1npl: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<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>
<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>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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&#8491;</td></tr>
<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>
<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>
<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>
</table>
</table>
== Function ==
[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>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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].
</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].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:10388566<ref>PMID:10388566</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1npl" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Narcissus pseudonarcissus]]
[[Category: Narcissus pseudonarcissus]]
[[Category: Grossmann, J G]]
[[Category: Grossmann JG]]
[[Category: Reynolds, C D]]
[[Category: Reynolds CD]]
[[Category: Rizkallah, P J]]
[[Category: Rizkallah PJ]]
[[Category: Sauerborn, M K]]
[[Category: Sauerborn MK]]
[[Category: Wright, L M]]
[[Category: Wright LM]]
[[Category: 3-mannose]]
[[Category: Agglutinin]]
[[Category: Daffodil]]
[[Category: Lectin]]
[[Category: Mannobiose]]
[[Category: Mannose-alpha1]]
[[Category: Sugar binding protein]]

Revision as of 11:52, 10 April 2024

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

Structural highlights

1npl is a 1 chain structure with sequence from Narcissus pseudonarcissus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).[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.

See Also

References

  1. ↑ Sauerborn MK, Wright LM, Reynolds CD, Grossmann JG, Rizkallah PJ. Insights into carbohydrate recognition by Narcissus pseudonarcissus lectin: the crystal structure at 2 A resolution in complex with alpha1-3 mannobiose. J Mol Biol. 1999 Jul 2;290(1):185-99. PMID:10388566 doi:10.1006/jmbi.1999.2862
  2. ↑ Heyder P, Gaipl US, Beyer TD, Voll RE, Kern PM, Stach C, Kalden JR, Herrmann M. Early detection of apoptosis by staining of acid-treated apoptotic cells with FITC-labeled lectin from Narcissus pseudonarcissus. Cytometry A. 2003 Oct;55(2):86-93. PMID:14505313 doi:10.1002/cyto.a.10078
  3. ↑ Balzarini J, Schols D, Neyts J, Van Damme E, Peumans W, De Clercq E. Alpha-(1-3) inhibitory to human immunodeficiency virus and cytomegalovirus infections in vitro. Antimicrob Agents Chemother. 1991 Mar;35(3):410-6. PMID:1645507 doi:10.1128/AAC.35.3.410
  4. ↑ Weiler BE, Schäcke H, Bachmann M, Brigido L, Gilbert M, Mills J, Matthes E, Forrest JM, Müller WE. Human immunodeficiency virus: novel enzyme-linked immunoassays for quantitation of envelope glycoprotein 120. J Virol Methods. 1991 May;32(2-3):287-301. PMID:1874921 doi:10.1016/0166-0934(91)90059-9
  5. ↑ Kaku H, Van Damme EJ, Peumans WJ, Goldstein IJ. Carbohydrate-binding specificity of the daffodil (Narcissus pseudonarcissus) and amaryllis (Hippeastrum hybr.) bulb lectins. Arch Biochem Biophys. 1990 Jun;279(2):298-304. PMID:2350177 doi:10.1016/0003-9861(90)90495-k
  6. ↑ Marchetti M, Mastromarino P, Rieti S, Seganti L, Orsi N. Inhibition of herpes simplex, rabies and rubella viruses by lectins with different specificities. Res Virol. 1995 May-Jun;146(3):211-5. PMID:7481093 doi:10.1016/0923-2516(96)80581-4

1npl, resolution 2.00Å

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