2qqw: Difference between revisions

Latest revision as of 09:27, 6 November 2024

Crystal structure of a cell-wall invertase (D23A) from Arabidopsis thaliana in complex with sucrose

Structural highlights

2qqw is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	FRU, GLC, MAN, NAG, PRD_900003, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

INV1_ARATH Beta-fructofuranosidase that can use sucrose and 1-kestose, and, to a lower extent, neokestose and levan, as substrates, but not inuline.^[1] ^[2]

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

In plants, cell-wall invertases fulfil important roles in carbohydrate partitioning, growth, development and crop yield. In this study, we report on different X-ray crystal structures of Arabidopsis thaliana cell-wall invertase 1 (AtcwINV1) mutants with sucrose. These structures reveal a detailed view of sucrose binding in the active site of the wild-type AtcwINV1. Compared to related enzyme-sucrose complexes, important differences in the orientation of the glucose subunit could be observed. The structure of the E203Q AtcwINV1 mutant showed a complete new binding modus, whereas the D23A, E203A and D239A structures most likely represent the productive binding modus. Together with a hydrophobic zone formed by the conserved W20, W47 and W82, the residues N22, D23, R148, E203, D149 and D239 are necessary to create the ideal sucrose-binding pocket. D239 can interact directly with the glucose moiety of sucrose, whereas K242 has an indirect role in substrate stabilization. Most probably, K242 keeps D239 in a favourable position upon substrate binding. Unravelling the exact position of sucrose in plant cell-wall invertases is a necessary step towards the rational design of superior invertases to further increase crop yield and biomass production.

Crystal structures of Arabidopsis thaliana cell-wall invertase mutants in complex with sucrose.,Lammens W, Le Roy K, Van Laere A, Rabijns A, Van den Ende W J Mol Biol. 2008 Mar 21;377(2):378-85. Epub 2008 Jan 5. PMID:18258263^[3]

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

References

↑ Matrai J, Lammens W, Jonckheer A, Le Roy K, Rabijns A, Van den Ende W, De Maeyer M. An alternate sucrose binding mode in the E203Q Arabidopsis invertase mutant: An X-ray crystallography and docking study. Proteins. 2007 Oct 26;. PMID:17963237 doi:10.1002/prot.21700
↑ Le Roy K, Lammens W, Verhaest M, De Coninck B, Rabijns A, Van Laere A, Van den Ende W. Unraveling the difference between invertases and fructan exohydrolases: a single amino acid (Asp-239) substitution transforms Arabidopsis cell wall invertase1 into a fructan 1-exohydrolase. Plant Physiol. 2007 Nov;145(3):616-25. Epub 2007 Sep 14. PMID:17873089 doi:pp.107.105049
↑ Lammens W, Le Roy K, Van Laere A, Rabijns A, Van den Ende W. Crystal structures of Arabidopsis thaliana cell-wall invertase mutants in complex with sucrose. J Mol Biol. 2008 Mar 21;377(2):378-85. Epub 2008 Jan 5. PMID:18258263 doi:10.1016/j.jmb.2007.12.074

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Matrai J, Lammens W, Jonckheer A, Le Roy K, Rabijns A, Van den Ende W, De Maeyer M. An alternate sucrose binding mode in the E203Q Arabidopsis invertase mutant: An X-ray crystallography and docking study. Proteins. 2007 Oct 26;. PMID:17963237 doi:10.1002/prot.21700

[2] Le Roy K, Lammens W, Verhaest M, De Coninck B, Rabijns A, Van Laere A, Van den Ende W. Unraveling the difference between invertases and fructan exohydrolases: a single amino acid (Asp-239) substitution transforms Arabidopsis cell wall invertase1 into a fructan 1-exohydrolase. Plant Physiol. 2007 Nov;145(3):616-25. Epub 2007 Sep 14. PMID:17873089 doi:pp.107.105049

[3] Lammens W, Le Roy K, Van Laere A, Rabijns A, Van den Ende W. Crystal structures of Arabidopsis thaliana cell-wall invertase mutants in complex with sucrose. J Mol Biol. 2008 Mar 21;377(2):378-85. Epub 2008 Jan 5. PMID:18258263 doi:10.1016/j.jmb.2007.12.074

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='2qqw' size='340' side='right'caption='[[2qqw]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qqw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QQW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qqw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QQW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ac1|2ac1]], [[2oxb|2oxb]], [[2qqv|2qqv]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ATBFRUCT1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-fructofuranosidase Beta-fructofuranosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.26 3.2.1.26] </span></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=2qqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qqw OCA], [https://pdbe.org/2qqw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qqw RCSB], [https://www.ebi.ac.uk/pdbsum/2qqw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qqw ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/INV1_ARATH INV1_ARATH]] Beta-fructofuranosidase that can use sucrose and 1-kestose, and, to a lower extent, neokestose and levan, as substrates, but not inuline.<ref>PMID:17963237</ref> <ref>PMID:17873089</ref>
+[https://www.uniprot.org/uniprot/INV1_ARATH INV1_ARATH] Beta-fructofuranosidase that can use sucrose and 1-kestose, and, to a lower extent, neokestose and levan, as substrates, but not inuline.<ref>PMID:17963237</ref> <ref>PMID:17873089</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qq/2qqw_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 38: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Beta-fructofuranosidase]]
 [[Category: Large Structures]]
-[[Category: Ende, W Van den]]
+[[Category: Lammens W]]
-[[Category: Laere, A Van]]
+[[Category: Le Roy K]]
-[[Category: Lammens, W]]
+[[Category: Rabijns A]]
-[[Category: Rabijns, A]]
+[[Category: Van Laere A]]
-[[Category: Roy, K Le]]
+[[Category: Van den Ende W]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Invertase]]

2qqw: Difference between revisions

Latest revision as of 09:27, 6 November 2024

Crystal structure of a cell-wall invertase (D23A) from Arabidopsis thaliana in complex with sucrose

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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