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| - | [[Image:2je9.gif|left|200px]]<br /><applet load="2je9" size="350" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="2je9, resolution 2.10Å" /> | |
| - | '''CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A-D-MANNOSE'''<br /> | |
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| - | ==About this Structure== | + | ==CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A-D-MANNOSE== |
| - | 2JE9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Dioclea_grandiflora Dioclea grandiflora] with <scene name='pdbligand=XMM:'>XMM</scene>, <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=MN:'>MN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Mn+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Xmm+Binding+Site+For+Chain+A'>AC3</scene>, <scene name='pdbsite=AC4:So4+Binding+Site+For+Chain+A'>AC4</scene>, <scene name='pdbsite=AC5:So4+Binding+Site+For+Chain+A'>AC5</scene>, <scene name='pdbsite=AC6:Ca+Binding+Site+For+Chain+B'>AC6</scene>, <scene name='pdbsite=AC7:Mn+Binding+Site+For+Chain+B'>AC7</scene>, <scene name='pdbsite=AC8:Xmm+Binding+Site+For+Chain+B'>AC8</scene>, <scene name='pdbsite=AC9:So4+Binding+Site+For+Chain+B'>AC9</scene>, <scene name='pdbsite=BC1:So4+Binding+Site+For+Chain+B'>BC1</scene>, <scene name='pdbsite=BC2:So4+Binding+Site+For+Chain+B'>BC2</scene>, <scene name='pdbsite=BC3:Ca+Binding+Site+For+Chain+C'>BC3</scene>, <scene name='pdbsite=BC4:Mn+Binding+Site+For+Chain+C'>BC4</scene>, <scene name='pdbsite=BC5:Xmm+Binding+Site+For+Chain+C'>BC5</scene>, <scene name='pdbsite=BC6:So4+Binding+Site+For+Chain+C'>BC6</scene>, <scene name='pdbsite=BC7:Ca+Binding+Site+For+Chain+D'>BC7</scene>, <scene name='pdbsite=BC8:Mn+Binding+Site+For+Chain+D'>BC8</scene> and <scene name='pdbsite=BC9:Xmm+Binding+Site+For+Chain+D'>BC9</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JE9 OCA].
| + | <StructureSection load='2je9' size='340' side='right'caption='[[2je9]], [[Resolution|resolution]] 2.10Å' scene=''> |
| - | [[Category: Dioclea grandiflora]] | + | == Structural highlights == |
| - | [[Category: Single protein]] | + | <table><tr><td colspan='2'>[[2je9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Macropsychanthus_grandiflorus Macropsychanthus grandiflorus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JE9 FirstGlance]. <br> |
| - | [[Category: Calvete, J.J.]]
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | [[Category: Cavada, B.S.]]
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</scene></td></tr> |
| - | [[Category: Nagano, C.S.]] | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2je9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2je9 OCA], [https://pdbe.org/2je9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2je9 RCSB], [https://www.ebi.ac.uk/pdbsum/2je9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2je9 ProSAT]</span></td></tr> |
| - | [[Category: Sanz, L.]] | + | </table> |
| - | [[Category: CA]]
| + | == Function == |
| - | [[Category: MN]]
| + | [https://www.uniprot.org/uniprot/LECA_DIOGR LECA_DIOGR] D-mannose/D-glucose-binding lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from rat. Induces lymphocyte proliferation and IFNG production. Shows toxicity against the aquatic snail B.glabrata at concentrations higher than 50 ug/ml.<ref>PMID:1398779</ref> <ref>PMID:7524287</ref> <ref>PMID:18472821</ref> <ref>PMID:9575151</ref> <ref>PMID:10747944</ref> <ref>PMID:19765980</ref> |
| - | [[Category: SO4]]
| + | == Evolutionary Conservation == |
| - | [[Category: XMM]]
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | [[Category: calcium]] | + | Check<jmol> |
| - | [[Category: carbohydrate binding protein]]
| + | <jmolCheckbox> |
| - | [[Category: cona-like]]
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/je/2je9_consurf.spt"</scriptWhenChecked> |
| - | [[Category: lectin]]
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | [[Category: legume lectin]] | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | [[Category: manganese]] | + | </jmolCheckbox> |
| - | [[Category: metal- binding]] | + | </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=2je9 ConSurf]. |
| - | [[Category: recombinant lectin]]
| + | <div style="clear:both"></div> |
| - | [[Category: sugar-binding protein]]
| + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | The structural ground underlying the pH-dependency of the dimer-tetramer transition of Diocleinae lectins was investigated by equilibrium sedimentation and X-ray crystal structure determination of wild-type and site-directed mutants of recombinant lectins. Synthetic genes coding for the full-length alpha-chains of the seed lectins of Dioclea guianensis (termed r-alphaDguia) and Dioclea grandiflora (termed r-alphaDGL) were designed and expressed in Escherichia coli. This pioneering approach, which will be described in detail in the present paper, yielded recombinant lectins displaying carbohydrate-binding activity, dimer-tetramer equilibria and crystal structures indistinguishable from their natural homologues. Conversion of the pH-stable tetrameric r-alphaDGL into a structure exhibiting pH-dependent dimer-tetramer transition was accomplished through mutations that abolished the interdimeric interactions at the central cavity of the tetrameric lectins. Both the central and the peripheral interacting regions bear structural information for formation of the canonical legume lectin tetramer. We hypothesize that the strength of the ionic contacts at these sites may be modulated by the pH, leading to dissociation of those lectin structures that are not locked into a pH-stable tetramer through interdimeric contacts networking the central cavity loops. |
| | | | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:44:47 2008''
| + | Insights into the structural basis of the pH-dependent dimer-tetramer equilibrium through crystallographic analysis of recombinant Diocleinae lectins.,Nagano CS, Calvete JJ, Barettino D, Perez A, Cavada BS, Sanz L Biochem J. 2008 Jan 15;409(2):417-28. PMID:17937659<ref>PMID:17937659</ref> |
| | + | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 2je9" style="background-color:#fffaf0;"></div> |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | + | [[Category: Macropsychanthus grandiflorus]] |
| | + | [[Category: Calvete JJ]] |
| | + | [[Category: Cavada BS]] |
| | + | [[Category: Nagano CS]] |
| | + | [[Category: Sanz L]] |
| Structural highlights
Function
LECA_DIOGR D-mannose/D-glucose-binding lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from rat. Induces lymphocyte proliferation and IFNG production. Shows toxicity against the aquatic snail B.glabrata at concentrations higher than 50 ug/ml.[1] [2] [3] [4] [5] [6]
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
The structural ground underlying the pH-dependency of the dimer-tetramer transition of Diocleinae lectins was investigated by equilibrium sedimentation and X-ray crystal structure determination of wild-type and site-directed mutants of recombinant lectins. Synthetic genes coding for the full-length alpha-chains of the seed lectins of Dioclea guianensis (termed r-alphaDguia) and Dioclea grandiflora (termed r-alphaDGL) were designed and expressed in Escherichia coli. This pioneering approach, which will be described in detail in the present paper, yielded recombinant lectins displaying carbohydrate-binding activity, dimer-tetramer equilibria and crystal structures indistinguishable from their natural homologues. Conversion of the pH-stable tetrameric r-alphaDGL into a structure exhibiting pH-dependent dimer-tetramer transition was accomplished through mutations that abolished the interdimeric interactions at the central cavity of the tetrameric lectins. Both the central and the peripheral interacting regions bear structural information for formation of the canonical legume lectin tetramer. We hypothesize that the strength of the ionic contacts at these sites may be modulated by the pH, leading to dissociation of those lectin structures that are not locked into a pH-stable tetramer through interdimeric contacts networking the central cavity loops.
Insights into the structural basis of the pH-dependent dimer-tetramer equilibrium through crystallographic analysis of recombinant Diocleinae lectins.,Nagano CS, Calvete JJ, Barettino D, Perez A, Cavada BS, Sanz L Biochem J. 2008 Jan 15;409(2):417-28. PMID:17937659[7]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Barral-Netto M, Santos SB, Barral A, Moreira LI, Santos CF, Moreira RA, Oliveira JT, Cavada BS. Human lymphocyte stimulation by legume lectins from the Diocleae tribe. Immunol Invest. 1992 Jul;21(4):297-303. PMID:1398779
- ↑ Gomes JC, Ferreira RR, Cavada BS, Moreira RA, Oliveira JT. Histamine release induced by glucose (mannose)-specific lectins isolated from Brazilian beans. Comparison with concanavalin A. Agents Actions. 1994 May;41(3-4):132-5. PMID:7524287
- ↑ Assreuy AM, Shibuya MD, Martins GJ, De Souza ML, Cavada BS, Moreira RA, Oliveira JT, Ribeiro RA, Flores CA. Anti-inflammatory effect of glucose-mannose binding lectins isolated from Brazilian beans. Mediators Inflamm. 1997;6(3):201-10. PMID:18472821 doi:http://dx.doi.org/10.1080/09629359791695
- ↑ Dam TK, Cavada BS, Grangeiro TB, Santos CF, de Sousa FA, Oscarson S, Brewer CF. Diocleinae lectins are a group of proteins with conserved binding sites for the core trimannoside of asparagine-linked oligosaccharides and differential specificities for complex carbohydrates. J Biol Chem. 1998 May 15;273(20):12082-8. PMID:9575151
- ↑ Dam TK, Cavada BS, Grangeiro TB, Santos CF, Ceccatto VM, de Sousa FA, Oscarson S, Brewer CF. Thermodynamic binding studies of lectins from the diocleinae subtribe to deoxy analogs of the core trimannoside of asparagine-linked oligosaccharides. J Biol Chem. 2000 May 26;275(21):16119-26. PMID:10747944 doi:http://dx.doi.org/10.1074/jbc.M000670200
- ↑ dos Santos AF, Cavada BS, da Rocha BA, do Nascimento KS, Sant'Ana AE. Toxicity of some glucose/mannose-binding lectins to Biomphalaria glabrata and Artemia salina. Bioresour Technol. 2010 Jan;101(2):794-8. doi: 10.1016/j.biortech.2009.07.062., Epub 2009 Sep 17. PMID:19765980 doi:http://dx.doi.org/10.1016/j.biortech.2009.07.062
- ↑ Nagano CS, Calvete JJ, Barettino D, Perez A, Cavada BS, Sanz L. Insights into the structural basis of the pH-dependent dimer-tetramer equilibrium through crystallographic analysis of recombinant Diocleinae lectins. Biochem J. 2008 Jan 15;409(2):417-28. PMID:17937659 doi:10.1042/BJ20070942
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