4amb: Difference between revisions
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<StructureSection load='4amb' size='340' side='right'caption='[[4amb]], [[Resolution|resolution]] 2.62Å' scene=''> | <StructureSection load='4amb' size='340' side='right'caption='[[4amb]], [[Resolution|resolution]] 2.62Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4amb]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4amb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_nogalater Streptomyces nogalater]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AMB FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUD:DEOXYURIDINE-5-DIPHOSPHATE'>DUD</scene></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.62Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUD:DEOXYURIDINE-5-DIPHOSPHATE'>DUD</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4amb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4amb OCA], [https://pdbe.org/4amb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4amb RCSB], [https://www.ebi.ac.uk/pdbsum/4amb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4amb ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q9RN61_STRNO Q9RN61_STRNO] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[Glycosyltransferase|Glycosyltransferase]] | *[[Glycosyltransferase 3D structures|Glycosyltransferase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Claesson | [[Category: Streptomyces nogalater]] | ||
[[Category: Dobritzsch | [[Category: Claesson M]] | ||
[[Category: Metsa-Ketela | [[Category: Dobritzsch D]] | ||
[[Category: Schneider | [[Category: Metsa-Ketela M]] | ||
[[Category: Siitonen | [[Category: Schneider G]] | ||
[[Category: Siitonen V]] | |||
Latest revision as of 14:30, 20 December 2023
Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalaterCrystal structure of the glycosyltransferase SnogD from Streptomyces nogalater
Structural highlights
FunctionPublication Abstract from PubMedThe glycosyltransferase SnogD from Streptomyces nogalater transfers a nogalamine moiety to the metabolic intermediate 3',4'-demethoxynogalose-1-hydroxynogalamycinone during the final steps of biosynthesis of the aromatic polyketide nogalamycin. The crystal structure of recombinant SnogD, as an apo-enzyme and with a bound nucleotide, 2-deoxyuridine-5'-diphosphate, was determined to 2.6 A resolution. Reductive methylation of SnogD was crucial for reproducible preparation of diffraction quality crystals due to creation of an additional intermolecular salt bridge between methylated lysine residue Lys384 and Glu374* from an adjacent molecule in the crystal lattice. SnogD is a dimer both in solution and in the crystal, and the enzyme subunit displays a fold characteristic of the GT-B family of glycosyltransferases. Binding of the nucleotide is associated with rearrangement of two active-site loops. Site-directed mutagenesis shows that two active-site histidine residues, His25 and His301, are critical for the glycosyltransferase activities of SnogD both in vivo and in vitro. The crystal structures and the functional data are consistent with a role for His301 in binding of the diphosphate group of the sugar donor substrate, and a function of His25 as a catalytic base in the glycosyl transfer reaction. Database The atomic coordinates and structure factors have been deposited with the RCSB Protein Data Bank under accession numbers 4AMB, 4AMG and 4AN4 Structured digital abstract * snogD and snogD bind by x-ray crystallography (View Interaction: 1, 2). Crystal structure of the glycosyltransferase SnogD from the biosynthetic pathway of nogalamycin in Streptomyces nogalater.,Claesson M, Siitonen V, Dobritzsch D, Metsa-Ketela M, Schneider G FEBS J. 2012 Sep;279(17):3251-63. doi: 10.1111/j.1742-4658.2012.08711.x. Epub, 2012 Aug 17. PMID:22804797[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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