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7dck
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==Crystal structure of phosphodiesterase tw9814== | ==Crystal structure of phosphodiesterase tw9814== | ||
| - | <StructureSection load='7dck' size='340' side='right'caption='[[7dck]]' scene=''> | + | <StructureSection load='7dck' size='340' side='right'caption='[[7dck]], [[Resolution|resolution]] 2.34Å' 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=7DCK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DCK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7dck]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Epsilonproteobacteria_bacterium_(ex_Lamellibrachia_satsuma) Epsilonproteobacteria bacterium (ex Lamellibrachia satsuma)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DCK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DCK 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=7dck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dck OCA], [https://pdbe.org/7dck PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dck RCSB], [https://www.ebi.ac.uk/pdbsum/7dck PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dck ProSAT]</span></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]] 2.34Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=7dck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dck OCA], [https://pdbe.org/7dck PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dck RCSB], [https://www.ebi.ac.uk/pdbsum/7dck PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dck ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/A0A426W059_9PROT A0A426W059_9PROT] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Metallo-beta-lactamase (MBL) superfamily proteins have a common alphabeta/betaalpha sandwich fold and perform a variety of functions through metal-mediated catalysis. However, because of the enormous scale of this superfamily, only a small percentage of the proteins belonging to the superfamily have been annotated structurally or functionally to date. Therefore, much remains unknown about the MBL superfamily proteins. Here, TW9814, a hypothetical MBL superfamily protein, was structurally and functionally investigated. Guided by the crystal structure of dimeric TW9814, it was demonstrated that TW9814 functions as a phosphodiesterase (PDE) in the presence of divalent metal ions such as manganese(II) or nickel(II). A docking model between TW9814 and the substrate bis(p-nitrophenyl)phosphate (bpNPP) showed the importance of the dimerization of TW9814 for its bpNPP-hydrolyzing activity and for the interaction between the enzyme and the substrate. TW9814 showed outstanding catalytic efficiency (kcat/Km) under alkaline conditions compared with other PDEs. The activity of TW9814 appears to be regulated through a disulfide bond, which is a feature that is not present in other MBL superfamily members. This study provides a platform for the functional characterization of other hypothetical proteins of the MBL or other superfamilies. | ||
| + | |||
| + | Structural and functional identification of the uncharacterized metallo-beta-lactamase superfamily protein TW9814 as a phosphodiesterase with unique metal coordination.,Heo Y, Park SB, Jeon YE, Yun JH, Jeong BG, Cha SS, Lee W Acta Crystallogr D Struct Biol. 2022 Apr 1;78(Pt 4):532-541. doi:, 10.1107/S2059798322002108. Epub 2022 Mar 17. PMID:35362475<ref>PMID:35362475</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7dck" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
Crystal structure of phosphodiesterase tw9814
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Categories: Large Structures | Cha SS | Heo Y | Lee W | Park JH | Park SB | Yun JH
