1ur9: Difference between revisions

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-{{Seed}}
-[[Image:1ur9.png|left|200px]]
-<!--
+==Interactions of a family 18 chitinase with the designed inhibitor HM508, and its degradation product, chitobiono-delta-lactone==
-The line below this paragraph, containing "STRUCTURE_1ur9", creates the "Structure Box" on the page.
+<StructureSection load='1ur9' size='340' side='right'caption='[[1ur9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1ur9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UR9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UR9 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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=GDL:2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE'>GDL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PHJ:N-[(AMINOOXY)CARBONYL]-N-PHENYLAMINE'>PHJ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1ur9|  PDB=1ur9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ur9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ur9 OCA], [https://pdbe.org/1ur9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ur9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ur9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ur9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q54276_SERMA Q54276_SERMA]
+== 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/ur/1ur9_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=1ur9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We describe enzymological and structural analyses of the interaction between the family 18 chitinase ChiB from Serratia marcescens and the designed inhibitor N,N'-diacetylchitobionoxime-N-phenylcarbamate (HM508). HM508 acts as a competitive inhibitor of this enzyme with a K(i) in the 50 microM range. Active site mutants of ChiB show K(i) values ranging from 1 to 200 microM, providing insight into some of the interactions that determine inhibitor affinity. Interestingly, the wild type enzyme slowly degrades HM508, but the inhibitor is essentially stable in the presence of the moderately active D142N mutant of ChiB. The crystal structure of the D142N-HM508 complex revealed that the two sugar moieties bind to the -2 and -1 subsites, whereas the phenyl group interacts with aromatic side chains that line the +1 and +2 subsites. Enzymatic degradation of HM508, as well as a Trp --&gt; Ala mutation in the +2 subsite of ChiB, led to reduced affinity for the inhibitor, showing that interactions between the phenyl group and the enzyme contribute to binding. Interestingly, a complex of enzymatically degraded HM508 with the wild type enzyme showed a chitobiono-delta-lactone bound in the -2 and -1 subsites, despite the fact that the equilibrium between the lactone and the hydroxy acid forms in solution lies far toward the latter. This shows that the active site preferentially binds the (4)E conformation of the -1 sugar, which resembles the proposed transition state of the reaction.
-===INTERACTIONS OF A FAMILY 18 CHITINASE WITH THE DESIGNED INHIBITOR HM508, AND ITS DEGRADATION PRODUCT, CHITOBIONO-DELTA-LACTONE===
+Interactions of a family 18 chitinase with the designed inhibitor HM508 and its degradation product, chitobiono-delta-lactone.,Vaaje-Kolstad G, Vasella A, Peter MG, Netter C, Houston DR, Westereng B, Synstad B, Eijsink VG, van Aalten DM J Biol Chem. 2004 Jan 30;279(5):3612-9. Epub 2003 Nov 3. PMID:14597613<ref>PMID:14597613</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ur9" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14597613}}, adds the Publication Abstract to the page
+*[[Chitinase 3D structures|Chitinase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14597613 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14597613}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-UR9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UR9 OCA].
-==Reference==
-Interactions of a family 18 chitinase with the designed inhibitor HM508 and its degradation product, chitobiono-delta-lactone., Vaaje-Kolstad G, Vasella A, Peter MG, Netter C, Houston DR, Westereng B, Synstad B, Eijsink VG, van Aalten DM, J Biol Chem. 2004 Jan 30;279(5):3612-9. Epub 2003 Nov 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14597613 14597613]
-[[Category: Chitinase]]
 [[Category: Serratia marcescens]]
-[[Category: Single protein]]
+[[Category: Eijsink VGH]]
-[[Category: Aalten, D M.F Van.]]
+[[Category: Houston DR]]
-[[Category: Eijsink, V G.H.]]
+[[Category: Netter C]]
-[[Category: Houston, D R.]]
+[[Category: Peter MG]]
-[[Category: Netter, C.]]
+[[Category: Synstad B]]
-[[Category: Peter, M G.]]
+[[Category: Vaaje-Kolstad G]]
-[[Category: Synstad, B.]]
+[[Category: Van Aalten DMF]]
-[[Category: Vaaje-Kolstad, G.]]
+[[Category: Vasella A]]
-[[Category: Vasella, A.]]
+[[Category: Westereng B]]
-[[Category: Westereng, B.]]
-[[Category: Chitin degradation]]
-[[Category: Chitinase]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Inhibition]]
-[[Category: Lactone]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 00:33:23 2008''