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| | <StructureSection load='5u38' size='340' side='right'caption='[[5u38]], [[Resolution|resolution]] 1.60Å' scene=''> | | <StructureSection load='5u38' size='340' side='right'caption='[[5u38]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5u38]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Platypodium_elegans Platypodium elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U38 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5U38 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5u38]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Platypodium_elegans Platypodium elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U38 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U38 FirstGlance]. <br> |
| - | </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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MMA:O1-METHYL-MANNOSE'>MMA</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]] 1.6Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5u38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u38 OCA], [http://pdbe.org/5u38 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u38 RCSB], [http://www.ebi.ac.uk/pdbsum/5u38 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u38 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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MMA:O1-METHYL-MANNOSE'>MMA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=5u38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u38 OCA], [https://pdbe.org/5u38 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u38 RCSB], [https://www.ebi.ac.uk/pdbsum/5u38 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u38 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/G1EUI6_9FABA G1EUI6_9FABA] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| | [[Category: Platypodium elegans]] | | [[Category: Platypodium elegans]] |
| - | [[Category: Araripe, D A]] | + | [[Category: Araripe DA]] |
| - | [[Category: Cavada, B S]] | + | [[Category: Cavada BS]] |
| - | [[Category: Leal, R B]] | + | [[Category: Leal RB]] |
| - | [[Category: Nascimento, K S]] | + | [[Category: Nascimento KS]] |
| - | [[Category: Neco, A H.B]] | + | [[Category: Neco AHB]] |
| - | [[Category: Osterne, V J.S]] | + | [[Category: Osterne VJS]] |
| - | [[Category: Pinto-Junior, V R]] | + | [[Category: Pinto-Junior VR]] |
| - | [[Category: Rocha, C R.C]] | + | [[Category: Rocha CRC]] |
| - | [[Category: Santiago, M Q]] | + | [[Category: Santiago MQ]] |
| - | [[Category: Silva, I B]] | + | [[Category: Silva IB]] |
| - | [[Category: Silva-Filho, J C]] | + | [[Category: Silva-Filho JC]] |
| - | [[Category: Lectin]]
| + | |
| - | [[Category: Man1-3man-ome]]
| + | |
| - | [[Category: Platypodium elegan]]
| + | |
| - | [[Category: Sugar binding protein]]
| + | |
| Structural highlights
5u38 is a 1 chain structure with sequence from Platypodium elegans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.6Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
G1EUI6_9FABA
Publication Abstract from PubMed
A native lectin (nPELa), purified from seeds of the species Platypodium elegans, Dalbergieae tribe, was crystallized and structurally characterized by X-ray diffraction crystallography and bioinformatics tools. The obtained crystals diffracted to 1.6A resolution, and nPELa structure were solved through molecular substitution. In addition, nPELa has a metal binding site and a conserved carbohydrate recognition domain (CRD) similar to other Dalbergieae tribe lectins, such as PAL (Pterocarpus angolensis) and CTL (Centrolobium tomentosum). Molecular docking analysis indicated high affinity of this lectin for different mannosides, mainly trimannosides, formed by alpha-1,3 or alpha-1,6 glycosidic bond, as evidenced by the obtained scores. In addition, molecular dynamics simulations were performed to demonstrate the structural behavior of nPELa in aqueous solution. In solution, nPELa was highly stable, and structural modifications in its carbohydrate recognition site allowed interaction between the lectin and the different ligands. Different modifications were observed during simulations for each one of the glycans, which included different hydrogen bonds and hydrophobic interactions through changes in the relevant residues. In addition, nPELa was evaluated for its nociceptive activity in mice and was reported to be the first lectin of the Dalbergieae tribe to show CRD-dependent hypernociceptive activity.
Structural studies and nociceptive activity of a native lectin from Platypodium elegans seeds (nPELa).,Cavada BS, Araripe DA, Silva IB, Pinto-Junior VR, Osterne VJS, Neco AHB, Laranjeira EPP, Lossio CF, Correia JLA, Pires AF, Assreuy AMS, Nascimento KS Int J Biol Macromol. 2017 Sep 1. pii: S0141-8130(17)32782-4. doi:, 10.1016/j.ijbiomac.2017.08.174. PMID:28867234[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Cavada BS, Araripe DA, Silva IB, Pinto-Junior VR, Osterne VJS, Neco AHB, Laranjeira EPP, Lossio CF, Correia JLA, Pires AF, Assreuy AMS, Nascimento KS. Structural studies and nociceptive activity of a native lectin from Platypodium elegans seeds (nPELa). Int J Biol Macromol. 2017 Sep 1. pii: S0141-8130(17)32782-4. doi:, 10.1016/j.ijbiomac.2017.08.174. PMID:28867234 doi:http://dx.doi.org/10.1016/j.ijbiomac.2017.08.174
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