7mfq
From Proteopedia
(Difference between revisions)
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==crystal structure of the L136 aminotransferase from acanthamoeba polyphaga mimivirus in complex with the TDP-viosamine external aldimine== | ==crystal structure of the L136 aminotransferase from acanthamoeba polyphaga mimivirus in complex with the TDP-viosamine external aldimine== | ||
| - | <StructureSection load='7mfq' size='340' side='right'caption='[[7mfq]]' scene=''> | + | <StructureSection load='7mfq' size='340' side='right'caption='[[7mfq]], [[Resolution|resolution]] 1.95Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MFQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MFQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7mfq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Apmv Apmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MFQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MFQ FirstGlance]. <br> |
| - | </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=7mfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mfq OCA], [https://pdbe.org/7mfq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mfq RCSB], [https://www.ebi.ac.uk/pdbsum/7mfq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mfq ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=T4K:(2R,3R,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)IMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL+[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>T4K</scene></td></tr> |
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7mfo|7mfo]], [[7mfp|7mfp]]</div></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MIMI_L136 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</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=7mfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mfq OCA], [https://pdbe.org/7mfq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mfq RCSB], [https://www.ebi.ac.uk/pdbsum/7mfq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mfq ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Acanthamoeba polyphaga Mimivirus, a complex virus that infects amoeba, was first reported in 2003. It is now known that its DNA genome encodes for nearly 1,000 proteins including enzymes that are required for the biosynthesis of the unusual sugar 4-amino-4,6-dideoxy-d-glucose, also known as d-viosamine. As observed in some bacteria, the pathway for the production of this sugar initiates with a nucleotide-linked sugar, which in the Mimivirus is thought to be UDP-d-glucose. The enzyme required for the installment of the amino group at the C-4' position of the pyranosyl moiety is encoded in the Mimivirus by the L136 gene. Here, we describe a structural and functional analysis of this pyridoxal 5'-phosphate-dependent enzyme, referred to as L136. For this analysis, three high-resolution X-ray structures were determined: the wildtype enzyme/pyridoxamine 5'-phosphate/dTDP complex and the site-directed mutant variant K185A in the presence of either UDP-4-amino-4,6-dideoxy-d-glucose or dTDP-4-amino-4,6-dideoxy-d-glucose. Additionally, the kinetic parameters of the enzyme utilizing either UDP-d-glucose or dTDP-d-glucose were measured and demonstrated that L136 is efficient with both substrates. This is in sharp contrast to the structurally related DesI from Streptomyces venezuelae, whose three-dimensional architecture was previously reported by this laboratory. As determined in this investigation, DesI shows a profound preference in its catalytic efficiency for the dTDP-linked sugar substrate. This difference can be explained in part by a hydrophobic patch in DesI that is missing in L136. Notably, the structure of L136 reported here represents the first three-dimensional model for a virally encoded PLP-dependent enzyme and thus provides new information on sugar aminotransferases in general. | ||
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| + | Characterization of an aminotransferase from Acanthamoeba polyphaga Mimivirus.,Seltzner CA, Ferek JD, Thoden JB, Holden HM Protein Sci. 2021 Jun 2. doi: 10.1002/pro.4139. PMID:34076307<ref>PMID:34076307</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7mfq" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Apmv]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Holden | + | [[Category: Holden, H M]] |
| - | [[Category: Seltzner | + | [[Category: Seltzner, C A]] |
| - | [[Category: Thoden | + | [[Category: Thoden, J B]] |
| + | [[Category: Aminotransferase]] | ||
| + | [[Category: Mimivirus]] | ||
| + | [[Category: Transferase]] | ||
| + | [[Category: Viosamine]] | ||
Revision as of 10:14, 14 July 2021
crystal structure of the L136 aminotransferase from acanthamoeba polyphaga mimivirus in complex with the TDP-viosamine external aldimine
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