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| | ==Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella catarrhalis in complex with Magnesium ion and Phosphate ion== | | ==Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella catarrhalis in complex with Magnesium ion and Phosphate ion== |
| - | <StructureSection load='4um5' size='340' side='right' caption='[[4um5]], [[Resolution|resolution]] 2.34Å' scene=''> | + | <StructureSection load='4um5' size='340' side='right'caption='[[4um5]], [[Resolution|resolution]] 2.34Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4um5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UM5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UM5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4um5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Moraxella_catarrhalis_BC8 Moraxella catarrhalis BC8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UM5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UM5 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.34Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4um6|4um6]], [[4um7|4um7]], [[4umd|4umd]], [[4ume|4ume]], [[4umf|4umf]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate-8-phosphatase 3-deoxy-manno-octulosonate-8-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.45 3.1.3.45] </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=4um5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4um5 OCA], [https://pdbe.org/4um5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4um5 RCSB], [https://www.ebi.ac.uk/pdbsum/4um5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4um5 ProSAT]</span></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=4um5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4um5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4um5 RCSB], [http://www.ebi.ac.uk/pdbsum/4um5 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A0A0J9X241_MORCA A0A0J9X241_MORCA] Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.[PIRNR:PIRNR006118] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4um5" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 3-deoxy-manno-octulosonate-8-phosphatase]] | + | [[Category: Large Structures]] |
| - | [[Category: Dhindwal, S]] | + | [[Category: Moraxella catarrhalis BC8]] |
| - | [[Category: Kumar, P]] | + | [[Category: Dhindwal S]] |
| - | [[Category: Tomar, S]]
| + | [[Category: Kumar P]] |
| - | [[Category: Had superfamily]] | + | [[Category: Tomar S]] |
| - | [[Category: Hydrolase]] | + | |
| Structural highlights
Function
A0A0J9X241_MORCA Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.[PIRNR:PIRNR006118]
Publication Abstract from PubMed
KdsC, the third enzyme of the 3-deoxy-D-manno-octulosonic acid (KDO) biosynthetic pathway, catalyzes a substrate-specific reaction to hydrolyze 3-deoxy-D-manno-octulosonate 8-phosphate to generate a molecule of KDO and phosphate. KdsC is a phosphatase that belongs to the C0 subfamily of the HAD superfamily. To understand the molecular basis for the substrate specificity of this tetrameric enzyme, the crystal structures of KdsC from Moraxella catarrhalis (Mc-KdsC) with several combinations of ligands, namely metal ion, citrate and products, were determined. Various transition states of the enzyme have been captured in these crystal forms. The ligand-free and ligand-bound crystal forms reveal that the binding of ligands does not cause any specific conformational changes in the active site. However, the electron-density maps clearly showed that the conformation of KDO as a substrate is different from the conformation adopted by KDO when it binds as a cleaved product. Furthermore, structural evidence for the existence of an intersubunit tunnel has been reported for the first time in the C0 subfamily of enzymes. A role for this tunnel in transferring water molecules from the interior of the tetrameric structure to the active-site cleft has been proposed. At the active site, water molecules are required for the formation of a water bridge that participates as a proton shuttle during the second step of the two-step phosphoryl-transfer reaction. In addition, as the KDO biosynthesis pathway is a potential antibacterial target, pharmacophore-based virtual screening was employed to identify inhibitor molecules for the Mc-KdsC enzyme.
Ligand-bound structures of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella catarrhalis reveal a water channel connecting to the active site for the second step of catalysis.,Dhindwal S, Priyadarshini P, Patil DN, Tapas S, Kumar P, Tomar S, Kumar P Acta Crystallogr D Biol Crystallogr. 2015 Feb;71(Pt 2):239-55. doi:, 10.1107/S1399004714025218. Epub 2015 Jan 23. PMID:25664734[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Dhindwal S, Priyadarshini P, Patil DN, Tapas S, Kumar P, Tomar S, Kumar P. Ligand-bound structures of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella catarrhalis reveal a water channel connecting to the active site for the second step of catalysis. Acta Crystallogr D Biol Crystallogr. 2015 Feb;71(Pt 2):239-55. doi:, 10.1107/S1399004714025218. Epub 2015 Jan 23. PMID:25664734 doi:http://dx.doi.org/10.1107/S1399004714025218
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