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1npl

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(New page: 200px<br /><applet load="1npl" size="450" color="white" frame="true" align="right" spinBox="true" caption="1npl, resolution 2.0&Aring;" /> '''MANNOSE-SPECIFIC AGGL...)
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[[Image:1npl.jpg|left|200px]]<br /><applet load="1npl" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1npl, resolution 2.0&Aring;" />
 
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'''MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM DAFFODIL (NARCISSUS PSEUDONARCISSUS) BULBS IN COMPLEX WITH MANNOSE-ALPHA1,3-MANNOSE'''<br />
 
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==Overview==
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==MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM DAFFODIL (NARCISSUS PSEUDONARCISSUS) BULBS IN COMPLEX WITH MANNOSE-ALPHA1,3-MANNOSE==
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Carbohydrate recognition by monocot mannose-binding lectins was studied, via the crystal structure determination of daffodil (Narcissus, pseudonarcissus) lectin. The lectin was extracted from daffodil bulbs, and, crystallised in the presence of alpha-1,3 mannobiose. Molecular, replacement methods were used to solve the structure using the partially, refined model of Hippeastrum hybrid agglutinin as a search model. The, structure was refined at 2.0 A resolution to a final R -factor of 18.7 %, and Rfreeof 26.7 %.The main feature of the daffodil lectin structure is, the presence of three fully occupied binding pockets per monomer, arranged, around the faces of a triangular beta-prism motif. The pockets have, identical topology, and can bind mono-, di- or oligosaccharides. Strand, exchange forms tightly bound dimers, and higher aggregation states are, achieved through hydrophobic patches on the surface, completing a tetramer, with internal 222-symmetry. There are therefore 12 fully occupied binding, pockets per tetrameric cluster. The tetramer persists in solution, as, shown with small-angle X-ray solution scattering. Extensive sideways and, out-of-plane interactions between tetramers, some mediated via the ligand, make up the bulk of the lattice contacts.A fourth binding site was also, observed. This is unique and has not been observed in similar structures., The site is only partially occupied by a ligand molecule due to the much, lower binding affinity. A comparison with the Galanthus nivalis, agglutinin/mannopentaose complex suggests an involvement of this site in, the recognition mechanism for naturally occurring glycans.
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<StructureSection load='1npl' size='340' side='right'caption='[[1npl]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1npl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Narcissus_pseudonarcissus Narcissus pseudonarcissus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NPL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NPL FirstGlance]. <br>
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</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&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PRD_900112:3alpha-alpha-mannobiose'>PRD_900112</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1npl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1npl OCA], [https://pdbe.org/1npl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1npl RCSB], [https://www.ebi.ac.uk/pdbsum/1npl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1npl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LEC_NARPS LEC_NARPS] D-mannose-binding lectin which binds alpha-D-linked mannose (PubMed:10388566, PubMed:1874921, PubMed:14505313, PubMed:2350177, PubMed:1645507). Displays a high affinity for alpha-(1-6)-mannose oligomers (PubMed:2350177, PubMed:1645507). Able to interact with both terminal and internal alpha-D-mannosyl residues (PubMed:2350177). Displays antiviral activity and therefore may contribute to defense against infections (PubMed:1645507, PubMed:7481093).<ref>PMID:10388566</ref> <ref>PMID:14505313</ref> <ref>PMID:1645507</ref> <ref>PMID:1874921</ref> <ref>PMID:2350177</ref> <ref>PMID:7481093</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/np/1npl_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1npl ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1NPL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Narcissus_pseudonarcissus Narcissus pseudonarcissus] with PO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NPL OCA].
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*[[Agglutinin 3D structures|Agglutinin 3D structures]]
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== References ==
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==Reference==
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<references/>
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Insights into carbohydrate recognition by Narcissus pseudonarcissus lectin: the crystal structure at 2 A resolution in complex with alpha1-3 mannobiose., Sauerborn MK, Wright LM, Reynolds CD, Grossmann JG, Rizkallah PJ, J Mol Biol. 1999 Jul 2;290(1):185-99. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10388566 10388566]
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Narcissus pseudonarcissus]]
[[Category: Narcissus pseudonarcissus]]
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[[Category: Single protein]]
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[[Category: Grossmann JG]]
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[[Category: Grossmann, J.G.]]
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[[Category: Reynolds CD]]
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[[Category: Reynolds, C.D.]]
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[[Category: Rizkallah PJ]]
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[[Category: Rizkallah, P.J.]]
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[[Category: Sauerborn MK]]
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[[Category: Sauerborn, M.K.]]
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[[Category: Wright LM]]
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[[Category: Wright, L.M.]]
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[[Category: PO4]]
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[[Category: 3-mannose]]
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[[Category: agglutinin]]
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[[Category: daffodil]]
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[[Category: lectin]]
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[[Category: mannobiose]]
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[[Category: mannose-alpha1]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:32:45 2007''
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Current revision

MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM DAFFODIL (NARCISSUS PSEUDONARCISSUS) BULBS IN COMPLEX WITH MANNOSE-ALPHA1,3-MANNOSE

PDB ID 1npl

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