7c3u: Difference between revisions
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==Crystal structure of NE0047 (N66A) mutant in complex with 8-azaguanine== | ==Crystal structure of NE0047 (N66A) mutant in complex with 8-azaguanine== | ||
<StructureSection load='7c3u' size='340' side='right'caption='[[7c3u]]' scene=''> | <StructureSection load='7c3u' size='340' side='right'caption='[[7c3u]], [[Resolution|resolution]] 1.86Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C3U FirstGlance]. <br> | <table><tr><td colspan='2'>[[7c3u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Niteu Niteu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C3U FirstGlance]. <br> | ||
</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=7c3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c3u OCA], [https://pdbe.org/7c3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c3u RCSB], [https://www.ebi.ac.uk/pdbsum/7c3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c3u ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZG:5-AMINO-1H-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-7-OL'>AZG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NE0047 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=228410 NITEU])</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=7c3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c3u OCA], [https://pdbe.org/7c3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c3u RCSB], [https://www.ebi.ac.uk/pdbsum/7c3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c3u ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Guanine deaminases (GDs) are essential enzymes that regulate the overall nucleobase pool. Since the deamination of guanine to xanthine results in the production of a mutagenic base, these enzymes have evolved to be very specific in nature. Surprisingly, they accept structurally distinct triazine ammeline, an intermediate in the melamine pathway, as one of the moonlighting substrates. Here, by employing NE0047 (a GD from Nitrosomonas europaea), we delineate the nuance in the catalytic mechanism that allows these two distinct substrates to be catalyzed. A combination of enzyme kinetics, X-ray crystallographic, and calorimetric studies reveal that GDs operate via a dual proton shuttle mechanism with two glutamates, E79 and E143, crucial for deamination. Additionally, N66 appears to be central for substrate anchoring and participates in catalysis. The study highlights the importance of closure of the catalytic loop and of maintenance of the hydrophobic core by capping residues like F141 and F48 for the creation of an apt environment for activation of the zinc-assisted catalysis. This study also analyzes evolutionarily distinct GDs and asserts that GDs incorporate subtle variations in the active site architectures while keeping the most critical active site determinants conserved. | |||
Structure Guided Mutagenesis Reveals the Substrate Determinants of Guanine Deaminase.,Singh J, Gaded V, Bitra A, Anand R J Struct Biol. 2021 May 16:107747. doi: 10.1016/j.jsb.2021.107747. PMID:34010666<ref>PMID:34010666</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7c3u" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Anand R]] | [[Category: Niteu]] | ||
[[Category: Bitra A]] | [[Category: Anand, R]] | ||
[[Category: Gaded V]] | [[Category: Bitra, A]] | ||
[[Category: Singh J]] | [[Category: Gaded, V]] | ||
[[Category: Singh, J]] | |||
[[Category: 8-azaguanine]] | |||
[[Category: Complex]] | |||
[[Category: Deaminase]] | |||
[[Category: Hydrolase]] | |||
Revision as of 17:49, 2 June 2021
Crystal structure of NE0047 (N66A) mutant in complex with 8-azaguanineCrystal structure of NE0047 (N66A) mutant in complex with 8-azaguanine
Structural highlights
Publication Abstract from PubMedGuanine deaminases (GDs) are essential enzymes that regulate the overall nucleobase pool. Since the deamination of guanine to xanthine results in the production of a mutagenic base, these enzymes have evolved to be very specific in nature. Surprisingly, they accept structurally distinct triazine ammeline, an intermediate in the melamine pathway, as one of the moonlighting substrates. Here, by employing NE0047 (a GD from Nitrosomonas europaea), we delineate the nuance in the catalytic mechanism that allows these two distinct substrates to be catalyzed. A combination of enzyme kinetics, X-ray crystallographic, and calorimetric studies reveal that GDs operate via a dual proton shuttle mechanism with two glutamates, E79 and E143, crucial for deamination. Additionally, N66 appears to be central for substrate anchoring and participates in catalysis. The study highlights the importance of closure of the catalytic loop and of maintenance of the hydrophobic core by capping residues like F141 and F48 for the creation of an apt environment for activation of the zinc-assisted catalysis. This study also analyzes evolutionarily distinct GDs and asserts that GDs incorporate subtle variations in the active site architectures while keeping the most critical active site determinants conserved. Structure Guided Mutagenesis Reveals the Substrate Determinants of Guanine Deaminase.,Singh J, Gaded V, Bitra A, Anand R J Struct Biol. 2021 May 16:107747. doi: 10.1016/j.jsb.2021.107747. PMID:34010666[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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