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| | ==The crystal structure of Bacillus subtilis YpgQ in complex with ADP== | | ==The crystal structure of Bacillus subtilis YpgQ in complex with ADP== |
| - | <StructureSection load='5dqw' size='340' side='right' caption='[[5dqw]], [[Resolution|resolution]] 2.15Å' scene=''> | + | <StructureSection load='5dqw' size='340' side='right'caption='[[5dqw]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5dqw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DQW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DQW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5dqw]] is a 2 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=5DQW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DQW FirstGlance]. <br> |
| - | </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=NI:NICKEL+(II)+ION'>NI</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]] 2.15Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5dqv|5dqv]]</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=NI:NICKEL+(II)+ION'>NI</scene></td></tr> |
| - | <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=5dqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dqw OCA], [http://pdbe.org/5dqw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dqw RCSB], [http://www.ebi.ac.uk/pdbsum/5dqw PDBsum]</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=5dqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dqw OCA], [https://pdbe.org/5dqw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dqw RCSB], [https://www.ebi.ac.uk/pdbsum/5dqw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dqw ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Jeon, Y J]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Song, W S]] | + | [[Category: Large Structures]] |
| - | [[Category: Yoon, S I]] | + | [[Category: Jeon YJ]] |
| - | [[Category: Hd domain]] | + | [[Category: Song WS]] |
| - | [[Category: Hydrolase]] | + | [[Category: Yoon SI]] |
| Structural highlights
Publication Abstract from PubMed
The optimal balance of cellular nucleotides and the efficient elimination of non-canonical nucleotides are critical to avoiding erroneous mutation during DNA replication. One such mechanism involves the degradation of excessive or abnormal nucleotides by nucleotide-hydrolyzing enzymes. YpgQ contains the histidine-aspartate (HD) domain that is involved in the hydrolysis of nucleotides or nucleic acids, but the enzymatic activity and substrate specificity of YpgQ have never been characterized. Here, we unravel the catalytic activity and structural features of YpgQ to report the first Mn2+-dependent pyrophosphohydrolase that hydrolyzes (deoxy)ribonucleoside triphosphate [(d)NTP] to (deoxy)ribonucleoside monophosphate and pyrophosphate using the HD domain. YpgQ from Bacillus subtilis (bsYpgQ) displays a helical structure and assembles into a unique dimeric architecture that has not been observed in other HD domain-containing proteins. Each bsYpgQ monomer accommodates a metal ion and a nucleotide substrate in a cavity located between the N- and C-terminal lobes. The metal cofactor is coordinated by the canonical residues of the HD domain, namely, two histidine residues and two aspartate residues, and is positioned in close proximity to the beta-phosphate group of the nucleotide, allowing us to propose a nucleophilic attack mechanism for the nucleotide hydrolysis reaction. YpgQ enzymes from other bacterial species also catalyze pyrophosphohydrolysis but exhibit different substrate specificity. Comparative structural and mutational studies demonstrated that residues outside the major substrate-binding site of bsYpgQ are responsible for the species-specific substrate preference. Taken together, our structural and biochemical analyses highlight the substrate-recognition mode and catalysis mechanism of YpgQ in pyrophosphohydrolysis.
Structural and biochemical characterization of bacterial YpgQ protein reveals a metal-dependent nucleotide pyrophosphohydrolase.,Jeon YJ, Park SC, Song WS, Kim OH, Oh BC, Yoon SI J Struct Biol. 2016 Apr 7. pii: S1047-8477(16)30061-2. doi:, 10.1016/j.jsb.2016.04.002. PMID:27062940[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Jeon YJ, Park SC, Song WS, Kim OH, Oh BC, Yoon SI. Structural and biochemical characterization of bacterial YpgQ protein reveals a metal-dependent nucleotide pyrophosphohydrolase. J Struct Biol. 2016 Apr 7. pii: S1047-8477(16)30061-2. doi:, 10.1016/j.jsb.2016.04.002. PMID:27062940 doi:http://dx.doi.org/10.1016/j.jsb.2016.04.002
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