View source for 7jid


==Crystal structure of the L780 UDP-rhamnose synthase from Acanthamoeba polyphaga mimivirus==
<StructureSection load='7jid' size='340' side='right'caption='[[7jid]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7jid]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JID FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AWU:[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>AWU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=7jid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jid OCA], [https://pdbe.org/7jid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jid RCSB], [https://www.ebi.ac.uk/pdbsum/7jid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jid ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/YL780_MIMIV YL780_MIMIV] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
For the field of virology, perhaps one of the most paradigm-shifting events so far in the 21(st) century was the identification of the giant double-stranded DNA virus that infects amoebae. Remarkably, this virus, known as Mimivirus, has a genome that encodes for nearly 1000 proteins, some of which are involved in the biosynthesis of unusual sugars. Indeed, the virus is coated by a layer of glycosylated fibers that contain d-glucose, N-acetyl-d-glucosamine, l-rhamnose, and 4-amino-4,6-dideoxy-d-glucose. Here we describe a combined structural and enzymological investigation of the protein encoded by the open-reading frame L780, which corresponds to an l-rhamnose synthase. The structure of the L780/NADP(+) /UDP-l-rhamnose ternary complex was determined to 1.45 A resolution and refined to an overall R-factor of 19.9 %. Each subunit of the dimeric protein adopts a bilobal-shaped appearance with the N-terminal domain harboring the dinucleotide binding site and the C-terminal domain positioning the UDP-sugar into the active site. The overall molecular architecture of L780 places it into the short chain dehydrogenase/reductase superfamily. Kinetic analyses indicate that the enzyme can function on either UDP- and dTDP-sugars but displays a higher catalytic efficiency with the UDP-linked substrate. Site-directed mutagenesis experiments suggest that both Cys 108 and Lys 175 play key roles in catalysis. This structure represents the first model of a viral UDP-l-rhamnose synthase and provides new details into these fascinating enzymes. This article is protected by copyright. All rights reserved.

The High-Resolution Structure of a UDP-l-Rhamnose Synthase from Acanthamoeba polyphaga Mimivirus.,Bockhaus NJ, Ferek JD, Thoden JB, Holden HM Protein Sci. 2020 Aug 14. doi: 10.1002/pro.3928. PMID:32797646<ref>PMID:32797646</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7jid" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Acanthamoeba polyphaga mimivirus]]
[[Category: Large Structures]]
[[Category: Bockhaus NJ]]
[[Category: Ferek JD]]
[[Category: Holden HM]]
[[Category: Thoden JB]]