1npl: Difference between revisions

Revision as of 15:08, 21 February 2008

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

OverviewOverview

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.

About this StructureAbout this Structure

1NPL is a Single protein structure of sequence from Narcissus pseudonarcissus with as ligand. Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Thu Feb 21 14:08:39 2008

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OCA

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-[[Image:1npl.jpg|left|200px]]<br /><applet load="1npl" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1npl.jpg|left|200px]]<br /><applet load="1npl" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1npl, resolution 2.0&Aring;" />
 '''MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM DAFFODIL (NARCISSUS PSEUDONARCISSUS) BULBS IN COMPLEX WITH MANNOSE-ALPHA1,3-MANNOSE'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-NPL 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].
+NPL 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 <scene name='pdbligand=PO4:'>PO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NPL OCA].
 ==Reference==
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 [[Category: Narcissus pseudonarcissus]]
 [[Category: Single protein]]
-[[Category: Grossmann, J.G.]]
+[[Category: Grossmann, J G.]]
-[[Category: Reynolds, C.D.]]
+[[Category: Reynolds, C D.]]
-[[Category: Rizkallah, P.J.]]
+[[Category: Rizkallah, P J.]]
-[[Category: Sauerborn, M.K.]]
+[[Category: Sauerborn, M K.]]
-[[Category: Wright, L.M.]]
+[[Category: Wright, L M.]]
 [[Category: PO4]]
 [[Category: 3-mannose]]
@@ Line 26: / Line 26: @@
 [[Category: mannose-alpha1]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:32:45 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:08:39 2008''