3e8m

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[[Image:3e8m.png|left|200px]]
 
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==Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate (KDN) Phosphatase Defines a New Clad Within the Type C0 HAD Subfamily==
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The line below this paragraph, containing "STRUCTURE_3e8m", creates the "Structure Box" on the page.
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<StructureSection load='3e8m' size='340' side='right'caption='[[3e8m]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3e8m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E8M FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
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{{STRUCTURE_3e8m| PDB=3e8m | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3e8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e8m OCA], [https://pdbe.org/3e8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e8m RCSB], [https://www.ebi.ac.uk/pdbsum/3e8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e8m ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/KDGGP_BACTN KDGGP_BACTN] Involved in the biosynthesis of 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid used in cell-wall polysaccharides (PubMed:18804026). Catalyzes the hydrolysis of 2-keto-3-deoxy-D-glycero-D-galacto-9-phosphonononic acid (KDN-9-P) to yield 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid (KDN) (PubMed:18804026, PubMed:18986982, PubMed:23848398). Also able to hydrolyze N-acetylneuraminate-9-phosphate (Neu5NAc-9-P), 2-keto-3-deoxy-D-manno-octulosonate-8-phosphate (KDO-8-P), phosphoenolpyruvate (PEP), gluconate 6-phosphate, tyrosine phosphate ester and glucose-6-P as substrate (PubMed:18804026, PubMed:18986982, PubMed:23848398).<ref>PMID:18804026</ref> <ref>PMID:18986982</ref> <ref>PMID:23848398</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e8/3e8m_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3e8m ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The phosphotransferases of the haloalkanoate dehalogenase superfamily (HADSF) act upon a wide range of metabolites in all eukaryotes and prokaryotes and thus constitute a significant force in cell function. The challenge posed for biochemical function assignment of HADSF members is the identification of the structural determinants that target a specific metabolite. The "8KDOP" subfamily of the HADSF is defined by the known structure and catalytic activity of 2-keto-3-deoxy-8-phospho-d-manno-octulosonic acid (KDO-8-P) phosphatase. Homologues of this enzyme have been uniformly annotated as KDO-8-P phosphatase. One such gene, BT1713, from the Bacteroides thetaiotaomicron genome was recently found to encode the enzyme 2-keto-3-deoxy-d-glycero-d-galacto-9-phosphonononic acid (KDN-9-P) phosphatase in the biosynthetic pathway of the 9-carbon alpha-keto acid, 2-keto-3-deoxy-d-glycero-d-galactonononic acid (KDN). To find the structural elements that provide substrate-specific interactions and to allow identification of genomic sequence markers, the x-ray crystal structures of BT1713 liganded to the cofactor Mg(2+)and complexed with tungstate or VO(3)(-)/Neu5Ac were determined to 1.1, 1.85, and 1.63 A resolution, respectively. The structures define the active site to be at the subunit interface and, as confirmed by steady-state kinetics and site-directed mutagenesis, reveal Arg-64(*), Lys-67(*), and Glu-56 to be the key residues involved in sugar binding that are essential for BT1713 catalytic function. Bioinformatic analyses of the differentially conserved residues between BT1713 and KDO-8-P phosphatase homologues guided by the knowledge of the structure-based specificity determinants define Glu-56 and Lys-67(*) to be the key residues that can be used in future annotations.
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===Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate (KDN) Phosphatase Defines a New Clad Within the Type C0 HAD Subfamily===
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Structure-function analysis of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphatase defines specificity elements in type C0 haloalkanoate dehalogenase family members.,Lu Z, Wang L, Dunaway-Mariano D, Allen KN J Biol Chem. 2009 Jan 9;284(2):1224-33. Epub 2008 Nov 5. PMID:18986982<ref>PMID:18986982</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_18986982}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3e8m" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18986982 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18986982}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[3e8m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E8M OCA].
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==Reference==
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<ref group="xtra">PMID:018986982</ref><references group="xtra"/>
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[[Category: Bacteroides thetaiotaomicron]]
[[Category: Bacteroides thetaiotaomicron]]
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[[Category: Allen, K N.]]
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[[Category: Large Structures]]
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[[Category: Dunaway-Mariano, D.]]
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[[Category: Allen KN]]
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[[Category: Lu, Z.]]
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[[Category: Dunaway-Mariano D]]
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[[Category: Wang, L.]]
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[[Category: Lu Z]]
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[[Category: 2-keto-3-deoxynononic acid 9-phosphate phosphohydrolase]]
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[[Category: Wang L]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Transferase]]
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Current revision

Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate (KDN) Phosphatase Defines a New Clad Within the Type C0 HAD Subfamily

PDB ID 3e8m

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