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| | ==Crystal structure of YrbI lacking the last 8 residues, in complex with Kdo and inorganic phosphate== | | ==Crystal structure of YrbI lacking the last 8 residues, in complex with Kdo and inorganic phosphate== |
| - | <StructureSection load='3i6b' size='340' side='right' caption='[[3i6b]], [[Resolution|resolution]] 2.49Å' scene=''> | + | <StructureSection load='3i6b' size='340' side='right'caption='[[3i6b]], [[Resolution|resolution]] 2.49Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3i6b]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_(strain_b) Escherichia coli (strain b)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I6B FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3i6b]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_B Escherichia coli B]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I6B FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</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]] 2.49Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2r8x|2r8x]], [[2r8y|2r8y]], [[2r8z|2r8z]], [[2r8e|2r8e]], [[3hyc|3hyc]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">c3958, kdsC, YrbI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37762 Escherichia coli (strain B)])</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=3i6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i6b OCA], [https://pdbe.org/3i6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i6b RCSB], [https://www.ebi.ac.uk/pdbsum/3i6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i6b ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3i6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i6b OCA], [http://pdbe.org/3i6b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i6b RCSB], [http://www.ebi.ac.uk/pdbsum/3i6b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3i6b ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KDSC_ECOL6 KDSC_ECOL6]] Involved in the biosynthesis of lipopolysaccharides (LPSs) (By similarity). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate. | + | [https://www.uniprot.org/uniprot/KDSC_ECOL6 KDSC_ECOL6] Involved in the biosynthesis of lipopolysaccharides (LPSs) (By similarity). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 3-deoxy-manno-octulosonate-8-phosphatase]] | + | [[Category: Escherichia coli B]] |
| - | [[Category: Biswas, T]] | + | [[Category: Large Structures]] |
| - | [[Category: Tsodikov, O V]] | + | [[Category: Biswas T]] |
| - | [[Category: Hydrolase]] | + | [[Category: Tsodikov OV]] |
| - | [[Category: Kdo]]
| + | |
| - | [[Category: Kdsc]]
| + | |
| - | [[Category: Lipopolysaccharide biosynthesis]]
| + | |
| - | [[Category: Magnesium]]
| + | |
| - | [[Category: Phosphatase]]
| + | |
| - | [[Category: Yrbi]]
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| Structural highlights
Function
KDSC_ECOL6 Involved in the biosynthesis of lipopolysaccharides (LPSs) (By similarity). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The phosphatase KdsC cleaves 3-deoxy-D-manno-octulosonate 8-phosphate to generate a molecule of inorganic phosphate and Kdo. Kdo is an essential component of the lipopolysaccharide envelope in Gram-negative bacteria. Because lipopolysaccharide is an important determinant of bacterial resistance and toxicity, KdsC is a potential target for novel antibacterial agents. KdsC belongs to the broad haloacid dehalogenase superfamily. In haloacid dehalogenase superfamily enzymes, substrate specificity and catalytic efficiency are generally dictated by a fold feature called the cap domain. It is therefore not clear why KdsC, which lacks a cap domain, is catalytically efficient and highly specific to 3-deoxy-D-manno-octulosonate 8-phosphate. Here, we present a set of seven structures of tetrameric Escherichia coli KdsC (ranging from 1.4 to 3.06 A in resolution) that model different intermediate states in its catalytic mechanism. A crystal structure of product-bound E. coli KdsC shows how the interface between adjacent monomers defines the active site pocket. Kdo is engaged in a network of polar and nonpolar interactions with residues at this interface, which explains substrate specificity. Furthermore, this structural and kinetic analysis strongly suggests that the binding of the flexible C-terminal region (tail) to the active site makes KdsC catalytically efficient by facilitating product release.
The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase.,Biswas T, Yi L, Aggarwal P, Wu J, Rubin JR, Stuckey JA, Woodard RW, Tsodikov OV J Biol Chem. 2009 Oct 30;284(44):30594-603. Epub 2009 Sep 2. PMID:19726684[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Biswas T, Yi L, Aggarwal P, Wu J, Rubin JR, Stuckey JA, Woodard RW, Tsodikov OV. The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase. J Biol Chem. 2009 Oct 30;284(44):30594-603. Epub 2009 Sep 2. PMID:19726684 doi:10.1074/jbc.M109.012278
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