Copper–oxygen Dynamics in Tyrosinase

2019 ◽  
Author(s):  
Nobutaka Fujieda ◽  
Sachiko Yanagisawa ◽  
Minoru Kubo ◽  
Genji Kurisu ◽  
Shinobu Itoh
Keyword(s):  
Catalytic Mechanism ◽  
Substrate Binding ◽  
Active Form ◽  
Copper Ion ◽  
Atomic Resolution ◽  
Oxygen Species ◽  
X Ray ◽  
Oxygen Dynamics ◽  
Insight Into ◽  
Copper Centre

To unveil the activation of dioxygen on the copper centre (Cu<sub>2</sub>O<sub>2</sub>core) of tyrosinase, we performed X-ray crystallograpy with active-form tyrosinase at near atomic resolution. This study provided a novel insight into the catalytic mechanism of the tyrosinase, including the rearrangement of copper-oxygen species as well as the intramolecular migration of copper ion induced by substrate-binding.<br>

scholarly journals Copper–oxygen Dynamics in Tyrosinase

2019 ◽  
Author(s):  
Nobutaka Fujieda ◽  
Sachiko Yanagisawa ◽  
Minoru Kubo ◽  
Genji Kurisu ◽  
Shinobu Itoh
Keyword(s):  
Catalytic Mechanism ◽  
Substrate Binding ◽  
Active Form ◽  
Copper Ion ◽  
Atomic Resolution ◽  
Oxygen Species ◽  
X Ray ◽  
Oxygen Dynamics ◽  
Insight Into ◽  
Copper Centre

To unveil the activation of dioxygen on the copper centre (Cu<sub>2</sub>O<sub>2</sub>core) of tyrosinase, we performed X-ray crystallograpy with active-form tyrosinase at near atomic resolution. This study provided a novel insight into the catalytic mechanism of the tyrosinase, including the rearrangement of copper-oxygen species as well as the intramolecular migration of copper ion induced by substrate-binding.<br>

scholarly journals An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures

2021 ◽  
Vol 7 (1) ◽  
pp. eabd8523
Author(s):  
Samuel L. Rose ◽  
Svetlana V. Antonyuk ◽  
Daisuke Sasaki ◽  
Keitaro Yamashita ◽  
Kunio Hirata ◽  
...  
Keyword(s):  
Bound States ◽  
Catalytic Mechanism ◽  
Catalytic Efficiency ◽  
Atomic Resolution ◽  
Reaction Intermediates ◽  
X Ray ◽  
Nitrite Reductases ◽  
Radiation Induced ◽  
Insight Into ◽  
Shed Light

Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK. Recently, we have identified two copies of nirK genes in several α-proteobacteria of the order Rhizobiales including Bradyrhizobium sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR (Br2DNiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (AxNiR) and green (AcNiR) subclasses, Br2DNiR, a blue CuNiR, shows a substantially lower catalytic efficiency despite a sequence identity of ~70%. Advanced synchrotron radiation and x-ray free-electron laser are used to obtain the most accurate (atomic resolution with unrestrained SHELX refinement) and damage-free (free from radiation-induced chemistry) structures, in as-isolated, substrate-bound, and product-bound states. This combination has shed light on the protonation states of essential catalytic residues, additional reaction intermediates, and how catalytic efficiency is modulated.

scholarly journals X-Ray Structure of 12-Oxophytodienoate Reductase 1 Provides Structural Insight into Substrate Binding and Specificity within the Family of OYE

Structure ◽  
2001 ◽  
Vol 9 (5) ◽  
pp. 419-429 ◽  
Author(s):  
Constanze Breithaupt ◽  
Jochen Strassner ◽  
Ulrike Breitinger ◽  
Robert Huber ◽  
Peter Macheroux ◽  
...  
Keyword(s):  
Substrate Binding ◽  
X Ray ◽  
The Family ◽  
Structural Insight ◽  
Insight Into

scholarly journals The First Structure of Dipeptidyl-peptidase III Provides Insight into the Catalytic Mechanism and Mode of Substrate Binding

2008 ◽  
Vol 283 (32) ◽  
pp. 22316-22324 ◽  
Author(s):  
Pravas Kumar Baral ◽  
Nina Jajčanin-Jozić ◽  
Sigrid Deller ◽  
Peter Macheroux ◽  
Marija Abramić ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Substrate Binding ◽  
Dipeptidyl Peptidase ◽  
Insight Into

scholarly journals Structural studies on dehydroshikimate dehydratase

2014 ◽  
Vol 70 (a1) ◽  
pp. C475-C475
Author(s):  
James Peek ◽  
Dinesh Christendat
Keyword(s):  
Sole Carbon Source ◽  
Catalytic Mechanism ◽  
Substrate Recognition ◽  
Structural Studies ◽  
Sugar Phosphate ◽  
X Ray ◽  
Structural Insight ◽  
Functional Relevance ◽  
Insight Into

The soil bacterium, Pseudomonas putida, is capable of using the alicyclic compound quinate as a sole carbon source. During this process, quinate is converted to 3-dehydroshikimate, which subsequently undergoes a dehydration to form protocatechuate. The latter transformation is performed by the enzyme dehydroshikimate dehydratase (DSD). We have recombinantly produced DSD from P. putida and are currently performing x-ray crystallographic studies on the enzyme to gain structural insight into its catalytic mechanism and mode of substrate recognition. Initial crystals of DSD diffracted to 2.7 Ä resolution, but exhibited strong twinning. A redesigned construct has recently yielded crystals that diffract to similar resolution, but with a significantly reduced tendency toward twinning. Interestingly, sequence analysis of P. putida DSD reveals that the protein is in fact a fusion of two distinct domains: an N-terminal sugar phosphate isomerase-like domain associated with DSD activity, and a C-terminal hydroxyphenylpyruvate dioxygenase (HPPD)-like domain with unknown functional significance. Structural characterization of the protein may provide novel insight into the functional relevance of the unusual HPPD-like domain.

scholarly journals Crystallization and Preliminary X-Ray Analysis of Rotavirus Protein VP6

1998 ◽  
Vol 72 (9) ◽  
pp. 7615-7619 ◽  
Author(s):  
Isabelle Petitpas ◽  
Jean Lepault ◽  
Patrice Vachette ◽  
Annie Charpilienne ◽  
Magali Mathieu ◽  
...  
Keyword(s):  
Atomic Resolution ◽  
Asymmetric Unit ◽  
Tubular Structures ◽  
Solvent Content ◽  
X Ray ◽  
X Ray Scattering ◽  
A Cell ◽  
Crystallization Conditions ◽  
Insight Into ◽  
Better Than

ABSTRACT As a first step to gain insight into the structure of the rotavirus virion at atomic resolution, we report here the expression, purification, and crystallization of recombinant rotavirus protein VP6. This protein has the property of polymerizing in the form of tubular structures in solution which have hindered crystallization thus far. Using a combination of electron microscopy and small-angle X-ray scattering, we found that addition of Ca2+ at concentrations higher than 100 mM results in depolymerization of the tubes, leading to an essentially monodisperse solution of trimeric VP6 even at high protein concentrations (higher than 10 mg/ml), thereby enabling us to search for crystallization conditions. We have thus obtained crystals of VP6 which diffract to better than 2.4 Å resolution and belong to the cubic space group P4132 with a cell dimension a of 160 Å. The crystals contain a trimer of VP6 lying along the diagonal of the cubic unit cell, resulting in one VP6 monomer per asymmetric unit and a solvent content of roughly 70%.

scholarly journals The structure of a family GH25 lysozyme fromAspergillus fumigatus

2010 ◽  
Vol 66 (9) ◽  
pp. 973-977 ◽  
Author(s):  
Justyna E. Korczynska ◽  
Steffen Danielsen ◽  
Ulrika Schagerlöf ◽  
Johan P. Turkenburg ◽  
Gideon J. Davies ◽  
...  
Keyword(s):  
Active Site ◽  
Glycoside Hydrolase ◽  
Catalytic Mechanism ◽  
Medical Application ◽  
Glycoside Hydrolase Family ◽  
X Ray ◽  
Fungal Structure ◽  
The Family ◽  
Hydrolase Family ◽  
Insight Into

Lysins are important biomolecules which cleave the bacterial cell-wall polymer peptidoglycan. They are finding increasing commercial and medical application. In order to gain an insight into the mechanism by which these enzymes operate, the X-ray structure of a CAZy family GH25 `lysozyme' fromAspergillus fumigatuswas determined. This is the first fungal structure from the family and reveals a modified α/β-barrel-like fold in which an eight-stranded β-barrel is flanked by three α-helices. The active site lies toward the bottom of a negatively charged pocket and its layout has much in common with other solved members of the GH25 and related GH families. A conserved active-site DXE motif may be implicated in catalysis, lending further weight to the argument that this glycoside hydrolase family operatesviaa `substrate-assisted' catalytic mechanism.

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