3vbi: Difference between revisions

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<StructureSection load='3vbi' size='340' side='right'caption='[[3vbi]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='3vbi' size='340' side='right'caption='[[3vbi]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3vbi]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus_sj1 Bacillus cereus sj1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VBI FirstGlance]. <br>
<table><tr><td colspan='2'>[[3vbi]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus_SJ1 Bacillus cereus SJ1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VBI FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0FX:DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE'>0FX</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</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]] 1.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vbj|3vbj]], [[3vbk|3vbk]], [[3vbl|3vbl]], [[3vbm|3vbm]], [[3vbn|3vbn]], [[3vbp|3vbp]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0FX:DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE'>0FX</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">antd, BCSJ1_02085 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=699184 Bacillus cereus SJ1])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Galactoside_O-acetyltransferase Galactoside O-acetyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.18 2.3.1.18] </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=3vbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vbi OCA], [https://pdbe.org/3vbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vbi RCSB], [https://www.ebi.ac.uk/pdbsum/3vbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vbi 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=3vbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vbi OCA], [https://pdbe.org/3vbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vbi RCSB], [https://www.ebi.ac.uk/pdbsum/3vbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vbi ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The unusual dideoxysugar D-anthrose has been identified as an important component in the endospores of such infectious agents as Bacillus anthracis and Bacillus cereus. Specifically, it is the terminal sugar on the bacterium's exosporium, and it provides a point of interaction between the spore and the host. The biosynthesis of D-anthrose involves numerous steps starting from alpha-D-glucose-1-phosphate. Here we present a combined structural and functional investigation of AntD from B. cereus. This enzyme plays a key role in D-anthrose biosynthesis by catalyzing the acylation of the C-4'' amino group of dTDP-4-amino-4,6-dideoxyglucose using 3-hydroxy-3-methylbutyryl-CoA as the acyl donor. For this investigation two ternary complexes of AntD were determined to 1.8 A resolution: one in which the protein contained bound beta-hydroxybutyryl-CoA and dTDP, and the second with CoA and dTDP-4-amino-4,6-dideoxyglucose. On the basis of these high-resolution structures, it was shown that the side chain of Asp 94 lies within hydrogen bonding distance to the sugar C-4'' amino group, and the side chain of Ser 84 resides near the carbonyl oxygen of beta-hydroxybutyryl-CoA. To test the roles of these residues in the catalytic mechanism of AntD, various site-directed mutant proteins were prepared and subjected to kinetic and structural analyses. The D94A and D94N mutant proteins demonstrated enzymatic activity, albeit with significantly reduced catalytic efficiencies. The S84A mutant protein showed an approximate tenfold decrease in activity. Interestingly, the S84C and S84T mutant proteins were both active, but demonstrated substrate inhibition. The three-dimensional structures of all of the mutant proteins were nearly identical to that of the wild-type enzyme, indicating that the changes in their kinetic parameters were not due to major conformational changes. Taken together, these data suggest that Asp 94 is important for substrate binding, but probably does not function as an enzymatic base, and that Ser 84 most likely plays a role in formation of an oxyanion hole.
Structural Studies on AntD: an N-Acyltransferase Involved in the Biosynthesis of D-Anthrose.,Kubiak RL, Holden HM Biochemistry. 2012 Jan 4. PMID:22220494<ref>PMID:22220494</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3vbi" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Galactoside O-acetyltransferase|Galactoside O-acetyltransferase]]
*[[Galactoside O-acetyltransferase|Galactoside O-acetyltransferase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus cereus sj1]]
[[Category: Bacillus cereus SJ1]]
[[Category: Galactoside O-acetyltransferase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Holden, H M]]
[[Category: Holden HM]]
[[Category: Kubiak, R L]]
[[Category: Kubiak RL]]
[[Category: Acylated sugar]]
[[Category: Anthrose]]
[[Category: Left-handed beta helix]]
[[Category: Sugar n-acylation]]
[[Category: Transferase]]

Latest revision as of 13:34, 1 March 2024

Crystal Structure of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP-4-amino-4,6-dideoxyglucose and Coenzyme ACrystal Structure of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP-4-amino-4,6-dideoxyglucose and Coenzyme A

Structural highlights

3vbi is a 3 chain structure with sequence from Bacillus cereus SJ1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

3vbi, resolution 1.80Å

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