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PDBsum entry 2dvb
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Sugar binding protein
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PDB id
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2dvb
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Contents |
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* Residue conservation analysis
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PDB id:
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Sugar binding protein
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Title:
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Crystal structure of peanut lectin gal-beta-1,6-galnac complex
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Structure:
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Galactose-binding lectin. Chain: a, b, c, d. Fragment: residues 1-236. Synonym: agglutinin, pna
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Source:
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Arachis hypogaea. Peanut. Organism_taxid: 3818
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Biol. unit:
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Tetramer (from
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Resolution:
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2.25Å
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R-factor:
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0.214
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R-free:
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0.266
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Authors:
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S.K.Natchiar,O.Srinivas,N.Mitra,A.Surolia,N.Jayaraman,M.Vijayan
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Key ref:
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S.K.Natchiar
et al.
(2006).
Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin.
Acta Crystallogr D Biol Crystallogr,
62,
1413-1421.
PubMed id:
DOI:
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Date:
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30-Jul-06
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Release date:
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07-Nov-06
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PROCHECK
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Headers
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References
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P02872
(LECG_ARAHY) -
Galactose-binding lectin from Arachis hypogaea
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Seq:
Struc:
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273 a.a.
232 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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DOI no:
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Acta Crystallogr D Biol Crystallogr
62:1413-1421
(2006)
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PubMed id:
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Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin.
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S.K.Natchiar,
O.Srinivas,
N.Mitra,
A.Surolia,
N.Jayaraman,
M.Vijayan.
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ABSTRACT
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Crystal structures of peanut lectin complexed with Galbeta1-3Gal,
methyl-T-antigen, Galbeta1-6GalNAc, Galalpha1-3Gal and Galalpha1-6Glc and that
of a crystal grown in the presence of Galalpha1-3Galbeta1-4Gal have been
determined using data collected at 100 K. The use of water bridges as a strategy
for generating carbohydrate specificity was previously deduced from the
complexes of the lectin with lactose (Galbeta1-4Glc) and T-antigen
(Galbeta1-3GalNAc). This has been confirmed by the analysis of the complexes
with Galbeta1-3Gal and methyl-T-antigen (Galbeta1-3GalNAc-alpha-OMe). A detailed
analysis of lectin-sugar interactions in the complexes shows that they are more
extensive when the beta-anomer is involved in the linkage. As expected, the
second sugar residue is ill-defined when the linkage is 1-->6. There are more
than two dozen water molecules which occur in the hydration shells of all
structures determined at resolutions better than 2.5 A. Most of them are
involved in stabilizing the structure, particularly loops. Water molecules
involved in lectin-sugar interactions are also substantially conserved. The
lectin molecule is fairly rigid and does not appear to be affected by changes in
temperature.
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Selected figure(s)
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Figure 2.
Figure 2 A PNA monomer with invariant water molecules and the
two metal ions. See text for details.
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Figure 6.
Figure 6 Stereoview of water bridges involving invariant water
molecules in the metal- and sugar-binding region.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2006,
62,
1413-1421)
copyright 2006.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Sharma,
and
M.Vijayan
(2011).
Influence of glycosidic linkage on the nature of carbohydrate binding in beta-prism I fold lectins: an X-ray and molecular dynamics investigation on banana lectin-carbohydrate complexes.
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Glycobiology,
21,
23-33.
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PDB codes:
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G.Pandey,
T.Fatma,
and
S.S.Komath
(2009).
Specific interaction of the legume lectins, concanavalin a and peanut agglutinin, with phycocyanin.
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Photochem Photobiol,
85,
1126-1133.
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C.Gondran,
M.P.Dubois,
S.Fort,
S.Cosnier,
and
S.Szunerits
(2008).
Detection of carbohydrate-binding proteins by oligosaccharide-modified polypyrrole interfaces using electrochemical surface plasmon resonance.
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Analyst,
133,
206-212.
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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.
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Links
