Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole (Q27652268)

6

0 references

Brandon Pybus

4

0 references

Daniel Herschlag

8

0 references

Jose M.m. Caaveiro

3

object named as

Jose M M Caaveiro

0 references

Paul A. Sigala

object named as

Paul A Sigala

1

0 references

Daniel A Kraut

object named as

Daniel A Kraut

2

0 references

author name string

Eliza A Ruben

Journal of the American Chemical Society

5

0 references

language of work or name

English

0 references

publication date

15 October 2008

0 references

published in

0 references

volume

130

0 references

page(s)

13696-708

0 references

issue

41

0 references

cites work

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Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole

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Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation

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X-ray structure of a serine protease acyl-enzyme complex at 0.95-A resolution

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Atomic (0.94 A) resolution structure of an inverting glycosidase in complex with substrate

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X-ray snapshots of serine protease catalysis reveal a tetrahedral intermediate

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Atomic resolution structure of native porcine pancreatic elastase at 1.1 A

20 March 2017

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Anatomy of a proficient enzyme: The structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog

20 March 2017

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Crystal structure of delta(5)-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin settles the correct hydrogen bonding scheme for transition state stabilization

20 March 2017

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Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase

20 March 2017

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Inhibition of elastase by N-sulfonylaryl beta-lactams: anatomy of a stable acyl-enzyme complex

20 March 2017

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Conformational changes in the crystal structure of rat glutathione transferase M1-1 with global substitution of 3-fluorotyrosine for tyrosine

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Crystal structure and enzyme mechanism of Delta 5-3-ketosteroid isomerase from Pseudomonas testosteroni

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Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates

20 March 2017

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Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis

20 March 2017

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Crystal structure of bovine low molecular weight phosphotyrosyl phosphatase complexed with the transition state analog vanadate

20 March 2017

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Use of 19F NMR to probe protein structure and conformational changes

20 March 2017

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A covalent enzyme-substrate intermediate with saccharide distortion in a mutant T4 lysozyme

20 March 2017

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Phasercrystallographic software

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Coot: model-building tools for molecular graphics

20 March 2017

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Refinement of macromolecular structures by the maximum-likelihood method

20 March 2017

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1H, 13C and 15N chemical shift referencing in biomolecular NMR

20 March 2017

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Calculation of protein extinction coefficients from amino acid sequence data

20 March 2017

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Catalytic proficiency: the unusual case of OMP decarboxylase

20 March 2017

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Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A

20 March 2017

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20 March 2017

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A low-barrier hydrogen bond in the catalytic triad of serine proteases

20 March 2017

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Do ligand binding and solvent exclusion alter the electrostatic character within the oxyanion hole of an enzymatic active site?

20 March 2017

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Progress in computational protein design

29 September 2017

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The geometry of interactions between catalytic residues and their substrates

29 September 2017

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Structural origins of efficient proton abstraction from carbon by a catalytic antibody

29 September 2017

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High-resolution crystallography and drug design

29 September 2017

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Structural and spectral response of Aequorea victoria green fluorescent proteins to chromophore fluorination.

29 September 2017

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Probing the Ser-Ser-Lys catalytic triad mechanism of peptide amidase: computational studies of the ground state, transition state, and intermediate

29 September 2017

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29 September 2017

1 reference

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De novo design of catalytic proteins

29 September 2017

1 reference

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Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?

29 September 2017

1 reference

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Catalysis by enzyme conformational change as illustrated by orotidine 5′-monophosphate decarboxylase

29 September 2017

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The rate of hydrolysis of phosphomonoester dianions and the exceptional catalytic proficiencies of protein and inositol phosphatases

29 September 2017

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Molecular dynamic study of orotidine-5'-monophosphate decarboxylase in ground state and in intermediate state: a role of the 203-218 loop dynamics

29 September 2017

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Probing protein electrostatics with a synthetic fluorescent amino acid.

29 September 2017

1 reference

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De novo design of biocatalysts

29 September 2017

1 reference

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Atomic motion in enzymatic reaction coordinates

29 September 2017

1 reference

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The structural basis for the remarkable catalytic proficiency of orotidine 5'-monophosphate decarboxylase

29 September 2017

1 reference

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Low dielectric response in enzyme active site

29 September 2017

1 reference

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Impaired transition state complementarity in the hydrolysis of O-arylphosphorothioates by protein-tyrosine phosphatases.

29 September 2017

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High-precision measurement of hydrogen bond lengths in proteins by nuclear magnetic resonance methods

29 September 2017

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Substituent effects on the binding of phenols to the D38N mutant of 3-oxo-delta5-steroid isomerase. A probe for the nature of hydrogen bonding to the intermediate

29 September 2017

1 reference

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Effects of both shortening and lengthening the active site nucleophile of Bacillus circulans xylanase on catalytic activity.

29 September 2017

1 reference

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Low-barrier hydrogen bonds and enzymic catalysis

29 September 2017

1 reference

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Crystal structure of the mutant yeast triosephosphate isomerase in which the catalytic base glutamic acid 165 is changed to aspartic acid

29 September 2017

1 reference

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The Cys(X)5Arg catalytic motif in phosphoester hydrolysis

29 September 2017

1 reference

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Dynamics of proteins: elements and function

29 September 2017

1 reference

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Conformational mechanisms for free energy transduction in protein systems: old ideas and new facts

29 September 2017

1 reference

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Crystallographic studies of the activity of hen egg-white lysozyme

29 September 2017

1 reference

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Estimation of the polarity of the protein interior by optical spectroscopy

29 September 2017

1 reference

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Transition-state stabilization in the mechanism of tyrosyl-tRNA synthetase revealed by protein engineering

29 September 2017

1 reference

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Enzymes work by solvation substitution rather than by desolvation

29 September 2017

1 reference

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Electrostatic effects in proteins

29 September 2017

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Crystallographic studies of the dynamic properties of lysozyme

29 September 2017

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Temperature-dependent X-ray diffraction as a probe of protein structural dynamics

29 September 2017

1 reference

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A model for thyroid hormone-receptor interactions

29 September 2017

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Transition state analog inhibitors and enzyme catalysis

29 September 2017

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Properties of thiol-subtilisin. The consequences of converting the active serine residue to cysteine in a serine protease

29 September 2017

1 reference

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Catalysis, binding and enzyme-substrate complementarity.

2 June 2018

1 reference

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Use of binding energy in catalysis analyzed by mutagenesis of the tyrosyl-tRNA synthetase.

2 June 2018

1 reference

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Structural comparisons of complexes of methotrexate analogues with Lactobacillus casei dihydrofolate reductase by two-dimensional 1H NMR at 500 MHz.

2 June 2018

1 reference

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Fluorine nuclear magnetic resonance of fluorinated ligands

2 June 2018

1 reference

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Mutation of essential catalytic residues in pig citrate synthase

2 June 2018

1 reference

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Subangstrom crystallography reveals that short ionic hydrogen bonds, and not a His-Asp low-barrier hydrogen bond, stabilize the transition state in serine protease catalysis.

2 June 2018

1 reference

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Positional ordering of reacting groups contributes significantly to the efficiency of proton transfer at an antibody active site

27 November 2018

1 reference

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X-ray structure of a ribonuclease A-uridine vanadate complex at 1.3 A resolution.

27 November 2018

1 reference

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Short hydrogen bonds in photoactive yellow protein

27 November 2018

1 reference

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The 0.83 A resolution crystal structure of alpha-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700827

Computational study of ketosteroid isomerase: insights from molecular dynamics simulation of enzyme bound substrate and intermediate.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700827

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.

27 November 2018

1 reference

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Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization.

27 November 2018

1 reference

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Noncoded amino acid replacement probes of the aspartate aminotransferase mechanism

27 November 2018

1 reference

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Reaction energetics of a mutant triosephosphate isomerase in which the active-site glutamate has been changed to aspartate

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700827

Role of Catalytic Residues in Enzymatic Mechanisms of Homologous Ketosteroid Isomerases†,‡

27 November 2018

1 reference

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Theoretical Investigation of the Relationship between Proton NMR Chemical Shift and Hydrogen Bond Strength

1 reference

12 December 2020

Forces, bond lengths, and reactivity: fundamental insight into the mechanism of enzyme catalysis

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Covalent versus Electrostatic Nature of the Strong Hydrogen Bond: Discrimination among Single, Double, and Asymmetric Single-Well Hydrogen Bonds by Variable-Temperature X-ray Crystallographic Methods in β-Diketone Enol RAHB Systems

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Processing of X-ray diffraction data collected in oscillation mode

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12 December 2020

Study of protein dynamics by X-ray diffraction

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Enzymatic Catalysis and Transition-State Theory

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Leaving group specificity in the chymotrypsin-catalyzed hydrolysis of peptides. Stereochemical interpretation

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12 December 2020

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Subtilisin. Stereochemical mechanism involving transition-state stabilization

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The Reactivity of Thiol-subtilisin, an Enzyme Containing a Synthetic Functional Group*

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12 December 2020

Details of the acyl-enzyme intermediate and the oxyanion hole in serine protease catalysis

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12 December 2020

Effects of tyrosine ring fluorination on rates and equilibria of formation of intermediates in the reactions of carbon-carbon lyases

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Gas-phase ionic reactions: dynamics and mechanism of nucleophilic displacements

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12 December 2020