3c1u

From Proteopedia

(Difference between revisions)

Revision as of 12:35, 5 August 2016

D192N mutant of Rhamnogalacturonan acetylesterase

Structural highlights

3c1u is a 1 chain structure with sequence from Aspac. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1k7c, 1dex, 1deo, 1pp4
Gene:	rha1 (ASPAC)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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).^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kauppinen S, Christgau S, Kofod LV, Halkier T, Dorreich K, Dalboge H. Molecular cloning and characterization of a rhamnogalacturonan acetylesterase from Aspergillus aculeatus. Synergism between rhamnogalacturonan degrading enzymes. J Biol Chem. 1995 Nov 10;270(45):27172-8. PMID:7592973
↑ Langkilde A, Kristensen SM, Lo Leggio L, Molgaard A, Jensen JH, Houk AR, Navarro Poulsen JC, Kauppinen S, Larsen S. Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase. Acta Crystallogr D Biol Crystallogr. 2008 Aug;D64(Pt 8):851-63. Epub 2008, Jul 17. PMID:18645234 doi:10.1107/S0907444908017083

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3c1u"

@@ Line 1: / Line 1: @@
 ==D192N mutant of Rhamnogalacturonan acetylesterase==
 <StructureSection load='3c1u' size='340' side='right' caption='[[3c1u]], [[Resolution|resolution]] 1.33&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3c1u]] is a 1 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C1U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3c1u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspac Aspac]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C1U FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1k7c|1k7c]], [[1dex|1dex]], [[1deo|1deo]], [[1pp4|1pp4]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rha1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5053 Aspergillus aculeatus])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rha1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5053 ASPAC])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c1u RCSB], [http://www.ebi.ac.uk/pdbsum/3c1u PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1u OCA], [http://pdbe.org/3c1u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c1u RCSB], [http://www.ebi.ac.uk/pdbsum/3c1u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3c1u ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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;">
@@ Line 28: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3c1u" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Aspergillus aculeatus]]
+[[Category: Aspac]]
 [[Category: Langkilde, A]]
 [[Category: Larsen, S]]

3c1u

From Proteopedia

Revision as of 12:35, 5 August 2016

D192N mutant of Rhamnogalacturonan acetylesterase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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