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6k37

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Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 in complex with NAD+ and the analog of reaction intermediate, 3-(1-aminoethyl)-nonanedioic acid

Structural highlights

6k37 is a 1 chain structure with sequence from Synechocystis sp. PCC 6803. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]^[1]

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sakaki K, Ohishi K, Shimizu T, Kobayashi I, Mori N, Matsuda K, Tomita T, Watanabe H, Tanaka K, Kuzuyama T, Nishiyama M. A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria. Nat Chem Biol. 2020 Feb 10. pii: 10.1038/s41589-019-0461-9. doi:, 10.1038/s41589-019-0461-9. PMID:32042199 doi:http://dx.doi.org/10.1038/s41589-019-0461-9
↑ Sakaki K, Ohishi K, Shimizu T, Kobayashi I, Mori N, Matsuda K, Tomita T, Watanabe H, Tanaka K, Kuzuyama T, Nishiyama M. A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria. Nat Chem Biol. 2020 Feb 10. pii: 10.1038/s41589-019-0461-9. doi:, 10.1038/s41589-019-0461-9. PMID:32042199 doi:http://dx.doi.org/10.1038/s41589-019-0461-9

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6k37"

Categories: Large Structures | Synechocystis sp. PCC 6803 | Nishiyama M | Sakaki K | Tomita T

@@ Line 3: / Line 3: @@
 <StructureSection load='6k37' size='340' side='right'caption='[[6k37]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6k37]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aphanocapsa_sp._(strain_n-1) Aphanocapsa sp. (strain n-1)]. 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 [http://proteopedia.org/fgij/fg.htm?mol=6K37 FirstGlance]. <br>
+<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='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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">slr0355 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1148 Aphanocapsa sp. (strain N-1)])</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'>[http://proteopedia.org/fgij/fg.htm?mol=6k37 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k37 OCA], [http://pdbe.org/6k37 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k37 RCSB], [http://www.ebi.ac.uk/pdbsum/6k37 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k37 ProSAT]</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=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 ==
@@ Line 22: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Nishiyama, M]]
+[[Category: Synechocystis sp. PCC 6803]]
-[[Category: Sakaki, K]]
+[[Category: Nishiyama M]]
-[[Category: Tomita, T]]
+[[Category: Sakaki K]]
-[[Category: Biotin biosynthesis]]
+[[Category: Tomita T]]
-[[Category: Biou]]
-[[Category: Dehydrogenase]]
-[[Category: Oxidoreductase]]
-[[Category: Synechocysti]]

6k37

From Proteopedia

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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