically active, protein cage from the floppy, open,
unliganded form of OMPDC. Such utilization of binding energy for ligand-driven
conformational changes provides a general mechanism to obtain specificity
in transition state binding. The rate enhancement that results from
the binding of carbon acid substrates to enzymes is partly due to
a reduction in the carbon acid pKa that
is associated with ligand binding. The binding of UMP to OMPDC results
in an unusually large >12 unit decrease in the pKa = 29 for abstraction of the C-6 substrate hydrogen,
due to stabilization of an enzyme-bound vinyl carbanion, which is
also an intermediate of OMPDC-catalyzed decarboxylation. The protein–ligand
interactions operate to stabilize the vinyl carbanion at the enzyme
active site compared to aqueous solution, rather than to stabilize
the transition state for the concerted electrophilic displacement
of CO2 by H+ that avoids formation of this reaction
intermediate. There is evidence that OMPDC induces strain into the
bound substrate. The interaction between the amide side chain of Gln-215
from the phosphodianion gripper loop and the hydroxymethylene side
chain of Ser-154 from the pyrimidine umbrella of ScOMPDC position the amide side chain to interact with the phosphodianion
of OMP. There are no direct stabilizing interactions between dianion
gripper protein side chains Gln-215, Tyr-217, and Arg-235 and the
pyrimidine ring at the decarboxylation transition state. Rather these
side chains function solely to hold OMPDC in the catalytically active
closed conformation. The hydrophobic side chains that line the active
site of OMPDC in the region of the departing CO2 product
may function to stabilize the decarboxylation transition state by
providing hydrophobic solvation of this product.
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Affiliation(s)
- John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Archie C. Reyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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4
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Reyes AC, Amyes TL, Richard JP. Enzyme Architecture: Erection of Active Orotidine 5'-Monophosphate Decarboxylase by Substrate-Induced Conformational Changes. J Am Chem Soc 2017; 139:16048-16051. [PMID: 29058891 PMCID: PMC5720041 DOI: 10.1021/jacs.7b08897] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Orotidine
5′-monophosphate decarboxylase (OMPDC) catalyzes
the decarboxylation of 5-fluoroorotate (FO) with kcat/Km = 1.4 ×
10–7 M–1 s–1. Combining this and related kinetic parameters shows that the 31
kcal/mol stabilization of the transition state for decarboxylation
of OMP provided by OMPDC represents the sum of 11.8 and 10.6 kcal/mol
stabilization by the substrate phosphodianion and the ribosyl ring,
respectively, and an 8.6 kcal/mol stabilization from the orotate ring.
The transition state for OMPDC-catalyzed decarboxylation of FO is stabilized by 5.2, 7.2, and 9.0 kcal/mol, respectively,
by 1.0 M phosphite dianion, d-glycerol 3-phosphate and d-erythritol 4-phosphate. The stabilization is due to the utilization
of binding interactions of the substrate fragments to drive an enzyme
conformational change, which locks the orotate ring of the whole substrate,
or the substrate pieces in a caged complex. We propose that enzyme-activation
is a possible, and perhaps probable, consequence of any substrate-induced
enzyme conformational change.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
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5
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Amyes TL, Malabanan MM, Zhai X, Reyes AC, Richard JP. Enzyme activation through the utilization of intrinsic dianion binding energy. Protein Eng Des Sel 2017; 30:157-165. [PMID: 27903763 DOI: 10.1093/protein/gzw064] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/14/2016] [Indexed: 11/12/2022] Open
Abstract
43 We consider 'the proposition that the intrinsic binding energy that results from the noncovalent interaction of a specific substrate with the active site of the enzyme is considerably larger than is generally believed. An important part of this binding energy may be utilized to provide the driving force for catalysis, so that the observed binding energy represents only what is left over after this utilization' [Jencks,W.P. (1975) Adv. Enzymol. Relat. Areas. Mol. Biol. , , 219-410]. The large ~12 kcal/mol intrinsic substrate phosphodianion binding energy for reactions catalyzed by triosephosphate isomerase (TIM), orotidine 5'-monophosphate decarboxylase and glycerol-3-phosphate dehydrogenase is divided into 4-6 kcal/mol binding energy that is expressed on the formation of the Michaelis complex in anchoring substrates to the respective enzyme, and 6-8 kcal/mol binding energy that is specifically expressed at the transition state in activating the respective enzymes for catalysis. A structure-based mechanism is described where the dianion binding energy drives a conformational change that activates these enzymes for catalysis. Phosphite dianion plays the active role of holding TIM in a high-energy closed active form, but acts as passive spectator in showing no effect on transition-state structure. The result of studies on mutant enzymes is presented, which support the proposal that the dianion-driven enzyme conformational change plays a role in enhancing the basicity of side chain of E167, the catalytic base, by clamping the base between a pair of hydrophobic side chains. The insight these results provide into the architecture of enzyme active sites and the development of strategies for the de novo design of protein catalysts is discussed.
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Affiliation(s)
- T L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - M M Malabanan
- Department of Biochemistry, Vanderbilt University, Nashville, TN37205-0146, USA
| | - X Zhai
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843-2128, USA
| | - A C Reyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - J P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
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6
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Reyes AC, Amyes TL, Richard JP. Enzyme Architecture: Self-Assembly of Enzyme and Substrate Pieces of Glycerol-3-Phosphate Dehydrogenase into a Robust Catalyst of Hydride Transfer. J Am Chem Soc 2016; 138:15251-15259. [PMID: 27792325 PMCID: PMC5291162 DOI: 10.1021/jacs.6b09936] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The stabilization of the transition
state for hlGPDH-catalyzed reduction of DHAP due
to the action of the phosphodianion
of DHAP and the cationic side chain of R269 is between 12.4 and 17
kcal/mol. The R269A mutation of glycerol-3-phosphate dehydrogenase
(hlGPDH) results in a 9.1 kcal/mol destabilization
of the transition state for enzyme-catalyzed reduction of dihydroxyacetone
phosphate (DHAP) by NADH, and there is a 6.7 kcal/mol stabilization of this transition state by 1.0 M guanidine cation (Gua+) [J. Am. Chem. Soc.2015, 137, 5312–5315]. The R269A mutant shows no detectable
activity toward reduction of glycolaldehyde (GA), or activation of
this reaction by 30 mM HPO32–. We report
the unprecedented self-assembly of R269A hlGPDH,
dianions (X2– = FPO32–, HPO32–, or SO42–), Gua+ and GA into a functioning catalyst of the reduction
of GA, and fourth-order reaction rate constants kcat/KGAKXKGua. The linear logarithmic correlation
(slope = 1.0) between values of kcat/KGAKX for dianion
activation of wildtype hlGPDH-catalyzed reduction
of GA and kcat/KGAKXKGua shows that the electrostatic interaction between exogenous dianions
and the side chain of R269 is not significantly perturbed by cutting hlGPDH into R269A and Gua+ pieces. The advantage
for connection of hlGPDH (R269A mutant + Gua+) and substrate pieces (GA + HPi) pieces, (ΔGS‡)HPi+E+Gua = 5.6 kcal/mol, is nearly equal to the sum
of the advantage to connection of the substrate pieces, (ΔGS‡)GA+HPi = 3.3 kcal/mol, for wildtype hlGPDH-catalyzed reaction of GA + HPi, and for connection
of the enzyme pieces, (ΔGS‡)E+Gua = 2.4
kcal/mol, for Gua+ activation of the R269A hlGPDH-catalyzed reaction of DHAP.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
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7
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Zhai X, Amyes TL, Richard JP. Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase. J Am Chem Soc 2015; 137:15185-97. [PMID: 26570983 PMCID: PMC4694050 DOI: 10.1021/jacs.5b09328] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The side chains of
Y208 and S211 from loop 7 of triosephosphate
isomerase (TIM) form hydrogen bonds to backbone amides and carbonyls
from loop 6 to stabilize the caged enzyme–substrate complex.
The effect of seven mutations [Y208T, Y208S, Y208A, Y208F, S211G,
S211A, Y208T/S211G] on the kinetic parameters for TIM catalyzed reactions
of the whole substrates dihydroxyacetone phosphate and d-glyceraldehyde
3-phosphate [(kcat/Km)GAP and (kcat/Km)DHAP] and of the substrate pieces
glycolaldehyde and phosphite dianion (kcat/KHPiKGA)
are reported. The linear logarithmic correlation between these kinetic
parameters, with slope of 1.04 ± 0.03, shows that most mutations
of TIM result in an identical change in the activation barriers for
the catalyzed reactions of whole substrate and substrate pieces, so
that the transition states for these reactions are stabilized by similar
interactions with the protein catalyst. The second linear logarithmic
correlation [slope = 0.53 ± 0.16] between kcat for isomerization of GAP and Kd⧧ for phosphite dianion binding to the transition
state for wildtype and many mutant TIM-catalyzed reactions of substrate
pieces shows that ca. 50% of the wildtype TIM dianion binding energy,
eliminated by these mutations, is expressed at the wildtype Michaelis
complex, and ca. 50% is only expressed at the wildtype transition
state. Negative deviations from this correlation are observed when
the mutation results in a decrease in enzyme reactivity at the catalytic
site. The main effect of Y208T, Y208S, and Y208A mutations is to cause
a reduction in the total intrinsic dianion binding energy, but the
effect of Y208F extends to the catalytic site.
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Affiliation(s)
- Xiang Zhai
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
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8
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Ma H, Szeler K, Kamerlin SCL, Widersten M. Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA). Chem Sci 2015; 7:1415-1421. [PMID: 29910900 PMCID: PMC5975929 DOI: 10.1039/c5sc03666f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/17/2015] [Indexed: 12/13/2022] Open
Abstract
Local mutations in the phosphate binding group of DERA alter global conformation dynamics, catalytic activities and reaction entropies.
DERA, 2-deoxyribose-5-phosphate aldolase, catalyzes the retro-aldol cleavage of 2-deoxy-ribose-5-phosphate (dR5P) into glyceraldehyde-3-phosphate (G3P) and acetaldehyde in a branch of the pentose phosphate pathway. In addition to the physiological reaction, DERA also catalyzes the reverse addition reaction and, hence, is an interesting candidate for bio-catalysis of carbo-ligation reactions, which are central to synthetic chemistry. An obstacle to overcome for this enzyme to become a truly useful biocatalyst, however, is to relax the very strict dependency of this enzyme on phosphorylated substrates. We have studied herein the role of the non-canonical phosphate-binding site of this enzyme, consisting of Ser238 and Ser239, by site-directed and site-saturation mutagenesis, coupled to kinetic analysis of mutants. In addition, we have performed molecular dynamics simulations on the wild-type and four mutant enzymes, to analyse how mutations at this phosphate-binding site may affect the protein structure and dynamics. Further examination of the S239P mutant revealed that this variant increases the enthalpy change at the transition state, relative to the wild-type enzyme, but concomitant loss in entropy causes an overall relative loss in the TS free energy change. This entropy loss, as measured by the temperature dependence of catalysed rates, was mirrored in both a drastic loss in dynamics of the enzyme, which contributes to phosphate binding, as well as an overall loss in anti-correlated motions distributed over the entire protein. Our combined data suggests that the degree of anticorrelated motions within the DERA structure is coupled to catalytic efficiency in the DERA-catalyzed retro-aldol cleavage reaction, and can be manipulated for engineering purposes.
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Affiliation(s)
- Huan Ma
- Department of Chemistry - BMC , Uppsala University , Box 576 , SE-751 23 Uppsala , Sweden .
| | - Klaudia Szeler
- Department of Cell and Molecular Biology , Uppsala University , Box 596 , SE-751 24 , Uppsala , Sweden .
| | - Shina C L Kamerlin
- Department of Cell and Molecular Biology , Uppsala University , Box 596 , SE-751 24 , Uppsala , Sweden .
| | - Mikael Widersten
- Department of Chemistry - BMC , Uppsala University , Box 576 , SE-751 23 Uppsala , Sweden .
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9
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Barrozo A, Duarte F, Bauer P, Carvalho ATP, Kamerlin SCL. Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily. J Am Chem Soc 2015; 137:9061-76. [PMID: 26091851 PMCID: PMC4513756 DOI: 10.1021/jacs.5b03945] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It is becoming widely accepted that catalytic promiscuity, i.e., the ability of a single enzyme to catalyze the turnover of multiple, chemically distinct substrates, plays a key role in the evolution of new enzyme functions. In this context, the members of the alkaline phosphatase superfamily have been extensively studied as model systems in order to understand the phenomenon of enzyme multifunctionality. In the present work, we model the selectivity of two multiply promiscuous members of this superfamily, namely the phosphonate monoester hydrolases from Burkholderia caryophylli and Rhizobium leguminosarum. We have performed extensive simulations of the enzymatic reaction of both wild-type enzymes and several experimentally characterized mutants. Our computational models are in agreement with key experimental observables, such as the observed activities of the wild-type enzymes, qualitative interpretations of experimental pH-rate profiles, and activity trends among several active site mutants. In all cases the substrates of interest bind to the enzyme in similar conformations, with largely unperturbed transition states from their corresponding analogues in aqueous solution. Examination of transition-state geometries and the contribution of individual residues to the calculated activation barriers suggest that the broad promiscuity of these enzymes arises from cooperative electrostatic interactions in the active site, allowing each enzyme to adapt to the electrostatic needs of different substrates. By comparing the structural and electrostatic features of several alkaline phosphatases, we suggest that this phenomenon is a generalized feature driving selectivity and promiscuity within this superfamily and can be in turn used for artificial enzyme design.
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Affiliation(s)
- Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Fernanda Duarte
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Paul Bauer
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
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10
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Fujihashi M, Mnpotra JS, Mishra RK, Pai EF, Kotra LP. Orotidine Monophosphate Decarboxylase--A Fascinating Workhorse Enzyme with Therapeutic Potential. J Genet Genomics 2015; 42:221-34. [PMID: 26059770 DOI: 10.1016/j.jgg.2015.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 04/13/2015] [Accepted: 04/15/2015] [Indexed: 10/23/2022]
Abstract
Orotidine 5'-monophosphate decarboxylase (ODCase) is known as one of the most proficient enzymes. The enzyme catalyzes the last reaction step of the de novo pyrimidine biosynthesis, the conversion from orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate. The enzyme is found in all three domains of life, Bacteria, Eukarya and Archaea. Multiple sequence alignment of 750 putative ODCase sequences resulted in five distinct groups. While the universally conserved DxKxxDx motif is present in all the groups, depending on the groups, several characteristic motifs and residues can be identified. Over 200 crystal structures of ODCases have been determined so far. The structures, together with biochemical assays and computational studies, elucidated that ODCase utilized both transition state stabilization and substrate distortion to accelerate the decarboxylation of its natural substrate. Stabilization of the vinyl anion intermediate by a conserved lysine residue at the catalytic site is considered the largest contributing factor to catalysis, while bending of the carboxyl group from the plane of the aromatic pyrimidine ring of OMP accounts for substrate distortion. A number of crystal structures of ODCases complexed with potential drug candidate molecules have also been determined, including with 6-iodo-uridine, a potential antimalarial agent.
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Affiliation(s)
- Masahiro Fujihashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Jagjeet S Mnpotra
- Department of Chemistry & Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, 27412, USA
| | - Ram Kumar Mishra
- Center for Molecular Design and Preformulations, and Toronto General Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Lakshmi P Kotra
- Center for Molecular Design and Preformulations, and Toronto General Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada; Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, M5S 3M2, Canada.
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11
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Reyes A, Zhai X, Morgan KT, Reinhardt CJ, Amyes TL, Richard JP. The activating oxydianion binding domain for enzyme-catalyzed proton transfer, hydride transfer, and decarboxylation: specificity and enzyme architecture. J Am Chem Soc 2015; 137:1372-82. [PMID: 25555107 PMCID: PMC4311969 DOI: 10.1021/ja5123842] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 11/29/2022]
Abstract
The kinetic parameters for activation of yeast triosephosphate isomerase (ScTIM), yeast orotidine monophosphate decarboxylase (ScOMPDC), and human liver glycerol 3-phosphate dehydrogenase (hlGPDH) for catalysis of reactions of their respective phosphodianion truncated substrates are reported for the following oxydianions: HPO3(2-), FPO3(2-), S2O3(2-), SO4(2-) and HOPO3(2-). Oxydianions bind weakly to these unliganded enzymes and tightly to the transition state complex (E·S(‡)), with intrinsic oxydianion Gibbs binding free energies that range from -8.4 kcal/mol for activation of hlGPDH-catalyzed reduction of glycolaldehyde by FPO3(2-) to -3.0 kcal/mol for activation of ScOMPDC-catalyzed decarboxylation of 1-β-d-erythrofuranosyl)orotic acid by HOPO3(2-). Small differences in the specificity of the different oxydianion binding domains are observed. We propose that the large -8.4 kcal/mol and small -3.8 kcal/mol intrinsic oxydianion binding energy for activation of hlGPDH by FPO3(2-) and S2O3(2-), respectively, compared with activation of ScTIM and ScOMPDC reflect stabilizing and destabilizing interactions between the oxydianion -F and -S with the cationic side chain of R269 for hlGPDH. These results are consistent with a cryptic function for the similarly structured oxydianion binding domains of ScTIM, ScOMPDC and hlGPDH. Each enzyme utilizes the interactions with tetrahedral inorganic oxydianions to drive a conformational change that locks the substrate in a caged Michaelis complex that provides optimal stabilization of the different enzymatic transition states. The observation of dianion activation by stabilization of active caged Michaelis complexes may be generalized to the many other enzymes that utilize substrate binding energy to drive changes in enzyme conformation, which induce tight substrate fits.
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Affiliation(s)
- Archie
C. Reyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Xiang Zhai
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Kelsey T. Morgan
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Christopher J. Reinhardt
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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12
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Xia G, Ruan C, Wang H. Highly sensitive detection of carbon dioxide by a pyrimido[1,2-a]benzimidazole derivative: combining experimental and theoretical studies. Analyst 2015; 140:5099-104. [DOI: 10.1039/c5an00947b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the present paper, a “light-up” chemsensor with a high specificity for carbon dioxide detection using a pyrimido[1,2-a]benzimidazole derivative (P1H) in liquid media has been developed.
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Affiliation(s)
- Guomin Xia
- College of Chemistry and Institute for Advanced Study
- Nanchang University
- Nanchang, China
| | - Chengyan Ruan
- College of Chemistry and Institute for Advanced Study
- Nanchang University
- Nanchang, China
| | - Hongming Wang
- College of Chemistry and Institute for Advanced Study
- Nanchang University
- Nanchang, China
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13
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Goldman L, Amyes TL, Goryanova B, Gerlt JA, Richard JP. Enzyme architecture: deconstruction of the enzyme-activating phosphodianion interactions of orotidine 5'-monophosphate decarboxylase. J Am Chem Soc 2014; 136:10156-65. [PMID: 24958125 PMCID: PMC4227808 DOI: 10.1021/ja505037v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Indexed: 12/12/2022]
Abstract
The mechanism for activation of orotidine 5'-monophosphate decarboxylase (OMPDC) by interactions of side chains from Gln215 and Try217 at a gripper loop and R235, adjacent to this loop, with the phosphodianion of OMP was probed by determining the kinetic parameters k(cat) and K(m) for all combinations of single, double, and triple Q215A, Y217F, and R235A mutations. The 12 kcal/mol intrinsic binding energy of the phosphodianion is shown to be equal to the sum of the binding energies of the side chains of R235 (6 kcal/mol), Q215 (2 kcal/mol), Y217 (2 kcal/mol), and hydrogen bonds to the G234 and R235 backbone amides (2 kcal/mol). Analysis of a triple mutant cube shows small (ca. 1 kcal/mol) interactions between phosphodianion gripper side chains, which are consistent with steric crowding of the side chains around the phosphodianion at wild-type OMPDC. These mutations result in the same change in the activation barrier to the OMPDC-catalyzed reactions of the whole substrate OMP and the substrate pieces (1-β-D-erythrofuranosyl)orotic acid (EO) and phosphite dianion. This shows that the transition states for these reactions are stabilized by similar interactions with the protein catalyst. The 12 kcal/mol intrinsic phosphodianion binding energy of OMP is divided between the 8 kcal/mol of binding energy, which is utilized to drive a thermodynamically unfavorable conformational change of the free enzyme, resulting in an increase in (k(cat))(obs) for OMPDC-catalyzed decarboxylation of OMP, and the 4 kcal/mol of binding energy, which is utilized to stabilize the Michaelis complex, resulting in a decrease in (K(m))(obs).
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Affiliation(s)
- Lawrence
M. Goldman
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Bogdana Goryanova
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John A. Gerlt
- Departments
of Biochemistry and Chemistry, University
of Illinois, Urbana, Illinois 61801, United
States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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14
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Richard JP, Amyes TL, Goryanova B, Zhai X. Enzyme architecture: on the importance of being in a protein cage. Curr Opin Chem Biol 2014; 21:1-10. [PMID: 24699188 DOI: 10.1016/j.cbpa.2014.03.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/01/2014] [Indexed: 11/30/2022]
Abstract
Substrate binding occludes water from the active sites of many enzymes. There is a correlation between the burden to enzymatic catalysis of deprotonation of carbon acids and the substrate immobilization at solvent-occluded active sites for ketosteroid isomerase (KSI--small burden, substrate pKa=13), triosephosphate isomerase (TIM, substrate pKa≈18) and diaminopimelate epimerase (DAP epimerase, large burden, substrate pKa≈29) catalyzed reaction. KSI binds substrates at a surface cleft, TIM binds substrate at an exposed 'cage' formed by closure of flexible loops; and, DAP epimerase binds substrate in a tight cage formed by an 'oyster-like' clamping motion of protein domains. Directed evolution of a solvent-occluded active site at a designed protein catalyst of the Kemp elimination reaction is discussed.
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA.
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - Bogdana Goryanova
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - Xiang Zhai
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
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15
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Zhai X, Amyes TL, Richard JP. Enzyme architecture: remarkably similar transition states for triosephosphate isomerase-catalyzed reactions of the whole substrate and the substrate in pieces. J Am Chem Soc 2014; 136:4145-8. [PMID: 24588650 PMCID: PMC3985921 DOI: 10.1021/ja501103b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Values of (kcat/Km)GAP for triosephosphate
isomerase-catalyzed reactions
of (R)-glyceraldehyde 3-phosphate and kcat/KHPiKGA for reactions of the substrate pieces glycolaldehyde
and HPO32– have been determined for wild-type
and the following TIM mutants: I172V, I172A, L232A, and P168A (TIM
from Trypanosoma brucei brucei); a
208-TGAG for 208-YGGS loop 7 replacement mutant (L7RM, TIM from chicken
muscle); and, Y208T, Y208S, Y208A, Y208F and S211A (yeast TIM). A
superb linear logarithmic correlation, with slope of 1.04 ± 0.03,
is observed between the kinetic parameters for wild-type and most
mutant enzymes, with positive deviations for L232A and L7RM. The unit
slope shows that most mutations result in an identical change in the
activation barriers for the catalyzed reactions of whole substrate
and substrate pieces, so that the two transition states are stabilized
by similar interactions with the protein catalyst. This is consistent
with a role for dianions as active spectators, which hold TIM in a
catalytically active caged form.
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Affiliation(s)
- Xiang Zhai
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
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