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PDBsum entry 1lu1
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Contents |
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* Residue conservation analysis
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PDB id:
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Lectin
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Title:
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The structure of the dolichos biflorus seed lectin in complex with the forssman disaccharide
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Structure:
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Lectin. Chain: a. Synonym: dbl. Engineered: yes. Other_details: dolichos biflorus seed lectin
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Source:
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Vigna unguiculata subsp. Cylindrica. Horse gram. Organism_taxid: 3840. Strain: subsp. Cylindrica. Organ: seed. Expressed in: escherichia coli. Expression_system_taxid: 562
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Biol. unit:
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Tetramer (from PDB file)
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Resolution:
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2.60Å
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R-factor:
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0.194
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R-free:
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0.234
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Authors:
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T.W.Hamelryck,R.Loris,J.Bouckaert,G.Strecker,A.Imberty,E.Fernandez, L.Wyns,M.E.Etzler
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Key ref:
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T.W.Hamelryck
et al.
(1999).
Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectin oligomers from Dolichos biflorus.
J Mol Biol,
286,
1161-1177.
PubMed id:
DOI:
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Date:
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24-Jul-98
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Release date:
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09-Dec-98
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PROCHECK
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Headers
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References
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P05045
(LEC1_VIGUC) -
Seed lectin subunit I from Vigna unguiculata subsp. cylindrica
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Seq:
Struc:
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275 a.a.
253 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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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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DOI no:
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J Mol Biol
286:1161-1177
(1999)
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PubMed id:
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Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectin oligomers from Dolichos biflorus.
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T.W.Hamelryck,
R.Loris,
J.Bouckaert,
M.H.Dao-Thi,
G.Strecker,
A.Imberty,
E.Fernandez,
L.Wyns,
M.E.Etzler.
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ABSTRACT
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The seed lectin (DBL) from the leguminous plant Dolichos biflorus has a unique
specificity among the members of the legume lectin family because of its high
preference for GalNAc over Gal. In addition, precipitation of blood group A+H
substance by DBL is slightly better inhibited by a blood group A trisaccharide
(GalNAc(alpha1-3)[Fuc(alpha1-2)]Gal) containing pentasaccharide, and about 40
times better by the Forssman disaccharide (GalNAc(alpha1-3)GalNAc) than by
GalNAc. We report the crystal structures of the DBL-blood group A trisaccharide
complex and the DBL-Forssman disaccharide complex.A comparison with the binding
sites of Gal-binding legume lectins indicates that the low affinity of DBL for
Gal is due to the substitution of a conserved aromatic residue by an aliphatic
residue (Leu127). Binding studies with a Leu127Phe mutant corroborate these
conclusions. DBL has a higher affinity for GalNAc because the N-acetyl group
compensates for the loss of aromatic stacking in DBL by making a hydrogen bond
with the backbone amide group of Gly103 and a hydrophobic contact with the
side-chains of Trp132 and Tyr104. Some legume lectins possess a hydrophobic
binding site that binds adenine and adenine-derived plant hormones, i.e.
cytokinins. The exact function of this binding site is unknown, but
adenine/cytokinin-binding legume lectins might be involved in storage of plant
hormones or plant growth regulation. The structures of DBL in complex with
adenine and of the dimeric stem and leaf lectin (DB58) from the same plant
provide the first structural data on these binding sites. Both oligomers possess
an unusual architecture, featuring an alpha-helix sandwiched between two
monomers. In both oligomers, this alpha-helix is directly involved in the
formation of the hydrophobic binding site. DB58 adopts a novel quaternary
structure, related to the quaternary structure of the DBL heterotetramer, and
brings the number of know legume lectin dimer types to four.
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Selected figure(s)
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Figure 3.
Figure 3. The overall structure of the DB58 dimer. The dimer
corresponds to dimer AC in the DBL tetramer (Figure 1(b). Metal
ions as in Figure 1(a).
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Figure 6.
Figure 6. Binding of iodinated lectins (wild-type DBL, WTSL;
native recombinant DBL, Native SL; and the Leu127Phe mutant,
L127F) to hog blood group A+H-Sepharose (BGS-Seph).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
286,
1161-1177)
copyright 1999.
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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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Google scholar
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PubMed id
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Reference
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L.L.Eggink,
M.Salas,
C.V.Hanson,
and
J.K.Hoober
(2010).
Peptide sugar mimetics prevent HIV type 1 replication in peripheral blood mononuclear cells in the presence of HIV-positive antiserum.
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AIDS Res Hum Retroviruses,
26,
149-160.
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B.A.Rocha,
F.B.Moreno,
P.Delatorre,
E.P.Souza,
E.S.Marinho,
R.G.Benevides,
J.K.Rustiguel,
L.A.Souza,
C.S.Nagano,
H.Debray,
A.H.Sampaio,
W.F.de Azevedo,
and
B.S.Cavada
(2009).
Purification, characterization, and preliminary X-ray diffraction analysis of a lactose-specific lectin from Cymbosema roseum seeds.
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Appl Biochem Biotechnol,
152,
383-393.
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F.S.Kittur,
H.Y.Yu,
D.R.Bevan,
and
A.Esen
(2009).
Homolog of the maize beta-glucosidase aggregating factor from sorghum is a jacalin-related GalNAc-specific lectin but lacks protein aggregating activity.
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Glycobiology,
19,
277-287.
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S.D'Auria,
L.Petrova,
C.John,
G.Russev,
A.Varriale,
and
V.Bogoeva
(2009).
Tumor-specific protein human galectin-1 interacts with anticancer agents.
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Mol Biosyst,
5,
1331-1336.
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K.Murata,
S.Kawai,
B.Mikami,
and
W.Hashimoto
(2008).
Superchannel of bacteria: biological significance and new horizons.
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Biosci Biotechnol Biochem,
72,
265-277.
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M.A.Wälti,
P.J.Walser,
S.Thore,
A.Grünler,
M.Bednar,
M.Künzler,
and
M.Aebi
(2008).
Structural basis for chitotetraose coordination by CGL3, a novel galectin-related protein from Coprinopsis cinerea.
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J Mol Biol,
379,
146-159.
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PDB codes:
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N.Ay,
K.Clauss,
O.Barth,
and
K.Humbeck
(2008).
Identification and characterization of novel senescence-associated genes from barley (Hordeum vulgare) primary leaves.
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Plant Biol (Stuttg),
10,
121-135.
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K.A.Kulkarni,
S.Katiyar,
A.Surolia,
M.Vijayan,
and
K.Suguna
(2007).
Generation of blood group specificity: new insights from structural studies on the complexes of A- and B-reactive saccharides with basic winged bean agglutinin.
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Proteins,
68,
762-769.
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PDB codes:
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P.Delatorre,
B.A.Rocha,
E.P.Souza,
T.M.Oliveira,
G.A.Bezerra,
F.B.Moreno,
B.T.Freitas,
T.Santi-Gadelha,
A.H.Sampaio,
W.F.Azevedo,
and
B.S.Cavada
(2007).
Structure of a lectin from Canavalia gladiata seeds: new structural insights for old molecules.
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BMC Struct Biol,
7,
52.
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PDB codes:
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R.Nash,
L.Neves,
R.Faast,
M.Pierce,
and
S.Dalton
(2007).
The lectin Dolichos biflorus agglutinin recognizes glycan epitopes on the surface of murine embryonic stem cells: a new tool for characterizing pluripotent cells and early differentiation.
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Stem Cells,
25,
974-982.
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I.I.Gubaidullin,
A.K.Baimiev,
A.V.Chemeris,
and
V.A.Vakhitov
(2006).
Construction of chimeric lectins with new sugar-binding properties.
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Dokl Biochem Biophys,
411,
349-350.
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K.A.Kulkarni,
S.Katiyar,
A.Surolia,
M.Vijayan,
and
K.Suguna
(2006).
Structural basis for the carbohydrate-specificity of basic winged-bean lectin and its differential affinity for Gal and GalNAc.
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Acta Crystallogr D Biol Crystallogr,
62,
1319-1324.
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PDB codes:
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L.Buts,
A.Garcia-Pino,
A.Imberty,
N.Amiot,
G.J.Boons,
S.Beeckmans,
W.Versées,
L.Wyns,
and
R.Loris
(2006).
Structural basis for the recognition of complex-type biantennary oligosaccharides by Pterocarpus angolensis lectin.
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FEBS J,
273,
2407-2420.
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PDB codes:
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M.Pathak,
B.Singh,
A.Sharma,
P.Agrawal,
S.B.Pasha,
H.R.Das,
and
R.H.Das
(2006).
Molecular cloning, expression, and cytokinin (6-benzylaminopurine) antagonist activity of peanut (Arachis hypogaea) lectin SL-I.
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Plant Mol Biol,
62,
529-545.
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S.S.Komath,
M.Kavitha,
and
M.J.Swamy
(2006).
Beyond carbohydrate binding: new directions in plant lectin research.
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Org Biomol Chem,
4,
973-988.
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W.Hashimoto,
K.Momma,
Y.Maruyama,
M.Yamasaki,
B.Mikami,
and
K.Murata
(2005).
Structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules.
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Biosci Biotechnol Biochem,
69,
673-692.
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M.S.Sujatha,
and
P.V.Balaji
(2004).
Identification of common structural features of binding sites in galactose-specific proteins.
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Proteins,
55,
44-65.
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M.Yamasaki,
S.Moriwaki,
O.Miyake,
W.Hashimoto,
K.Murata,
and
B.Mikami
(2004).
Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold.
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J Biol Chem,
279,
31863-31872.
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PDB code:
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W.Hashimoto,
M.Yamasaki,
T.Itoh,
K.Momma,
B.Mikami,
and
K.Murata
(2004).
Super-channel in bacteria: structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules.
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J Biosci Bioeng,
98,
399-413.
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A.Rabijns,
C.Verboven,
P.Rougé,
A.Barre,
E.J.Van Damme,
W.J.Peumans,
and
C.J.De Ranter
(2001).
Structure of a legume lectin from the bark of Robinia pseudoacacia and its complex with N-acetylgalactosamine.
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Proteins,
44,
470-478.
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PDB codes:
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L.M.Brill,
C.J.Evans,
and
A.M.Hirsch
(2001).
Expression of MsLEC1- and MsLEC2-antisense genes in alfalfa plant lines causes severe embryogenic, developmental and reproductive abnormalities.
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Plant J,
25,
453-461.
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S.Elgavish,
and
B.Shaanan
(2001).
Chemical characteristics of dimer interfaces in the legume lectin family.
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Protein Sci,
10,
753-761.
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PDB code:
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A.Medeiros,
S.Bianchi,
J.J.Calvete,
H.Balter,
S.Bay,
A.Robles,
D.Cantacuzène,
M.Nimtz,
P.M.Alzari,
and
E.Osinaga
(2000).
Biochemical and functional characterization of the Tn-specific lectin from Salvia sclarea seeds.
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Eur J Biochem,
267,
1434-1440.
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J.Bouckaert,
T.Hamelryck,
L.Wyns,
and
R.Loris
(1999).
Novel structures of plant lectins and their complexes with carbohydrates.
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Curr Opin Struct Biol,
9,
572-577.
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J.Bouckaert,
T.W.Hamelryck,
L.Wyns,
and
R.Loris
(1999).
The crystal structures of Man(alpha1-3)Man(alpha1-O)Me and Man(alpha1-6)Man(alpha1-O)Me in complex with concanavalin A.
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J Biol Chem,
274,
29188-29195.
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PDB codes:
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J.Jiménez-Barbero,
J.L.Asensio,
F.J.Cañada,
and
A.Poveda
(1999).
Free and protein-bound carbohydrate structures.
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Curr Opin Struct Biol,
9,
549-555.
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M.Vijayan,
and
N.Chandra
(1999).
Lectins.
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Curr Opin Struct Biol,
9,
707-714.
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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
