3vmm

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<StructureSection load='3vmm' size='340' side='right'caption='[[3vmm]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='3vmm' size='340' side='right'caption='[[3vmm]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vmm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VMM FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vmm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VMM FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=P0D:(2S)-3-[(S)-[(1R)-1-AMINOETHYL](PHOSPHONOOXY)PHOSPHORYL]-2-BENZYLPROPANOIC+ACID'>P0D</scene></td></tr>
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</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>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bacD, BSU37710, ipa-83d ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=P0D:(2S)-3-[(S)-[(1R)-1-AMINOETHYL](PHOSPHONOOXY)PHOSPHORYL]-2-BENZYLPROPANOIC+ACID'>P0D</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/L-amino-acid_alpha-ligase L-amino-acid alpha-ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.28 6.3.2.28] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vmm OCA], [https://pdbe.org/3vmm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vmm RCSB], [https://www.ebi.ac.uk/pdbsum/3vmm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vmm 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=3vmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vmm OCA], [https://pdbe.org/3vmm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vmm RCSB], [https://www.ebi.ac.uk/pdbsum/3vmm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vmm ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/BACD_BACSU BACD_BACSU]] Catalyzes the formation of alpha-dipeptides from various L-amino acids in the presence of ATP. Has a broad substrate specificity. Does not accept lysine, arginine, glutamate, aspartate and proline as a substrate. Probably catalyzes the ligation of L-alanine and L-anticapsin to produce the final bacilysin antibiotic.
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[https://www.uniprot.org/uniprot/BACD_BACSU BACD_BACSU] Catalyzes the formation of alpha-dipeptides from various L-amino acids in the presence of ATP. Has a broad substrate specificity. Does not accept lysine, arginine, glutamate, aspartate and proline as a substrate. Probably catalyzes the ligation of L-alanine and L-anticapsin to produce the final bacilysin antibiotic.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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BacD is an ATP-dependent dipeptide ligase responsible for the biosynthesis of L-alanyl-L-anticapsin, a precursor of an antibiotic produced by Bacillus spp. In contrast to the well-studied and phylogenetically related D-alanine: D-alanine ligase (Ddl), BacD synthesizes dipeptides using L-amino acids as substrates and has a low substrate specificity in vitro. The enzyme is of great interest because of its potential application in industrial protein engineering for the environmentally friendly biological production of useful peptide compounds, such as physiologically active peptides, artificial sweeteners and antibiotics, but the determinants of its substrate specificity and its catalytic mechanism have not yet been established due to a lack of structural information. In this study, we report the crystal structure of BacD in complex with ADP and an intermediate analog, phosphorylated phosphinate L-alanyl-L-phenylalanine, refined to 2.5-A resolution. The complex structure reveals that ADP and two magnesium ions bind in a manner similar to that of Ddl. However, the dipeptide orientation is reversed, and, concomitantly, the entrance to the amino acid binding cavity differs in position. Enzymatic characterization of two mutants, Y265F and S185A, demonstrates that these conserved residues are not catalytic residues at least in the reaction where L-phenylalanine is used as a substrate. On the basis of the biochemical and the structural data, we propose a reaction scheme and a catalytic mechanism for BacD.
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Structural and enzymatic characterization of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis.,Shomura Y, Hinokuchi E, Ikeda H, Senoo A, Takahashi Y, Saito JI, Komori H, Shibata N, Yonetani Y, Higuchi Y Protein Sci. 2012 Mar 9. doi: 10.1002/pro.2058. PMID:22407814<ref>PMID:22407814</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3vmm" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Vibrio subtilis ehrenberg 1835]]
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[[Category: Bacillus subtilis]]
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[[Category: L-amino-acid alpha-ligase]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Higuchi, Y]]
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[[Category: Higuchi Y]]
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[[Category: Shomura, Y]]
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[[Category: Shomura Y]]
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[[Category: Amino acid ligase]]
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[[Category: Atp binding]]
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[[Category: Atp-grasp domain]]
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[[Category: Ligase]]
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Current revision

Crystal structure of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis

PDB ID 3vmm

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