1fdy: Difference between revisions

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-[[Image:1fdy.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1fdy", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1fdy|  PDB=1fdy  |  SCENE=  }}
-'''N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH HYDROXYPYRUVATE'''
+==N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH HYDROXYPYRUVATE==
+<StructureSection load='1fdy' size='340' side='right'caption='[[1fdy]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1fdy]] is a 4 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=1FDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FDY 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]] 2.45&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PY:3-HYDROXYPYRUVIC+ACID'>3PY</scene></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=1fdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fdy OCA], [https://pdbe.org/1fdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fdy RCSB], [https://www.ebi.ac.uk/pdbsum/1fdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fdy ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NANA_ECOLI NANA_ECOLI] Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate.[HAMAP-Rule:MF_01237]
+== 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/fd/1fdy_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1fdy ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We describe here a sub-family of enzymes related both structurally and functionally to N-acetylneuraminate lyase. Two members of this family (N-acetylneuraminate lyase and dihydrodipicolinate synthase) have known three-dimensional structures and we now proceed to show their structural and functional relationship to two further proteins, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase and D-4-deoxy-5-oxoglucarate dehydratase. These enzymes are all thought to involve intermediate Schiff-base formation with their respective substrates. In order to understand the nature of this intermediate, we have determined the three-dimensional structure of N-acetylneuraminate lyase in complex with hydroxypyruvate (a product analogue) and in complex with one of its products (pyruvate). From these structures we deduce the presence of a closely similar Schiff-base forming motif in all members of the N-acetylneuraminate lyase sub-family. A fifth protein, MosA, is also confirmed to be a member of the sub-family although the involvement of an intermediate Schiff-base in its proposed reaction is unclear.
-==Overview==
+Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase.,Lawrence MC, Barbosa JA, Smith BJ, Hall NE, Pilling PA, Ooi HC, Marcuccio SM J Mol Biol. 1997 Feb 21;266(2):381-99. PMID:9047371<ref>PMID:9047371</ref>
-We describe here a sub-family of enzymes related both structurally and functionally to N-acetylneuraminate lyase. Two members of this family (N-acetylneuraminate lyase and dihydrodipicolinate synthase) have known three-dimensional structures and we now proceed to show their structural and functional relationship to two further proteins, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase and D-4-deoxy-5-oxoglucarate dehydratase. These enzymes are all thought to involve intermediate Schiff-base formation with their respective substrates. In order to understand the nature of this intermediate, we have determined the three-dimensional structure of N-acetylneuraminate lyase in complex with hydroxypyruvate (a product analogue) and in complex with one of its products (pyruvate). From these structures we deduce the presence of a closely similar Schiff-base forming motif in all members of the N-acetylneuraminate lyase sub-family. A fifth protein, MosA, is also confirmed to be a member of the sub-family although the involvement of an intermediate Schiff-base in its proposed reaction is unclear.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-FDY 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=1FDY OCA].
+</div>
+<div class="pdbe-citations 1fdy" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase., Lawrence MC, Barbosa JA, Smith BJ, Hall NE, Pilling PA, Ooi HC, Marcuccio SM, J Mol Biol. 1997 Feb 21;266(2):381-99. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9047371 9047371]
+*[[N-acetylneuraminate lyase 3D structures|N-acetylneuraminate lyase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: N-acetylneuraminate lyase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Barbosa JARG]]
-[[Category: Barbosa, J A.R G.]]
+[[Category: Hall NE]]
-[[Category: Hall, N E.]]
+[[Category: Lawrence MC]]
-[[Category: Lawrence, M C.]]
+[[Category: Marcuccio SM]]
-[[Category: Marcuccio, S M.]]
+[[Category: Ooi HC]]
-[[Category: Ooi, H C.]]
+[[Category: Pilling PA]]
-[[Category: Pilling, P A.]]
+[[Category: Smith BJ]]
-[[Category: Smith, B J.]]
-[[Category: Aldolase]]
-[[Category: Alpha-keto-acid lyase]]
-[[Category: Carbon-carbon lyase]]
-[[Category: Lyase]]
-[[Category: Oxo-acid lyase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 16:12:58 2008''