(Q27658062)

English

X-ray Crystallographic Analysis of the 6-Aminohexanoate Cyclic Dimer Hydrolase: CATALYTIC MECHANISM AND EVOLUTION OF AN ENZYME RESPONSIBLE FOR NYLON-6 BYPRODUCT DEGRADATION

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X-ray Crystallographic Analysis of the 6-Aminohexanoate Cyclic Dimer Hydrolase: CATALYTIC MECHANISM AND EVOLUTION OF AN ENZYME RESPONSIBLE FOR NYLON-6 BYPRODUCT DEGRADATION (English)

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author name string

Kengo Yasuhira

1

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Naoki Shibata

2

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Go Mongami

3

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Yuki Uedo

4

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Yu Atsumi

5

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Yasuyuki Kawashima

6

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Atsushi Hibino

7

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Yusuke Tanaka

8

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Young-Ho Lee

9

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Dai-ichiro Kato

10

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Masahiro Takeo

11

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Yoshiki Higuchi

12

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Seiji Negoro

13

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language of work or name

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publication date

8 January 2010

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Journal of Biological Chemistry

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285

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2

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1239-48

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Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a β-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

20 March 2017

Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

20 March 2017

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=2801252

20 March 2017

Hydrolysis of third-generation cephalosporins by class C beta-lactamases. Structures of a transition state analog of cefotoxamine in wild-type and extended spectrum enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

20 March 2017

The crystal structure of phosphonate-inhibited D-Ala-D-Ala peptidase reveals an analogue of a tetrahedral transition state

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

20 March 2017

Structural adaptations in a membrane enzyme that terminates endocannabinoid signaling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

20 March 2017

An alternative mechanism for amidase signature enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

20 March 2017

Structure of malonamidase E2 reveals a novel Ser-cisSer-Lys catalytic triad in a new serine hydrolase fold that is prevalent in nature

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

20 March 2017

An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

20 March 2017

EstB from Burkholderia gladioli: A novel esterase with a β-lactamase fold reveals steric factors to discriminate between esterolytic and β-lactam cleaving activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

20 March 2017

Elimination of the hydrolytic water molecule in a class A beta-lactamase mutant: crystal structure and kinetics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

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=2801252

20 March 2017

Plasmid dependence of Pseudomonas sp. strain NK87 enzymes that degrade 6-aminohexanoate-cyclic dimer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

20 March 2017

6-Aminohexanoate oligomer hydrolases from the alkalophilic bacteria Agromyces sp. strain KY5R and Kocuria sp. strain KY2.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

29 September 2017

Crystallization and X-ray diffraction analysis of 6-aminohexanoate-cyclic-dimer hydrolase from Arthrobacter sp. KI72.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

29 September 2017

A second fatty acid amide hydrolase with variable distribution among placental mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

29 September 2017

Nucleotide sequences of the Pseudomonas savastanoi indoleacetic acid genes show homology with Agrobacterium tumefaciens T-DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

29 September 2017

X-ray crystallographic analysis of 6-aminohexanoate-dimer hydrolase: molecular basis for the birth of a nylon oligomer-degrading enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

29 September 2017

Biodegradation of nylon oligomers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

29 September 2017

Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

29 September 2017

High homology between 6-aminohexanoate-cyclic-dimer hydrolases of Flavobacterium and Pseudomonas strains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

29 September 2017

6-Aminohexanoic acid cyclic dimer hydrolase. A new cyclic amide hydrolase produced by Achromobacter guttatus KI74

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

29 September 2017

Bacterial lipolytic enzymes: classification and properties

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

2 June 2018

A plasmid encoding enzymes for nylon oligomer degradation: nucleotide sequence and analysis of pOAD2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

2 June 2018

A general method for introducing a series of mutations into cloned DNA using the polymerase chain reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2801252

2 June 2018

Structural basis for tRNA-dependent amidotransferase function.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M109.041285

21 January 2018

The signature amidase from Sulfolobus solfataricus belongs to the CX3C subgroup of enzymes cleaving both amides and nitriles. Ser195 and Cys145 are predicted to be the active site nucleophiles

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M109.041285

21 January 2018

The screening, characterization, and use of omega-laurolactam hydrolase: a new enzymatic synthesis of 12-aminolauric acid

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M109.041285

21 January 2018

A novel aryl acylamidase from Nocardia farcinica hydrolyses polyamide

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M109.041285

21 January 2018

Processing of X-ray diffraction data collected in oscillation mode

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M109.041285

21 January 2018

[27] Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M109.041285

21 January 2018

Identification of Glu166 as the general base in the acylation reaction of class A beta-lactamases through QM/MM modeling

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M109.041285

21 January 2018

Genetic organization of nylon-oligomer-degrading enzymes from alkalophilic bacterium, Agromyces sp. KY5R.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M109.041285

21 January 2018

Mutational analysis of 6-aminohexanoate-dimer hydrolase: relationship between nylon oligomer hydrolytic and esterolytic activities.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M109.041285

21 January 2018

Molecular design of a nylon-6 byproduct-degrading enzyme from a carboxylesterase with a beta-lactamase fold.

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M109.041285

21 January 2018

PROCHECK: a program to check the stereochemical quality of protein structures

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M109.041285

21 January 2018

Ammonia channel couples glutaminase with transamidase reactions in GatCAB

1 reference

https://pubmed.ncbi.nlm.nih.gov/19889645

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Arg-158 is critical in both binding the substrate and stabilizing the transition-state oxyanion for the enzymatic reaction of malonamidase E2

1 reference

https://pubmed.ncbi.nlm.nih.gov/19889645

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Arabidopsis amidase 1, a member of the amidase signature family

1 reference

https://pubmed.ncbi.nlm.nih.gov/19889645

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The catalytic mechanism of amidase also involves nitrile hydrolysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/19889645

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1074/JBC.M109.041285

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