3c1u: Difference between revisions

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-{{Seed}}
-[[Image:3c1u.jpg|left|200px]]
-<!--
+==D192N mutant of Rhamnogalacturonan acetylesterase==
-The line below this paragraph, containing "STRUCTURE_3c1u", creates the "Structure Box" on the page.
+<StructureSection load='3c1u' size='340' side='right'caption='[[3c1u]], [[Resolution|resolution]] 1.33&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'>[[3c1u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_aculeatus Aspergillus aculeatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C1U 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]] 1.33&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-{{STRUCTURE_3c1u|  PDB=3c1u  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1u OCA], [https://pdbe.org/3c1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c1u RCSB], [https://www.ebi.ac.uk/pdbsum/3c1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c1u ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RHA1_ASPAC RHA1_ASPAC] Plays a key role in the degradation of rhamnogalacturonan in the cell wall. Acts in synergy together with rhamnogalacturonase A (RGase A) and rhamnogalacturonase B (RGase B).<ref>PMID:7592973</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/c1/3c1u_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=3c1u ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+An extremely low-field signal (at approximately 18 p.p.m.) in the (1)H NMR spectrum of rhamnogalacturonan acetylesterase (RGAE) shows the presence of a short strong hydrogen bond in the structure. This signal was also present in the mutant RGAE D192N, in which Asp192, which is part of the catalytic triad, has been replaced with Asn. A careful analysis of wild-type RGAE and RGAE D192N was conducted with the purpose of identifying possible candidates for the short hydrogen bond with the 18 p.p.m. deshielded proton. Theoretical calculations of chemical shift values were used in the interpretation of the experimental (1)H NMR spectra. The crystal structure of RGAE D192N was determined to 1.33 A resolution and refined to an R value of 11.6% for all data. The structure is virtually identical to the high-resolution (1.12 A) structure of the wild-type enzyme except for the interactions involving the mutation and a disordered loop. Searches of the Cambridge Structural Database were conducted to obtain information on the donor-acceptor distances of different types of hydrogen bonds. The short hydrogen-bond interactions found in RGAE have equivalents in small-molecule structures. An examination of the short hydrogen bonds in RGAE, the calculated pK(a) values and solvent-accessibilities identified a buried carboxylic acid carboxylate hydrogen bond between Asp75 and Asp87 as the likely origin of the 18 p.p.m. signal. Similar hydrogen-bond interactions between two Asp or Glu carboxy groups were found in 16% of a homology-reduced set of high-quality structures extracted from the PDB. The shortest hydrogen bonds in RGAE are all located close to the active site and short interactions between Ser and Thr side-chain OH groups and backbone carbonyl O atoms seem to play an important role in the stability of the protein structure. These results illustrate the significance of short strong hydrogen bonds in proteins.
-===D192N mutant of Rhamnogalacturonan acetylesterase===
+Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase.,Langkilde A, Kristensen SM, Lo Leggio L, Molgaard A, Jensen JH, Houk AR, Navarro Poulsen JC, Kauppinen S, Larsen S Acta Crystallogr D Biol Crystallogr. 2008 Aug;D64(Pt 8):851-63. Epub 2008, Jul 17. PMID:18645234<ref>PMID:18645234</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18645234}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3c1u" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18645234 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18645234}}
+__TOC__
+</StructureSection>
-==About this Structure==
-C1U is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_aculeatus Aspergillus aculeatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1U OCA].
-==Reference==
-Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase., Langkilde A, Kristensen SM, Lo Leggio L, Molgaard A, Jensen JH, Houk AR, Navarro Poulsen JC, Kauppinen S, Larsen S, Acta Crystallogr D Biol Crystallogr. 2008 Aug;64(Pt 8):851-63. Epub 2008, Jul 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18645234 18645234]
-Crystal packing in two pH-dependent crystal forms of rhamnogalacturonan acetylesterase., Molgaard A, Larsen S, Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):472-8. Epub 2004, Feb 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14993671 14993671]
-A branched N-linked glycan at atomic resolution in the 1.12 A structure of rhamnogalacturonan acetylesterase., Molgaard A, Larsen S, Acta Crystallogr D Biol Crystallogr. 2002 Jan;58(Pt 1):111-9. Epub 2001, Dec 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11752785 11752785]
-Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases., Molgaard A, Kauppinen S, Larsen S, Structure. 2000 Apr 15;8(4):373-83. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10801485 10801485]
-Crystallization and preliminary X-ray diffraction studies of the heterogeneously glycosylated enzyme rhamnogalacturonan acetylesterase from Aspergillus aculeatus., Molgaard A, Petersen JF, Kauppinen S, Dalboge H, Johnsen AH, Navarro Poulsen JC, Larsen S, Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):1026-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9757128 9757128]
 [[Category: Aspergillus aculeatus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Langkilde, A.]]
+[[Category: Langkilde A]]
-[[Category: Larsen, S.]]
+[[Category: Larsen S]]
-[[Category: Leggio, L Lo.]]
+[[Category: Lo Leggio L]]
-[[Category: Molgaard, A.]]
+[[Category: Molgaard A]]
-[[Category: Poulsen, J C.Navarro.]]
+[[Category: Navarro Poulsen JC]]
-[[Category: Glycoprotein]]
-[[Category: Pectin degradation]]
-[[Category: Sgnh hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug  6 12:57:22 2008''