6k37
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 in complex with NAD+ and the analog of reaction intermediate, 3-(1-aminoethyl)-nonanedioic acid== | |
| + | <StructureSection load='6k37' size='340' side='right'caption='[[6k37]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6k37]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803 Synechocystis sp. PCC 6803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K37 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K37 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]] 2.5Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CWL:(3R)-3-[(1R)-1-azanylethyl]nonanedioic+acid'>CWL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=6k37 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k37 OCA], [https://pdbe.org/6k37 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k37 RCSB], [https://www.ebi.ac.uk/pdbsum/6k37 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k37 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/BIOU_SYNY3 BIOU_SYNY3] A 'suicide' enzyme that participates in biotin synthesis. Catalyzes the formation of (S)-8-amino-7-oxononanoate (DAN-carbamic acid) from (7R,8S)-8-amino-7-(carboxyamino)nonanoate (DAN), a function equivalent to the cannonical BioA reaction and the first half-reaction of BioD. The cellular requirement for biotin is thought be low enough that this single turnover enzyme supplies a sufficient amount of the cofactor. Overall it catalyzes three reactions: formation of a covalent linkage with 8-amino-7-oxononanoate to yield a BioU-DAN conjugate at the epsilon-amino group of Lys124 of BioU using NAD(P)H, carboxylation of the conjugate to form BioU-DAN-carbamic acid, and release of DAN-carbamic acid using NAD(P)+ (By similarity) (PubMed:32042199). A coupled Synechocystis BioU/BioD assay produces dethiobiotin from DAN. Complements a bioA deletion in E.coli but not a bioD1 deletion (PubMed:32042199).[HAMAP-Rule:MF_00852]<ref>PMID:32042199</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | In biotin biosynthesis, the conversion of pimeloyl intermediates to biotin is catalyzed by a universal set of four enzymes: BioF, BioA, BioD and BioB. We found that the gene homologous to bioA, the product of which is involved in the conversion of 8-amino-7-oxononanoate (AON) to 7,8-diaminononanoate (DAN), is missing in the genome of the cyanobacterium Synechocystis sp. PCC 6803. We provide structural and biochemical evidence showing that a novel dehydrogenase, BioU, is involved in biotin biosynthesis and functionally replaces BioA. This enzyme catalyzes three reactions: formation of covalent linkage with AON to yield a BioU-DAN conjugate at the epsilon-amino group of Lys124 of BioU using NAD(P)H, carboxylation of the conjugate to form BioU-DAN-carbamic acid, and release of DAN-carbamic acid using NAD(P)(+). In this biosynthetic pathway, BioU is a suicide enzyme that loses the Lys124 amino group after a single round of reaction. | ||
| - | + | A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria.,Sakaki K, Ohishi K, Shimizu T, Kobayashi I, Mori N, Matsuda K, Tomita T, Watanabe H, Tanaka K, Kuzuyama T, Nishiyama M Nat Chem Biol. 2020 Feb 10. pii: 10.1038/s41589-019-0461-9. doi:, 10.1038/s41589-019-0461-9. PMID:32042199<ref>PMID:32042199</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 6k37" style="background-color:#fffaf0;"></div> |
| - | [[Category: Nishiyama | + | == References == |
| - | [[Category: Sakaki | + | <references/> |
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Synechocystis sp. PCC 6803]] | ||
| + | [[Category: Nishiyama M]] | ||
| + | [[Category: Sakaki K]] | ||
| + | [[Category: Tomita T]] | ||
Current revision
Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 in complex with NAD+ and the analog of reaction intermediate, 3-(1-aminoethyl)-nonanedioic acid
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