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3e84

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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

Structural highlights

3e84 is a 4 chain structure with sequence from Bacteroides thetaiotaomicron. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.85Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3]

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 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.

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^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wang L, Lu Z, Allen KN, Mariano PS, Dunaway-Mariano D. Human symbiont Bacteroides thetaiotaomicron synthesizes 2-keto-3-deoxy-D-glycero-D- galacto-nononic acid (KDN). Chem Biol. 2008 Sep 22;15(9):893-7. doi: 10.1016/j.chembiol.2008.08.005. PMID:18804026 doi:http://dx.doi.org/10.1016/j.chembiol.2008.08.005
↑ Lu Z, Wang L, Dunaway-Mariano D, Allen KN. 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. J Biol Chem. 2009 Jan 9;284(2):1224-33. Epub 2008 Nov 5. PMID:18986982 doi:10.1074/jbc.M807056200
↑ Daughtry KD, Huang H, Malashkevich V, Patskovsky Y, Liu W, Ramagopal U, Sauder JM, Burley SK, Almo SC, Dunaway-Mariano D, Allen KN. Structural Basis for the Divergence of Substrate Specificity and Biological Function within HAD Phosphatases in Lipopolysaccharide and Sialic Acid Biosynthesis. Biochemistry. 2013 Aug 13;52(32):5372-86. doi: 10.1021/bi400659k. Epub 2013 Jul, 29. PMID:23848398 doi:10.1021/bi400659k
↑ Lu Z, Wang L, Dunaway-Mariano D, Allen KN. 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. J Biol Chem. 2009 Jan 9;284(2):1224-33. Epub 2008 Nov 5. PMID:18986982 doi:10.1074/jbc.M807056200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3e84"

@@ Line 1: / Line 1: @@
 ==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==
-<StructureSection load='3e84' size='340' side='right' caption='[[3e84]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<StructureSection load='3e84' size='340' side='right'caption='[[3e84]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3e84]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_thetaiotaomicron"_distaso_1912 "bacillus thetaiotaomicron" distaso 1912]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E84 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3e84]] 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=3E84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E84 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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=WO4:TUNGSTATE(VI)ION'>WO4</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]] 1.85&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3e81|3e81]], [[3e8m|3e8m]]</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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=WO4:TUNGSTATE(VI)ION'>WO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BT1713 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 "Bacillus thetaiotaomicron" Distaso 1912])</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=3e84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e84 OCA], [https://pdbe.org/3e84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e84 RCSB], [https://www.ebi.ac.uk/pdbsum/3e84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e84 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=3e84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e84 OCA], [http://pdbe.org/3e84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e84 RCSB], [http://www.ebi.ac.uk/pdbsum/3e84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e84 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e8/3e84_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e8/3e84_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus thetaiotaomicron distaso 1912]]
+[[Category: Bacteroides thetaiotaomicron]]
-[[Category: Allen, K N]]
+[[Category: Large Structures]]
-[[Category: Dunaway-Mariano, D]]
+[[Category: Allen KN]]
-[[Category: Lu, Z]]
+[[Category: Dunaway-Mariano D]]
-[[Category: Wang, L]]
+[[Category: Lu Z]]
-[[Category: 2-keto-3-deoxynononic acid 9-phosphate phosphohydrolase]]
+[[Category: Wang L]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Transferase]]

3e84

From Proteopedia

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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