Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6

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Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6 is …
instance of (P31):
scholarly articleQ13442814

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P819ADS bibcode2014PLoSO...992249S
P356DOI10.1371/JOURNAL.PONE.0092249
P932PMC publication ID3962378
P698PubMed publication ID24657997
P5875ResearchGate publication ID261033671

P50authorEiji MasaiQ42634099
P2093author name stringKeisuke Sugimoto
Masao Fukuda
Toshiya Senda
Miki Senda
Daisuke Kasai
P2860cites workAcid-base catalysis in the extradiol catechol dioxygenase reaction mechanism: site-directed mutagenesis of His-115 and His-179 in Escherichia coli 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB).Q45112105
Evolution of a new bacterial pathway for 4-nitrotoluene degradationQ46272784
Combined spectroscopic/computational studies on Fe- and Mn-dependent superoxide dismutases: insights into second-sphere tuning of active site properties.Q54502825
Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditionsQ27619532
Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenaseQ27631079
Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenaseQ27639570
Crystal Structures of Fe2+ Dioxygenase Superoxo, Alkylperoxo, and Bound Product IntermediatesQ27644520
Swapping metals in Fe- and Mn-dependent dioxygenases: Evidence for oxygen activation without a change in metal redox stateQ27650648
A hyperactive cobalt-substituted extradiol-cleaving catechol dioxygenaseQ27666296
Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonadQ27729302
Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102Q27732711
Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanolQ27766353
Refinement of macromolecular structures by the maximum-likelihood methodQ27861011
PHENIX: building new software for automated crystallographic structure determinationQ27861044
Features and development of CootQ27861079
The CCP4 suite: programs for protein crystallographyQ27861090
Characterizing the promiscuity of LigAB, a lignin catabolite degrading extradiol dioxygenase from Sphingomonas paucimobilis SYK-6Q28659011
MOLREP: an Automated Program for Molecular ReplacementQ29642797
Thermophilic adaptation of proteinsQ34188393
Evolutionary relationships among extradiol dioxygenasesQ35614251
Crystallization and preliminary X-ray analysis of the reduced Rieske-type [2Fe-2S] ferredoxin derived from Pseudomonas sp. strain KKS102.Q36580630
Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds.Q36703545
Mechanism of extradiol aromatic ring-cleaving dioxygenasesQ37039723
Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenasesQ37096285
Crystallization and preliminary crystallographic analysis of gallate dioxygenase DesB from Sphingobium sp. SYK-6.Q37420359
Characterization of the 3-O-methylgallate dioxygenase gene and evidence of multiple 3-O-methylgallate catabolic pathways in Sphingomonas paucimobilis SYK-6.Q41073376
Characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6.Q41835059
Definitive evidence for monoanionic binding of 2,3-dihydroxybiphenyl to 2,3-dihydroxybiphenyl 1,2-dioxygenase from UV resonance Raman spectroscopy, UV/Vis absorption spectroscopy, and crystallography.Q43915522
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P433issue3
P407language of work or nameEnglishQ1860
P304page(s)e92249
P577publication date2014-01-01
P1433published inPLOS OneQ564954
P1476titleMolecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6
P478volume9

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cites work (P2860)
Q57818201Anaerobic Protein Purification and Kinetic Analysis via Oxygen Electrode for Studying DesB Dioxygenase Activity and Inhibition
Q50101369Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism
Q51117645Characterization of an extradiol dioxygenase involved in the catabolism of lignin-derived biphenyl.
Q51291151Crystal structure of the TK2203 protein from Thermococcus kodakarensis, a putative extradiol dioxygenase.
Q97652798Iron acquisition system of Sphingobium sp. strain SYK-6, a degrader of lignin-derived aromatic compounds
Q38958193Proteins analysed as virtual knots
Q51551281Purification and partial characterization of the extradiol dioxygenase, 2'-carboxy-2,3-dihydroxybiphenyl 1,2-dioxygenase, in the fluorene degradation pathway from Rhodococcus sp. strain DFA3.
Q91619811Regulation of vanillate and syringate catabolism by a MarR-type transcriptional regulator DesR in Sphingobium sp. SYK-6
Q27701537Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold

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