Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-Methyluracil

Prokofev, I.I.; Lashkov, A.A.; Габдулхаков, А.Г.; Балаев, В.В.; Миронов, А.; Betzel, Christian; Mikhailov, A.M.

doi:10.1134/s1063774518030239

Cited by 2 publications

(11 citation statements)

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“…The structural organization of the enzyme VchUPh is similar to that of the VchUPh structures reported previously [6,[8][9][10]. Each subunit of the VchUPh molecule, which exists as a toroidal homohexamer with a diameter of ~106 Å, is composed of 253 residues (the molecular weight is 27.5 kDa).…”

Section: Three-dimensional Organization Of the Vchuph Structuresupporting

confidence: 77%

“…The protein crystallization by the vapor-diffusion technique was described in [8,10]. The protein concentration was 15 mg/mL in 0.1 M Tris-HCl buffer.…”

Section: Crystallizationmentioning

confidence: 99%

“…Alternative conformations of long secondary-structure elements (β-stands and loops) of the protein tertiary structure in the absence of specific bound ligands were analyzed. Previously, alternative conformations in the atomic-resolution UPh structures were observed only in complexes of UPh with functionally important ligands bound at partial occupancy [6,10,11].…”

Section: Introductionmentioning

confidence: 98%

“…Currently, great attention is given to the evaluation of the enzyme specificity of UPh and the development of reversible competitive inhibitors, the decrease in the concentration of which leads to the restoration of UPh activity. The structures of the protein from different organisms and its complexes with various ligands were determined and characterized at a resolution of up to 1.2 Å [4][5][6][7][8][9][10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

“…This issue can be addressed by determining the crystal structures of the protein and its complexes with high accuracy by means of X-ray crystal-lography. According to our experience, an analysis of the structures determined at atomic and subatomic resolution makes it possible not only to reveal the structural features of the protein and its complexes but also to elucidate the mechanism of action of the enzyme as a biological machine relying on experimental data by analyzing alternative conformations, anisotropic displacement parameters, and active-site protonation states [6,10,11].…”

Section: Introductionmentioning

confidence: 99%

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Crystallization in Microgravity and the Atomic-Resolution Structure of Uridine Phosphorylase from Vibrio cholerae

et al. 2021

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Uridine phosphorylases are known as key targets for the development of new anticancer and antiparasitic agents. Crystals of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae were grown in microgravity by the capillary counter-diffusion method on board of the International Space Station. The three-dimensional structure of this enzyme was determined at atomic (1.04 Å) resolution (RCSB PDB ID: 6Z9Z). Alternative conformations of long fragments (β-strands and adjacent loops) of the protein molecule were found for the first time in the three-dimensional structure of uridine phosphorylase in the absence of specific bound ligands. Apparently, these alternative conformations are related to the enzyme function. Conformational analysis with Markov state models demonstrated that conformational rearrangements can occur in the ligand-free state of the enzyme.

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Section: Three-dimensional Organization Of the Vchuph Structuresupporting

confidence: 77%

“…The protein crystallization by the vapor-diffusion technique was described in [8,10]. The protein concentration was 15 mg/mL in 0.1 M Tris-HCl buffer.…”

Section: Crystallizationmentioning

confidence: 99%