4z8b: Difference between revisions

Latest revision as of 10:58, 10 January 2024

crystal structure of a DGL mutant - H51G H131N

Structural highlights

4z8b is a 1 chain structure with sequence from Macropsychanthus grandiflorus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.951Å
Ligands:	CA, GOL, MN, SO4, XMM
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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]

Publication Abstract from PubMed

The structural basis of the pH dependency of the dimer-tetramer transition exhibited by Brinda's type II Diocleinae lectins was investigated by equilibrium sedimentation and X-ray crystal structure determination of recombinant wild-type and site-directed single and double mutants of the pH-stable tetrameric Dioclea grandiflora lectin (r-alphaDGL). Releasing the peripheral site interdimeric contact between R60 and D78 rendered a mutant displaying dimer-tetramer equilibrium in the pH range equivalent to pKa+/-1 of the gamma-COOH. Mutation of both histidines 51 and 131, but not the mutation of each His separately, abolished the formation of the Diocleinae canonical tetramer in the pH range 2.5-8.5. The X-ray structure of the double mutant r-alphaDGL H51G/H131N suggests that H131 plays a crucial role in networking loop 114-125 residues from all four subunits at the central cavity of the tetrameric lectin, and that H51 maintains the central cavity loops in a proper spatial orientation to make H131-mediated interdimer contacts.

Quaternary structure of Dioclea grandiflora lectin assessed by equilibrium sedimentation and crystallographic analysis of recombinant mutants.,Zamora-Caballero S, Perez A, Sanz L, Bravo J, Calvete JJ FEBS Lett. 2015 Jul 27. pii: S0014-5793(15)00645-6. doi:, 10.1016/j.febslet.2015.07.020. PMID:26226421^[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:https://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:https://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:https://dx.doi.org/10.1016/j.biortech.2009.07.062
↑ Zamora-Caballero S, Perez A, Sanz L, Bravo J, Calvete JJ. Quaternary structure of Dioclea grandiflora lectin assessed by equilibrium sedimentation and crystallographic analysis of recombinant mutants. FEBS Lett. 2015 Jul 27. pii: S0014-5793(15)00645-6. doi:, 10.1016/j.febslet.2015.07.020. PMID:26226421 doi:https://dx.doi.org/10.1016/j.febslet.2015.07.020

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OCA

[1] 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

[2] 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

[3] 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:https://dx.doi.org/10.1080/09629359791695

[4] 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

[5] 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:https://dx.doi.org/10.1074/jbc.M000670200

[6] s 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:https://dx.doi.org/10.1016/j.biortech.2009.07.062

[7] Zamora-Caballero S, Perez A, Sanz L, Bravo J, Calvete JJ. Quaternary structure of Dioclea grandiflora lectin assessed by equilibrium sedimentation and crystallographic analysis of recombinant mutants. FEBS Lett. 2015 Jul 27. pii: S0014-5793(15)00645-6. doi:, 10.1016/j.febslet.2015.07.020. PMID:26226421 doi:https://dx.doi.org/10.1016/j.febslet.2015.07.020

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@@ Line 3: / Line 3: @@
 <StructureSection load='4z8b' size='340' side='right'caption='[[4z8b]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4z8b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Diogr Diogr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z8B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z8B FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4z8b]] is a 1 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=4Z8B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z8B FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.951&#8491;</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=4z8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8b OCA], [http://pdbe.org/4z8b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z8b RCSB], [http://www.ebi.ac.uk/pdbsum/4z8b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4z8b ProSAT]</span></td></tr>
+<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=GOL:GLYCEROL'>GOL</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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4z8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8b OCA], [https://pdbe.org/4z8b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z8b RCSB], [https://www.ebi.ac.uk/pdbsum/4z8b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z8b ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Diogr]]
 [[Category: Large Structures]]
-[[Category: Bravo, J]]
+[[Category: Macropsychanthus grandiflorus]]
-[[Category: Calvete, J J]]
+[[Category: Bravo J]]
-[[Category: Perez, A]]
+[[Category: Calvete JJ]]
-[[Category: Sanz, L]]
+[[Category: Perez A]]
-[[Category: Zamora-Caballero, S]]
+[[Category: Sanz L]]
-[[Category: Dioclea grandiflora]]
+[[Category: Zamora-Caballero S]]
-[[Category: H31a-h151n mutant]]
-[[Category: Lectin]]
-[[Category: Sugar binding protein]]

4z8b: Difference between revisions

Latest revision as of 10:58, 10 January 2024

crystal structure of a DGL mutant - H51G H131N

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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