PDBsum entry 1npl

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Sugar binding protein PDB id
Protein chain
109 a.a. *
PO4 ×3
Waters ×97
* Residue conservation analysis
PDB id:
Name: Sugar binding protein
Title: Mannose-specific agglutinin (lectin) from daffodil (narcissu pseudonarcissus) bulbs in complex with mannose-alpha1,3-man
Structure: Protein (agglutinin). Chain: a. Synonym: daffodil lectin. Other_details: from daffodil plant family of amaryllidaceae
Source: Narcissus pseudonarcissus. Daffodil. Organism_taxid: 39639. Strain: dutch master. Organ: bulbs
Biol. unit: Tetramer (from PDB file)
2.00Å     R-factor:   0.187     R-free:   0.267
Authors: M.K.Sauerborn,L.M.Wright,C.D.Reynolds,J.G.Grossmann,P.J.Rizk
Key ref:
M.K.Sauerborn et al. (1999). Insights into carbohydrate recognition by Narcissus pseudonarcissus lectin: the crystal structure at 2 A resolution in complex with alpha1-3 mannobiose. J Mol Biol, 290, 185-199. PubMed id: 10388566 DOI: 10.1006/jmbi.1999.2862
17-Dec-98     Release date:   23-Dec-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q40423  (Q40423_9ASPA) -  Dimeric mannose specific lectin protein
115 a.a.
109 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)


DOI no: 10.1006/jmbi.1999.2862 J Mol Biol 290:185-199 (1999)
PubMed id: 10388566  
Insights into carbohydrate recognition by Narcissus pseudonarcissus lectin: the crystal structure at 2 A resolution in complex with alpha1-3 mannobiose.
M.K.Sauerborn, L.M.Wright, C.D.Reynolds, J.G.Grossmann, P.J.Rizkallah.
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.
  Selected figure(s)  
Figure 1.
Figure 1. NPL packing diagram, projected down the z-axis, showing subunits A (green), B (orange), C (yellow), and D (purple) of one lectin tetramer. Interfaces between two monomers (1), two dimers (2), and two tetramers (3) are indicated. Interface 4, the contact along the z-axis, is not shown. The projection comprises one unit-cell thickness in the direction out of the plane of the paper (z-direction). Figure prepared with SETOR (Evans, 1993).
Figure 3.
Figure 3. Illustration of the dimer interface showing molecule A in green (ribbon model) and molecule D in purple (space filling model). Molecule A demonstrates the triangular b-prism motif with its 12th strand fitting in a cleft of molecule D. The three main CRDs (I-III) are occupied by a1-3 mannobioses (blue). CRDIV containing an additional a1-3 mannobiose (light blue), is formed by three tryptophan residues (red). Figure prepared with SETOR (Evans, 1993).
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 290, 185-199) copyright 1999.  
  Figures were selected by the author.  
    Author's comment    
  The significance of this structure is that it is tetrameric, as confirmed by the small angle X-ray scattering profile. This is a feature common to all amaryllidaceae lectins, but not the lilyaceae or alliaceae lectins. The geometry of binding also indicates one possible geometry of the binding of a full peptido-glycan, evidence for which is still missing. Additionally, there is a clear indication for sugar ligands being able to cross link between tetramers, both in-plane and out-of-pl
Pierre Rizkallah

Literature references that cite this PDB file's key reference

  PubMed id Reference
18074341 A.D.Hill, and P.J.Reilly (2008).
A Gibbs free energy correlation for automated docking of carbohydrates.
  J Comput Chem, 29, 1131-1141.  
17954971 A.Sharma, D.Chandran, D.D.Singh, and M.Vijayan (2007).
Multiplicity of carbohydrate-binding sites in beta-prism fold lectins: occurrence and possible evolutionary implications.
  J Biosci, 32, 1089-1110.  
17632570 J.Balzarini (2007).
Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy.
  Nat Rev Microbiol, 5, 583-597.  
17609367 S.Naithani, T.Chookajorn, D.R.Ripoll, and J.B.Nasrallah (2007).
Structural modules for receptor dimerization in the S-locus receptor kinase extracellular domain.
  Proc Natl Acad Sci U S A, 104, 12211-12216.  
16170324 S.A.McMahon, J.L.Miller, J.A.Lawton, D.E.Kerkow, A.Hodes, M.A.Marti-Renom, S.Doulatov, E.Narayanan, A.Sali, J.F.Miller, and P.Ghosh (2005).
The C-type lectin fold as an evolutionary solution for massive sequence variation.
  Nat Struct Mol Biol, 12, 886-892.
PDB codes: 1yu0 1yu1 1yu2 1yu3 1yu4
15649901 W.Liu, N.Yang, J.Ding, R.H.Huang, Z.Hu, and D.C.Wang (2005).
Structural mechanism governing the quaternary organization of monocot mannose-binding lectin revealed by the novel monomeric structure of an orchid lectin.
  J Biol Chem, 280, 14865-14876.
PDB codes: 1xd5 1xd6
15388953 A.H.Parret, L.Wyns, R.De Mot, and R.Loris (2004).
Overexpression, purification and crystallization of bacteriocin LlpA from Pseudomonas sp. BW11M1.
  Acta Crystallogr D Biol Crystallogr, 60, 1922-1924.  
12964193 A.Laederach, and P.J.Reilly (2003).
Specific empirical free energy function for automated docking of carbohydrates to proteins.
  J Comput Chem, 24, 1748-1757.  
12736266 S.Walter, and H.Schrempf (2003).
Oligomerization, membrane anchoring, and cellulose-binding characteristics of AbpS, a receptor-like Streptomyces protein.
  J Biol Chem, 278, 26639-26647.  
11856826 G.Ramachandraiah, N.R.Chandra, A.Surolia, and M.Vijayan (2002).
Re-refinement using reprocessed data to improve the quality of the structure: a case study involving garlic lectin.
  Acta Crystallogr D Biol Crystallogr, 58, 414-420.
PDB code: 1kj1
12351829 W.Liu, Y.L.Hu, M.Wang, Y.Xiang, Z.Hu, and D.C.Wang (2002).
Purification, crystallization and preliminary X-ray diffraction analysis of a novel mannose-binding lectin from Gastrodia elata with antifungal properties.
  Acta Crystallogr D Biol Crystallogr, 58, 1833-1835.  
11502201 K.Mann, C.M.Farias, F.G.Del Sol, C.F.Santos, T.B.Grangeiro, C.S.Nagano, B.S.Cavada, and J.J.Calvete (2001).
The amino-acid sequence of the glucose/mannose-specific lectin isolated from Parkia platycephala seeds reveals three tandemly arranged jacalin-related domains.
  Eur J Biochem, 268, 4414-4422.  
10931189 E.J.Van Damme, C.H.Astoul, A.Barre, P.Rougé, and W.J.Peumans (2000).
Cloning and characterization of a monocot mannose-binding lectin from Crocus vernus (family Iridaceae).
  Eur J Biochem, 267, 5067-5077.  
10813817 G.Ramachandraiah, and N.R.Chandra (2000).
Sequence and structural determinants of mannose recognition.
  Proteins, 39, 358-364.  
10508764 J.Bouckaert, T.Hamelryck, L.Wyns, and R.Loris (1999).
Novel structures of plant lectins and their complexes with carbohydrates.
  Curr Opin Struct Biol, 9, 572-577.  
10607664 M.Vijayan, and N.Chandra (1999).
  Curr Opin Struct Biol, 9, 707-714.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.