1hl2: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1hl2.gif|left|200px]]<br /><applet load="1hl2" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1hl2, resolution 1.8&Aring;" />
-'''CRYSTAL STRUCTURE OF N-ACETYLNEURAMINATE LYASE FROM E. COLI MUTANT L142R IN COMPLEX WITH B-HYDROXYPYRUVATE'''<br />
-==Overview==
+==Crystal structure of N-acetylneuraminate lyase from E. coli mutant L142R in complex with b-hydroxypyruvate==
-N-acetylneuraminate lyase (NAL) and dihydrodipicolinate synthase (DHDPS), belong to the NAL subfamily of (betaalpha)(8)-barrels. They share a common, catalytic step but catalyze reactions in different biological pathways. By, rational design, we have introduced various mutations into the NAL, scaffold from Escherichia coli to switch the activity toward DHDPS. These, mutants were tested with respect to their catalytic properties in vivo and, in vitro as well as their stability. One point mutation (L142R) was, sufficient to create an enzyme that could complement a bacterial auxotroph, lacking the gene for DHDPS as efficiently as DHDPS itself. In vitro, this, mutant had an increased DHDPS activity of up to 19-fold as defined by the, specificity constant k(cat)K(M) for the new substrate, l-aspartate-beta-semialdehyde when compared with the residual activity of, NAL wild-type, mainly because of an increased turnover rate. At the same, time, mutant L142R maintained much of its original NAL activity. We have, solved the crystal structure of mutant L142R at 1.8 A resolution in, complex with the inhibitor beta-hydroxypyruvate. This structure reveals, that the conformations of neighboring active site residues are left, virtually unchanged by the mutation. The high flexibility of R142 may, favor its role in assisting in catalysis. Perhaps, nature has exploited, the catalytic promiscuity of many enzymes to evolve novel enzymes or, biological pathways during the course of evolution.
+<StructureSection load='1hl2' size='340' side='right'caption='[[1hl2]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1hl2]] 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=1HL2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HL2 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]] 1.8&#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=1hl2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hl2 OCA], [https://pdbe.org/1hl2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hl2 RCSB], [https://www.ebi.ac.uk/pdbsum/1hl2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hl2 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/hl/1hl2_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=1hl2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+N-acetylneuraminate lyase (NAL) and dihydrodipicolinate synthase (DHDPS) belong to the NAL subfamily of (betaalpha)(8)-barrels. They share a common catalytic step but catalyze reactions in different biological pathways. By rational design, we have introduced various mutations into the NAL scaffold from Escherichia coli to switch the activity toward DHDPS. These mutants were tested with respect to their catalytic properties in vivo and in vitro as well as their stability. One point mutation (L142R) was sufficient to create an enzyme that could complement a bacterial auxotroph lacking the gene for DHDPS as efficiently as DHDPS itself. In vitro, this mutant had an increased DHDPS activity of up to 19-fold as defined by the specificity constant k(cat)K(M) for the new substrate l-aspartate-beta-semialdehyde when compared with the residual activity of NAL wild-type, mainly because of an increased turnover rate. At the same time, mutant L142R maintained much of its original NAL activity. We have solved the crystal structure of mutant L142R at 1.8 A resolution in complex with the inhibitor beta-hydroxypyruvate. This structure reveals that the conformations of neighboring active site residues are left virtually unchanged by the mutation. The high flexibility of R142 may favor its role in assisting in catalysis. Perhaps, nature has exploited the catalytic promiscuity of many enzymes to evolve novel enzymes or biological pathways during the course of evolution.
-==About this Structure==
+Mimicking natural evolution in vitro: an N-acetylneuraminate lyase mutant with an increased dihydrodipicolinate synthase activity.,Joerger AC, Mayer S, Fersht AR Proc Natl Acad Sci U S A. 2003 May 13;100(10):5694-9. Epub 2003 Apr 23. PMID:12711733<ref>PMID:12711733</ref>
-HL2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=3PY:'>3PY</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/N-acetylneuraminate_lyase N-acetylneuraminate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.3 4.1.3.3] Known structural/functional Site: <scene name='pdbsite=CAT:3py+Binding+Site+For+Chain+D'>CAT</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HL2 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Mimicking natural evolution in vitro: an N-acetylneuraminate lyase mutant with an increased dihydrodipicolinate synthase activity., Joerger AC, Mayer S, Fersht AR, Proc Natl Acad Sci U S A. 2003 May 13;100(10):5694-9. Epub 2003 Apr 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12711733 12711733]
+</div>
+<div class="pdbe-citations 1hl2" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[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: Fersht AR]]
-[[Category: Fersht, A.R.]]
+[[Category: Joerger AC]]
-[[Category: Joerger, A.C.]]
-[[Category: 3PY]]
-[[Category: carbohydrate metabolism]]
-[[Category: class i aldolase]]
-[[Category: lyase]]
-[[Category: n-acetylneuraminate lyase]]
-[[Category: schiff base]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 09:50:04 2008''