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Structure paper

TitleRevealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level.
Journal, issue, pagesNat Commun, Vol. 9, Page 3243-3243, Year 2018
Publish dateJun 17, 2018 (structure data deposition date)
AuthorsRen, W. / Pengelly, R. / Farren-Dai, M. / Shamsi Kazem Abadi, S. / Oehler, V. / Akintola, O. / Draper, J. / Meanwell, M. / Chakladar, S. / Swiderek, K. ...Ren, W. / Pengelly, R. / Farren-Dai, M. / Shamsi Kazem Abadi, S. / Oehler, V. / Akintola, O. / Draper, J. / Meanwell, M. / Chakladar, S. / Swiderek, K. / Moliner, V. / Britton, R. / Gloster, T.M. / Bennet, A.J.
External linksNat Commun / PubMed:30104598
MethodsX-ray diffraction
Resolution1.22 - 2.2 Å
Structure data

PDB-6gta:
Alpha-galactosidase mutant D378A from Thermotoga maritima in complex with intact cyclohexene-based carbasugar mimic of galactose with 3,5 difluorophenyl leaving group
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-6gvd:
Alpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose
Method: X-RAY DIFFRACTION / Resolution: 1.22 Å

PDB-6gwf:
Alpha-galactosidase mutant D387A from Thermotoga maritima in complex with intact cyclohexene-based carbasugar mimic of galactose with 2,4-dinitro leaving group
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-6gwg:
Alpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose covalently linked to the nucleophile
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-6gx8:
Alpha-galactosidase from Thermotoga maritima in complex with hydrolysed cyclohexene-based carbasugar mimic of galactose
Method: X-RAY DIFFRACTION / Resolution: 1.42 Å

Chemicals

ChemComp-SO4:
SULFATE ION

ChemComp-MG:
Unknown entry

ChemComp-F9W:
(1~{R},2~{S},3~{S},6~{S})-6-[3,5-bis(fluoranyl)phenoxy]-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol

ChemComp-HOH:
WATER

ChemComp-FDK:
(1~{S},2~{S},3~{S},4~{S})-5-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol

ChemComp-FEQ:
(1~{S},2~{S},5~{S},6~{R})-5-(2,4-dinitrophenoxy)-6-fluoranyl-3-(hydroxymethyl)cyclohex-3-ene-1,2-diol

ChemComp-FEK:
(1~{S},2~{S},3~{S})-3-fluoranyl-6-(hydroxymethyl)cyclohex-5-ene-1,2,4-triol

ChemComp-GOL:
GLYCEROL

ChemComp-FH2:
(1~{S},2~{S},3~{S},4~{S})-3-fluoranyl-6-(hydroxymethyl)cyclohex-5-ene-1,2,4-triol

Source
  • thermotoga maritima (strain atcc 43589 / msb8 / dsm 3109 / jcm 10099) (bacteria)
  • thermotoga maritima msb8 (bacteria)
KeywordsHYDROLASE / glycoside hydrolase / galactosidase / carbohydrate processing enzyme / inhibitor

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