Evidence map›Paper›PMID 19923719›Full record

ArticleActa crystallographica. Section D, Biological crystallography2009

A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase.

Artem Y Lyubimov, Lin Chen, Nicole S Sampson, Alice Vrielink

Abstract read
In one paragraph

Article in Acta crystallographica. Section D, Biological crystallography, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Crystallization and preliminary X-ray analysis of pyridoxine 4-oxidase, the first enzyme in pyridoxine degradation pathway I.Acta crystallographica. Section F, Structural biology and crystallization communications · 2012
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Artem Y LyubimovDepartment of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Sinsheimer Laboratories, Santa Cruz, CA 95064, USA.
Lin Chen
Nicole S Sampson
Alice Vrielink

Funding

CHOLESTEROL OXIDASE LOOP RESIDUES &CATALYSISR01HL053306 · NHLBI · STATE UNIVERSITY NEW YORK STONY BROOK · PI SAMPSON, NICOLE S · 2001 to 2009
$2.6M
NHLBI NIH HHS R01 HL053306
6 · The paper itself

Abstract

Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3beta-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH...pi interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall k(cat). Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 A resolution) reveals significant perturbations in the active site. As predicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and Glu361 form unusual hydrogen bonds to the functional group of Asp485 and are displaced from the positions they occupy in the wild-type active site. The overall effect is to disrupt the stabilization of the reduced FAD cofactor during catalysis. Furthermore, a narrow transient channel that is shown to form when the wild-type Asn485 forms the NH...pi interaction with FAD and that has been proposed to function as an access route of molecular oxygen, is not observed in either of the mutant structures, suggesting that the dynamics of the active site are altered.

Indexed as

BiocatalysisCholesterol OxidaseCrystallography, X-RayHydrogen BondingHydrogen-Ion ConcentrationIsomerismModels, MolecularMutationOxidation-ReductionProtein Structure, TertiaryCholesterol Oxidase

Identifiers

PMID19923719
PMCPMC3089011

What OpenQuestion holds

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.