(Q27644728)

English

A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization

scientific article

In more languages

Statements

scholarly article

0 references

A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization (English)

0 references

0 references

author name string

Andrew T Torelli

1

0 references

Jolanta Krucinska

2

0 references

Joseph E Wedekind

3

0 references

language of work or name

0 references

publication date

July 2007

0 references

0 references

13

0 references

1052-70

0 references

7

0 references

Crystal structure of the leadzyme at 1.8 A resolution: metal ion binding and the implications for catalytic mechanism and allo site ion regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

The course of phosphorus in the reaction of N-acetyl-L-glutamate kinase, determined from the structures of crystalline complexes, including a complex with an AlF(4)(-) transition state mimic

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Tools for the automatic identification and classification of RNA base pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Ligand-induced structural changes in adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Transition state stabilization by a catalytic RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Artificial evolution of an enzyme active site: structural studies of three highly active mutants of Escherichia coli alkaline phosphatase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

A model of the transition state in the alkaline phosphatase reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

The sulfuryl transfer mechanism. Crystal structure of a vanadate complex of estrogen sulfotransferase and mutational analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

X-ray structure of the magnesium(II).ADP.vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Crystal structures of rat acid phosphatase complexed with the transition-state analogs vanadate and molybdate. Implications for the reaction mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

X-ray structures of the myosin motor domain of Dictyostelium discoideum complexed with MgADP.BeFx and MgADP.AlF4-

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Enzyme-Catalyzed Phosphoryl Transfer Reactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Raster3D: photorealistic molecular graphics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Detection, delineation, measurement and display of cavities in macromolecular structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

The CCP4 suite: programs for protein crystallography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

The finer things in X-ray diffraction data collection

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Further additions to MolScript version 1.4, including reading and contouring of electron-density maps

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Improved methods for building protein models in electron density maps and the location of errors in these models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Ribozyme structures and mechanisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Structural basis of glmS ribozyme activation by glucosamine-6-phosphate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Tertiary contacts distant from the active site prime a ribozyme for catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Functional involvement of G8 in the hairpin ribozyme cleavage mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

Enzyme catalysis: not different, just better

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

20 March 2017

The Cambridge Structural Database: a quarter of a million crystal structures and rising

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

7 April 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

27 November 2018

Active site labeling of G8 in the hairpin ribozyme: implications for structure and mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

A Trojan horse transition state analogue generated by MgF3- formation in an enzyme active site.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Trapped water molecules are essential to structural dynamics and function of a ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Radiation damage in macromolecular cryocrystallography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Nucleobase catalysis in ribozyme mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

When to believe what you see.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Enzyme inhibitors as chemical tools to study enzyme catalysis: rational design, synthesis, and applications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

The catalytic diversity of RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Role of an active site adenine in hairpin ribozyme catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Ribozyme catalysis: not different, just worse

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

The power of vanadate in crystallographic investigations of phosphoryl transfer enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

The chemistry and biochemistry of vanadium and the biological activities exerted by vanadium compounds

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

The hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

The catalytic mechanism of the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

The role of metal ions in RNA catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Comparative analysis of hairpin ribozyme structures and interference data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Sodium alpha-glucoheptonate dihydrate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Mg2+-independent hairpin ribozyme catalysis in hydrated RNA films.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Ribozyme cleavage of a 2,5-phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Structure and function of the hammerhead ribozyme: an unfinished story

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Active site of RNase: neutron diffraction study of a complex with uridine vanadate, a transition-state analog

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Specific association between an endoribonucleolytic sequence from a satellite RNA and a substrate analogue containing a 2'-5' phosphodiester

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

29 September 2017

Pentavalent Organo-Vanadates as Transition State Analogues for Phosphoryl Transfer Reactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

2 June 2018

Nucleobase catalysis in the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

2 June 2018

Rapid loss of structural motifs in the manganese complex of oxygenic photosynthesis by X-ray irradiation at 10-300 K.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

2 June 2018

Rescue of an abasic hairpin ribozyme by cationic nucleobases: evidence for a novel mechanism of RNA catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

2 June 2018

Purification, crystallization, and X-ray diffraction analysis of small ribozymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

2 June 2018

Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

2 June 2018

General acid catalysis by the hepatitis delta virus ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

27 November 2018

Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

27 November 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

27 November 2018

Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

27 November 2018

A conformational switch controls hepatitis delta virus ribozyme catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

27 November 2018

Catalytic properties of hairpin ribozymes derived from Chicory yellow mottle virus and arabis mosaic virus satellite RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1894929

27 November 2018

Specificity of the hairpin ribozyme. Sequence requirements surrounding the cleavage site

1 reference

https://pubmed.ncbi.nlm.nih.gov/17488874

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium

1 reference

https://pubmed.ncbi.nlm.nih.gov/17488874

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/17488874

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Solid state coordination chemistry: structural consequences of variations in tether length in the oxovanadium-copper-bisterpy-[O3P(CH2)nPO3]4- system, n= 1-6 (bisterpy = 2,2':4',4'':2'',2'''-quarterpyridyl-6',6''-di-2-pyridine)

1 reference

https://pubmed.ncbi.nlm.nih.gov/17488874

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/17488874

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Role of Solvent Dynamics in Stabilizing the Transition State of RNA Hydrolysis by Hairpin Ribozyme.

1 reference

https://pubmed.ncbi.nlm.nih.gov/17488874

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Enzymatic Catalysis and Transition-State Theory

1 reference

https://pubmed.ncbi.nlm.nih.gov/17488874

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The geometry of the transition state in the hydrolysis of phosphate esters

1 reference

https://pubmed.ncbi.nlm.nih.gov/17488874

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Pb(II)-catalysed cleavage of the sugar–phosphate backbone of yeast tRNAPhe—implications for lead toxicity and self-splicing RNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/17488874

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Purine functional groups in essential residues of the hairpin ribozyme required for catalytic cleavage of RNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/17488874

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Four ribose 2'-hydroxyl groups essential for catalytic function of the hairpin ribozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/17488874

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The solvent-protected core of the hairpin ribozyme-substrate complex

1 reference

https://pubmed.ncbi.nlm.nih.gov/17488874

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1261/RNA.510807

0 references

0 references

0 references

ResearchGate publication ID

0 references

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q27644728&oldid=1954733880"