(Q27652755)

English

Specificity and Reactivity in Menaquinone Biosynthesis: The Structure of Escherichia coli MenD (2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase)

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scholarly article

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25 December 2019

Specificity and reactivity in menaquinone biosynthesis: the structure of Escherichia coli MenD (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase) (English)

1 reference

Europe PubMed Central

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25 December 2019

Escherichia coli

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William Nigel Hunter

3

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25 December 2019

author name string

Alice Dawson

1

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25 December 2019

Paul K Fyfe

2

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25 December 2019

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publication date

1 November 2008

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25 December 2019

number of pages

16

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Journal of Molecular Biology

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25 December 2019

384

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25 December 2019

1353-1368

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25 December 2019

5

1 reference

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25 December 2019

Structure of isochorismate synthase in complex with magnesium

1 reference

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Glyoxylate carboligase lacks the canonical active site glutamate of thiamine-dependent enzymes

1 reference

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20 March 2017

Structure ofStaphylococcus aureus1,4-dihydroxy-2-naphthoyl-CoA synthase (MenB) in complex with acetoacetyl-CoA

1 reference

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20 March 2017

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1 reference

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MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

Lysine 190 is the catalytic base in MenF, the menaquinone-specific isochorismate synthase from Escherichia coli: implications for an enzyme family

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

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1 reference

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20 March 2017

Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis

1 reference

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Modern analytical ultracentrifugation in protein science: a tutorial review

1 reference

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1 reference

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Electrostatics of nanosystems: application to microtubules and the ribosome

1 reference

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The high-resolution crystal structure of the molybdate-dependent transcriptional regulator (ModE) from Escherichia coli: a novel combination of domain folds

1 reference

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20 March 2017

The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes

1 reference

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20 March 2017

Inference of macromolecular assemblies from crystalline state

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

The Buccaneer software for automated model building. 1. Tracing protein chains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

Scaling and assessment of data quality

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

Coot: model-building tools for molecular graphics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

Refinement of macromolecular structures by the maximum-likelihood method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

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=3656419

20 March 2017

PRODRG: a tool for high-throughput crystallography of protein-ligand complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

Maximum-likelihood density modification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

Size-Distribution Analysis of Macromolecules by Sedimentation Velocity Ultracentrifugation and Lamm Equation Modeling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

Remarks about protein structure precision

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

Automated MAD and MIR structure solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

Dali: a network tool for protein structure comparison

1 reference

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20 March 2017

Solvent content of protein crystals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

Vitamin K-dependent gamma-glutamylcarboxylation: an ancient posttranslational modification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

Structure of naphthoate synthase (MenB) from Mycobacterium tuberculosis in both native and product-bound forms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

20 March 2017

The universal protein resource (UniProt)

1 reference

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7 April 2017

Determination of the stereochemistry of 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate, a key intermediate in menaquinone biosynthesis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

29 September 2017

Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

29 September 2017

Structure, mechanism and catalytic duality of thiamine-dependent enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

29 September 2017

The 1',4'-iminopyrimidine tautomer of thiamin diphosphate is poised for catalysis in asymmetric active centers on enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

29 September 2017

The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

29 September 2017

Crystallization and preliminary X-ray analysis of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase (MenD) from Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

29 September 2017

Current mechanistic understanding of thiamin diphosphate-dependent enzymatic reactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

29 September 2017

Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): a perspective on enzymatic mechanisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

29 September 2017

Microbial ubiquinones: multiple roles in respiration, gene regulation and oxidative stress management

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

29 September 2017

Three-dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 A resolution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

2 June 2018

Identification and characterization of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase in the menaquinone biosynthesis of Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

27 November 2018

Changes in the redox state and composition of the quinone pool of Escherichia coli during aerobic batch-culture growth.

1 reference

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27 November 2018

Structure and mechanism of the ThDP-dependent benzaldehyde lyase from Pseudomonas fluorescens

1 reference

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27 November 2018

A molecular switch and proton wire synchronize the active sites in thiamine enzymes

1 reference

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27 November 2018

Tetrahedral intermediates in thiamin diphosphate-dependent decarboxylations exist as a 1',4'-imino tautomeric form of the coenzyme, unlike the michaelis complex or the free coenzyme.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656419

27 November 2018

Steady-State Kinetics and Molecular Evolution of Escherichia coli MenD [(1R,6R)-2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate Synthase], an Anomalous Thiamin Diphosphate-Dependent Decarboxylase−Carboligase

1 reference

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27 November 2018

Domain relationships in thiamine diphosphate-dependent enzymes

1 reference

https://pubmed.ncbi.nlm.nih.gov/18983854

12 December 2020

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The crystal structure of thiamine pyrophosphate

1 reference

https://pubmed.ncbi.nlm.nih.gov/18983854

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A thiamin diphosphate binding fold revealed by comparison of the crystal structures of transketolase, pyruvate oxidase and pyruvate decarboxylase

1 reference

https://pubmed.ncbi.nlm.nih.gov/18983854

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The biosynthesis of shikimate metabolites

1 reference

https://pubmed.ncbi.nlm.nih.gov/18983854

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

How Thiamin Diphosphate Is Activated in Enzymes

1 reference

https://pubmed.ncbi.nlm.nih.gov/18983854

12 December 2020

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1 reference

https://pubmed.ncbi.nlm.nih.gov/18983854

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1016/J.JMB.2008.10.048

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Europe PubMed Central

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25 December 2019

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Europe PubMed Central

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25 December 2019

1 reference

Europe PubMed Central

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25 December 2019

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