1x8f: Difference between revisions

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-[[Image:1x8f.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1x8f", creates the "Structure Box" on the page.
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-{{STRUCTURE_1x8f|  PDB=1x8f  |  SCENE=  }}
-'''Crystal Structure Of apo-Kdo8P Synthase'''
+==Crystal Structure Of apo-Kdo8P Synthase==
+<StructureSection load='1x8f' size='340' side='right'caption='[[1x8f]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1x8f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X8F FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</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=1x8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x8f OCA], [https://pdbe.org/1x8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x8f RCSB], [https://www.ebi.ac.uk/pdbsum/1x8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x8f ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KDSA_ECOLI KDSA_ECOLI] Synthesis of KDO 8-P which is required for lipid A maturation and cellular growth.[HAMAP-Rule:MF_00056]
+== 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/x8/1x8f_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1x8f ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The enzyme 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS) catalyses the condensation of arabinose 5-phosphate (A5P) and phosphoenol pyruvate (PEP) to obtain 3-deoxy-D-manno-2-octulosonate-8-phosphate (KDO8P). We have elucidated initial modes of ligand binding in KDO8PS binary complexes by X-ray crystallography. Structures of the apo-enzyme and of binary complexes with the substrate PEP, the product KDO8P and the catalytically inactive 1-deoxy analog of arabinose 5-phosphate (1dA5P) were obtained. The KDO8PS active site resembles an irregular funnel with positive electrostatic potential situated at the bottom of the PEP-binding sub-site, which is the primary attractive force towards negatively charged phosphate moieties of all ligands. The structures of the ligand-free apo-KDO8PS and the binary complex with the product KDO8P visualize for the first time the role of His202 as an active-site gate. Examination of the crystal structures of KDO8PS with the KDO8P or 1dA5P shows these ligands bound to the enzyme in the PEP-binding sub-site, and not as expected to the A5P sub-site. Taken together, the structures presented here strengthen earlier evidence that this enzyme functions predominantly through positional catalysis, map out the roles of active-site residues and provide evidence that explains the total lack of catalytic reversibility.
-==Overview==
+Crystal structures of Escherichia coli KDO8P synthase complexes reveal the source of catalytic irreversibility.,Vainer R, Belakhov V, Rabkin E, Baasov T, Adir N J Mol Biol. 2005 Aug 19;351(3):641-52. PMID:16023668<ref>PMID:16023668</ref>
-The enzyme 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS) catalyses the condensation of arabinose 5-phosphate (A5P) and phosphoenol pyruvate (PEP) to obtain 3-deoxy-D-manno-2-octulosonate-8-phosphate (KDO8P). We have elucidated initial modes of ligand binding in KDO8PS binary complexes by X-ray crystallography. Structures of the apo-enzyme and of binary complexes with the substrate PEP, the product KDO8P and the catalytically inactive 1-deoxy analog of arabinose 5-phosphate (1dA5P) were obtained. The KDO8PS active site resembles an irregular funnel with positive electrostatic potential situated at the bottom of the PEP-binding sub-site, which is the primary attractive force towards negatively charged phosphate moieties of all ligands. The structures of the ligand-free apo-KDO8PS and the binary complex with the product KDO8P visualize for the first time the role of His202 as an active-site gate. Examination of the crystal structures of KDO8PS with the KDO8P or 1dA5P shows these ligands bound to the enzyme in the PEP-binding sub-site, and not as expected to the A5P sub-site. Taken together, the structures presented here strengthen earlier evidence that this enzyme functions predominantly through positional catalysis, map out the roles of active-site residues and provide evidence that explains the total lack of catalytic reversibility.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-X8F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X8F OCA].
+</div>
+<div class="pdbe-citations 1x8f" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Crystal structures of Escherichia coli KDO8P synthase complexes reveal the source of catalytic irreversibility., Vainer R, Belakhov V, Rabkin E, Baasov T, Adir N, J Mol Biol. 2005 Aug 19;351(3):641-52. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16023668 16023668]
+*[[Kdo-8-phosphate synthase|Kdo-8-phosphate synthase]]
-[[Category: 3-deoxy-8-phosphooctulonate synthase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Adir, N.]]
+[[Category: Adir N]]
-[[Category: Baasov, T.]]
+[[Category: Baasov T]]
-[[Category: Belakhov, V.]]
+[[Category: Belakhov V]]
-[[Category: Rabkin, E.]]
+[[Category: Rabkin E]]
-[[Category: Vainer, R.]]
+[[Category: Vainer R]]
-[[Category: Beta-alpha-barrel]]
-[[Category: Lipopolysaccharide]]
-[[Category: Lyase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 14:42:06 2008''