7kzd: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Crystal structure of KabA from Bacillus cereus UW85 in complex with the reduced internal aldimine and with bound Glutarate== | ==Crystal structure of KabA from Bacillus cereus UW85 in complex with the reduced internal aldimine and with bound Glutarate== | ||
<StructureSection load='7kzd' size='340' side='right'caption='[[7kzd]]' scene=''> | <StructureSection load='7kzd' size='340' side='right'caption='[[7kzd]], [[Resolution|resolution]] 1.90Å' 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=7KZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KZD FirstGlance]. <br> | <table><tr><td colspan='2'>[[7kzd]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KZD 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=7kzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kzd OCA], [https://pdbe.org/7kzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kzd RCSB], [https://www.ebi.ac.uk/pdbsum/7kzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kzd 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GUA:GLUTARIC+ACID'>GUA</scene>, <scene name='pdbligand=PLR:(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL+DIHYDROGEN+PHOSPHATE'>PLR</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;'>[[7kz3|7kz3]], [[7kz5|7kz5]], [[7kz6|7kz6]]</div></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">kabA, GE376_30835 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1396 ATCC 14579])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aspartate_transaminase Aspartate transaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.1 2.6.1.1] </span></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=7kzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kzd OCA], [https://pdbe.org/7kzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kzd RCSB], [https://www.ebi.ac.uk/pdbsum/7kzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kzd ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Kanosamine is an antibiotic and antifungal monosaccharide. The kanosamine biosynthetic pathway from glucose 6-phosphate in Bacillus cereus UW85 was recently reported, and the functions of each of the three enzymes in the pathway, KabA, KabB and KabC, were demonstrated. KabA, a member of a subclass of the VIbeta family of PLP-dependent aminotransferases, catalyzes the second step in the pathway, generating kanosamine 6-phosphate (K6P) using l-glutamate as the amino-donor. KabA catalysis was shown to be extremely efficient, with a second-order rate constant with respect to K6P transamination of over 10(7) M(-1)s(-1). Here we report the high-resolution structure of KabA in both the PLP- and PMP-bound forms. In addition, co-crystallization with K6P allowed the structure of KabA in complex with the covalent PLP-K6P adduct to be solved. Co-crystallization or soaking with glutamate or 2-oxoglutarate did not result in crystals with either substrate/product. Reduction of the PLP-KabA complex with sodium cyanoborohydride gave an inactivated enzyme, and crystals of the reduced KabA were soaked with the l-glutamate analog glutarate to mimic the KabA-PLP-l-glutamate complex. Together these four structures give a complete picture of how the active site of KabA recognizes substrates for each half-reaction. The KabA structure is discussed in the context of homologous aminotransferases. | |||
Snapshots along the catalytic path of KabA, a PLP-dependent aminotransferase required for kanosamine biosynthesis in Bacillus cereus UW85.,Prasertanan T, Palmer DRJ, Sanders DAR J Struct Biol. 2021 May 11;213(2):107744. doi: 10.1016/j.jsb.2021.107744. PMID:33984505<ref>PMID:33984505</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7kzd" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Aspartate transaminase]] | |||
[[Category: Atcc 14579]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Palmer | [[Category: Palmer, D R.J]] | ||
[[Category: Prasertanan T]] | [[Category: Prasertanan, T]] | ||
[[Category: Sanders | [[Category: Sanders, D A.R]] | ||
[[Category: Aminotransferase]] | |||
[[Category: Biosynthesis]] | |||
[[Category: Biosynthetic protein]] | |||
[[Category: Kaba]] | |||
[[Category: Kanosamine]] | |||
[[Category: Transferase]] | |||
Revision as of 14:51, 2 June 2021
Crystal structure of KabA from Bacillus cereus UW85 in complex with the reduced internal aldimine and with bound Glutarate
| ||||||||||||
