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3wnz

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==Crystal structure of Bacillus subtilis YwfE, an L-amino acid ligase, with bound ADP-Mg-Pi==
==Crystal structure of Bacillus subtilis YwfE, an L-amino acid ligase, with bound ADP-Mg-Pi==
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<StructureSection load='3wnz' size='340' side='right' caption='[[3wnz]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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<StructureSection load='3wnz' size='340' side='right'caption='[[3wnz]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3wnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WNZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WNZ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3wnz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WNZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WNZ FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.9&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vmm|3vmm]], [[3wo0|3wo0]], [[3wo1|3wo1]]</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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-amino-acid_alpha-ligase L-amino-acid alpha-ligase], with EC number [http://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=3wnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wnz OCA], [https://pdbe.org/3wnz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wnz RCSB], [https://www.ebi.ac.uk/pdbsum/3wnz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wnz ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wnz OCA], [http://pdbe.org/3wnz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wnz RCSB], [http://www.ebi.ac.uk/pdbsum/3wnz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wnz ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://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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l-Amino acid ligase (Lal) catalyzes the formation of a dipeptide from two l-amino acids in an ATP-dependent manner and belongs to the ATP-grasp superfamily. Bacillus subtilis YwfE, the first identified Lal, produces the dipeptide antibiotic bacilysin, which consists of l-Ala and l-anticapsin. Its substrate specificity is restricted to smaller amino acids such as l-Ala for the N-terminal end of the dipeptide, whereas a wide range of hydrophobic amino acids including l-Phe and l-Met are recognized for the C-terminal end in vitro. We determined the crystal structures of YwfE with bound ADP-Mg(2+)-Pi and ADP-Mg(2+)-l-Ala at 1.9 and 2.0 A resolutions, respectively. On the basis of these structures, we generated point mutants of residues that are considered to participate in the recognition of l-Ala and measured their ATPase activity. The conserved Arg328 is suggested to be a crucial residue for l-Ala recognition and catalysis. The mutation of Trp332 to Ala caused the enzyme to hydrolyze ATP, even in the absence of l-Ala, and the structure of this mutant protein appeared to show a cavity in the N-terminal substrate-binding pocket. These results suggest that Trp332 plays a key role in restricting the substrate specificity to smaller amino acids such as l-Ala. Moreover, Trp332 mutants can alter the substrate specificity and activity depending on the size and shape of substituted amino acids. These observations provide sufficient scope for the rational design of Lal to produce desirable dipeptides. We propose that the positioning of the conserved Arg residue in Lal is important for enantioselective recognition of l-amino acids.
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Single Mutation Alters the Substrate Specificity of l-Amino Acid Ligase.,Tsuda T, Asami M, Koguchi Y, Kojima S Biochemistry. 2014 Apr 29;53(16):2650-60. doi: 10.1021/bi500292b. Epub 2014 Apr, 17. PMID:24702628<ref>PMID:24702628</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 3wnz" 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: L-amino-acid alpha-ligase]]
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[[Category: Bacillus subtilis subsp. subtilis str. 168]]
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[[Category: Kojima, S]]
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[[Category: Large Structures]]
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[[Category: Tsuda, T]]
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[[Category: Kojima S]]
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[[Category: Atp binding]]
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[[Category: Tsuda T]]
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[[Category: Atp-grasp fold]]
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[[Category: Ligase]]
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Current revision

Crystal structure of Bacillus subtilis YwfE, an L-amino acid ligase, with bound ADP-Mg-Pi

PDB ID 3wnz

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