 |
PDBsum entry 1a3k
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
J Biol Chem
273:13047-13052
(1998)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
X-ray crystal structure of the human galectin-3 carbohydrate recognition domain at 2.1-A resolution.
|
|
J.Seetharaman,
A.Kanigsberg,
R.Slaaby,
H.Leffler,
S.H.Barondes,
J.M.Rini.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Galectins are a family of lectins which share similar carbohydrate recognition
domains (CRDs) and affinity for small beta-galactosides, but which show
significant differences in binding specificity for more complex glycoconjugates.
We report here the x-ray crystal structure of the human galectin-3 CRD, in
complex with lactose and N-acetyllactosamine, at 2.1-A resolution. This
structure represents the first example of a CRD determined from a galectin which
does not show the canonical 2-fold symmetric dimer organization. Comparison with
the published structures of galectins-1 and -2 provides an explanation for the
differences in carbohydrate-binding specificity shown by galectin-3, and for the
fact that it fails to form dimers by analogous CRD-CRD interactions.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 2.
Fig. 2. The human galectin-3 carbohydrate binding site.
Residues interacting with the bound LacNAc moiety through direct
and water mediated hydrogen bonds or through van der Waals
contacts are shown. The bound LacNAc moiety is shown with yellow
bonds. Oxygen and nitrogen atoms are colored red and blue,
respectively. Water molecules are labeled W1-W3. Potential
hydrogen bonds are shown as dotted lines.
|
|
Figure 3.
Fig. 3. Electrostatic potential of the galectin-3-C
surface viewed into the carbohydrate binding site. The molecular
surface was generated using GRASP (31) with a probe radius of
1.4 Å. Blue and red indicate positive and negative
electrostatic potentials respectively. The bound LacNAc moiety
is shown in stick representation in yellow.
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(1998,
273,
13047-13052)
copyright 1998.
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
C.Diehl,
O.Engström,
T.Delaine,
M.Håkansson,
S.Genheden,
K.Modig,
H.Leffler,
U.Ryde,
U.J.Nilsson,
and
M.Akke
(2010).
Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3.
|
| |
J Am Chem Soc,
132,
14577-14589.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.Salomonsson,
M.C.Carlsson,
V.Osla,
R.Hendus-Altenburger,
B.Kahl-Knutson,
C.T.Oberg,
A.Sundin,
R.Nilsson,
E.Nordberg-Karlsson,
U.J.Nilsson,
A.Karlsson,
J.M.Rini,
and
H.Leffler
(2010).
Mutational tuning of galectin-3 specificity and biological function.
|
| |
J Biol Chem,
285,
35079-35091.
|
|
|
|
|
|
|
K.C.Haudek,
R.J.Patterson,
and
J.L.Wang
(2010).
SR proteins and galectins: what's in a name?
|
| |
Glycobiology,
20,
1199-1207.
|
|
|
|
|
|
|
T.Horlacher,
M.A.Oberli,
D.B.Werz,
L.Kröck,
S.Bufali,
R.Mishra,
J.Sobek,
K.Simons,
M.Hirashima,
T.Niki,
and
P.H.Seeberger
(2010).
Determination of carbohydrate-binding preferences of human galectins with carbohydrate microarrays.
|
| |
Chembiochem,
11,
1563-1573.
|
|
|
|
|
|
|
C.Meynier,
M.Feracci,
M.Espeli,
F.Chaspoul,
P.Gallice,
C.Schiff,
F.Guerlesquin,
and
P.Roche
(2009).
NMR and MD investigations of human galectin-1/oligosaccharide complexes.
|
| |
Biophys J,
97,
3168-3177.
|
|
|
|
|
|
|
G.R.Vasta
(2009).
Roles of galectins in infection.
|
| |
Nat Rev Microbiol,
7,
424-438.
|
|
|
|
|
|
|
J.W.Dennis,
I.R.Nabi,
and
M.Demetriou
(2009).
Metabolism, cell surface organization, and disease.
|
| |
Cell,
139,
1229-1241.
|
|
|
|
|
|
|
J.W.Dennis,
K.S.Lau,
M.Demetriou,
and
I.R.Nabi
(2009).
Adaptive regulation at the cell surface by N-glycosylation.
|
| |
Traffic,
10,
1569-1578.
|
|
|
|
|
|
|
M.Nagae,
N.Nishi,
T.Murata,
T.Usui,
T.Nakamura,
S.Wakatsuki,
and
R.Kato
(2009).
Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain.
|
| |
Glycobiology,
19,
112-117.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.S.Oakley,
V.Majam,
B.Mahajan,
N.Gerald,
V.Anantharaman,
J.M.Ward,
L.J.Faucette,
T.F.McCutchan,
H.Zheng,
M.Terabe,
J.A.Berzofsky,
L.Aravind,
and
S.Kumar
(2009).
Pathogenic roles of CD14, galectin-3, and OX40 during experimental cerebral malaria in mice.
|
| |
PLoS One,
4,
e6793.
|
|
|
|
|
|
|
R.A.de Boer,
A.A.Voors,
P.Muntendam,
W.H.van Gilst,
and
D.J.van Veldhuisen
(2009).
Galectin-3: a novel mediator of heart failure development and progression.
|
| |
Eur J Heart Fail,
11,
811-817.
|
|
|
|
|
|
|
R.D.Cummings
(2009).
The repertoire of glycan determinants in the human glycome.
|
| |
Mol Biosyst,
5,
1087-1104.
|
|
|
|
|
|
|
D.Zhou,
H.Ge,
J.Sun,
Y.Gao,
M.Teng,
and
L.Niu
(2008).
Crystal structure of the C-terminal conserved domain of human GRP, a galectin-related protein, reveals a function mode different from those of galectins.
|
| |
Proteins,
71,
1582-1588.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.M.Rapoport,
O.V.Kurmyshkina,
and
N.V.Bovin
(2008).
Mammalian galectins: structure, carbohydrate specificity, and functions.
|
| |
Biochemistry (Mosc),
73,
393-405.
|
|
|
|
|
|
|
H.Ahmed,
and
G.R.Vasta
(2008).
Unlike mammalian GRIFIN, the zebrafish homologue (DrGRIFIN) represents a functional carbohydrate-binding galectin.
|
| |
Biochem Biophys Res Commun,
371,
350-355.
|
|
|
|
|
|
|
H.Forsman,
E.Salomonsson,
K.Onnheim,
J.Karlsson,
A.Björstad,
H.Leffler,
J.Bylund,
A.Karlsson,
and
C.Dahlgren
(2008).
The beta-galactoside binding immunomodulatory lectin galectin-3 reverses the desensitized state induced in neutrophils by the chemotactic peptide f-Met-Leu-Phe: role of reactive oxygen species generated by the NADPH-oxidase and inactivation of the agonist.
|
| |
Glycobiology,
18,
905-912.
|
|
|
|
|
|
|
H.J.Gould,
and
B.J.Sutton
(2008).
IgE in allergy and asthma today.
|
| |
Nat Rev Immunol,
8,
205-217.
|
|
|
|
|
|
|
M.A.Wälti,
S.Thore,
M.Aebi,
and
M.Künzler
(2008).
Crystal structure of the putative carbohydrate recognition domain of human galectin-related protein.
|
| |
Proteins,
72,
804-808.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.Tamura,
K.Kasai,
T.Itagaki,
T.Nonaka,
and
Y.Arata
(2008).
Identification of a second, non-conserved amino acid that contributes to the unique sugar binding properties of the nematode galectin LEC-1.
|
| |
Biol Pharm Bull,
31,
1254-1257.
|
|
|
|
|
|
|
S.R.Stowell,
C.M.Arthur,
K.A.Slanina,
J.R.Horton,
D.F.Smith,
and
R.D.Cummings
(2008).
Dimeric Galectin-8 induces phosphatidylserine exposure in leukocytes through polylactosamine recognition by the C-terminal domain.
|
| |
J Biol Chem,
283,
20547-20559.
|
|
|
|
|
|
|
T.Zhuang,
H.S.Lee,
B.Imperiali,
and
J.H.Prestegard
(2008).
Structure determination of a Galectin-3-carbohydrate complex using paramagnetism-based NMR constraints.
|
| |
Protein Sci,
17,
1220-1231.
|
|
|
|
|
|
|
D.Delacour,
C.Greb,
A.Koch,
E.Salomonsson,
H.Leffler,
A.Le Bivic,
and
R.Jacob
(2007).
Apical sorting by galectin-3-dependent glycoprotein clustering.
|
| |
Traffic,
8,
379-388.
|
|
|
|
|
|
|
E.Lippert,
W.Falk,
F.Bataille,
T.Kaehne,
M.Naumann,
M.Goeke,
H.Herfarth,
J.Schoelmerich,
and
G.Rogler
(2007).
Soluble galectin-3 is a strong, colonic epithelial-cell-derived, lamina propria fibroblast-stimulating factor.
|
| |
Gut,
56,
43-51.
|
|
|
|
|
|
|
L.Feng,
H.S.Lee,
and
J.H.Prestegard
(2007).
NMR resonance assignments for sparsely 15N labeled proteins.
|
| |
J Biomol NMR,
38,
213-219.
|
|
|
|
|
|
|
P.M.Collins,
K.I.Hidari,
and
H.Blanchard
(2007).
Slow diffusion of lactose out of galectin-3 crystals monitored by X-ray crystallography: possible implications for ligand-exchange protocols.
|
| |
Acta Crystallogr D Biol Crystallogr,
63,
415-419.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.W.Snyder,
G.Lee,
P.E.Marszalek,
R.L.Clark,
and
E.J.Toone
(2007).
A stochastic, cantilever approach to the evaluation of solution phase thermodynamic quantities.
|
| |
Proc Natl Acad Sci U S A,
104,
2579-2584.
|
|
|
|
|
|
|
R.D.Seidel,
T.Zhuang,
and
J.H.Prestegard
(2007).
Bound-state residual dipolar couplings for rapidly exchanging ligands of His-tagged proteins.
|
| |
J Am Chem Soc,
129,
4834-4839.
|
|
|
|
|
|
|
S.Ramasamy,
S.Duraisamy,
S.Barbashov,
T.Kawano,
S.Kharbanda,
and
D.Kufe
(2007).
The MUC1 and galectin-3 oncoproteins function in a microRNA-dependent regulatory loop.
|
| |
Mol Cell,
27,
992.
|
|
|
|
|
|
|
Y.Arata,
N.Ishii,
M.Tamura,
T.Nonaka,
and
K.Kasai
(2007).
Identification of the amino acid residue in the nematode galectin LEC-1 responsible for its unique sugar binding property: analysis by combination of site-directed mutagenesis and frontal affinity chromatography.
|
| |
Biol Pharm Bull,
30,
2012-2017.
|
|
|
|
|
|
|
J.S.Woo,
J.H.Imm,
C.K.Min,
K.J.Kim,
S.S.Cha,
and
B.H.Oh
(2006).
Structural and functional insights into the B30.2/SPRY domain.
|
| |
EMBO J,
25,
1353-1363.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.J.Pieters
(2006).
Inhibition and detection of galectins.
|
| |
Chembiochem,
7,
721-728.
|
|
|
|
|
|
|
S.Yao,
M.S.Liu,
S.L.Masters,
J.G.Zhang,
J.J.Babon,
N.A.Nicola,
S.E.Nicholson,
and
R.S.Norton
(2006).
Dynamics of the SPRY domain-containing SOCS box protein 2: flexibility of key functional loops.
|
| |
Protein Sci,
15,
2761-2772.
|
|
|
|
|
|
|
T.Zhuang,
H.Leffler,
and
J.H.Prestegard
(2006).
Enhancement of bound-state residual dipolar couplings: conformational analysis of lactose bound to Galectin-3.
|
| |
Protein Sci,
15,
1780-1790.
|
|
|
|
|
|
|
V.N.Kasho,
I.N.Smirnova,
and
H.R.Kaback
(2006).
Sequence alignment and homology threading reveals prokaryotic and eukaryotic proteins similar to lactose permease.
|
| |
J Mol Biol,
358,
1060-1070.
|
|
|
|
|
|
|
K.Xie,
S.C.Song,
S.L.Spitalnik,
and
J.E.Wedekind
(2005).
Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition.
|
| |
Acta Crystallogr D Biol Crystallogr,
61,
1386-1394.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.Ballell,
K.J.Alink,
M.Slijper,
C.Versluis,
R.M.Liskamp,
and
R.J.Pieters
(2005).
A new chemical probe for proteomics of carbohydrate-binding proteins.
|
| |
Chembiochem,
6,
291-295.
|
|
|
|
|
|
|
G.R.Vasta,
H.Ahmed,
and
E.W.Odom
(2004).
Structural and functional diversity of lectin repertoires in invertebrates, protochordates and ectothermic vertebrates.
|
| |
Curr Opin Struct Biol,
14,
617-630.
|
|
|
|
|
|
|
T.Mizushima,
T.Hirao,
Y.Yoshida,
S.J.Lee,
T.Chiba,
K.Iwai,
Y.Yamaguchi,
K.Kato,
T.Tsukihara,
and
K.Tanaka
(2004).
Structural basis of sugar-recognizing ubiquitin ligase.
|
| |
Nat Struct Mol Biol,
11,
365-370.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.G.Ford,
T.Weimar,
T.Köhli,
and
R.J.Woods
(2003).
Molecular dynamics simulations of galectin-1-oligosaccharide complexes reveal the molecular basis for ligand diversity.
|
| |
Proteins,
53,
229-240.
|
|
|
|
|
|
|
P.R.Dormitzer,
Z.Y.Sun,
G.Wagner,
and
S.C.Harrison
(2002).
The rhesus rotavirus VP4 sialic acid binding domain has a galectin fold with a novel carbohydrate binding site.
|
| |
EMBO J,
21,
885-897.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
E.Altman,
B.A.Harrison,
R.K.Latta,
K.K.Lee,
J.F.Kelly,
and
P.Thibault
(2001).
Galectin-3-mediated adherence of Proteus mirabilis to Madin-Darby canine kidney cells.
|
| |
Biochem Cell Biol,
79,
783-788.
|
|
|
|
|
|
|
J.D.Schrag,
J.J.Bergeron,
Y.Li,
S.Borisova,
M.Hahn,
D.Y.Thomas,
and
M.Cygler
(2001).
The Structure of calnexin, an ER chaperone involved in quality control of protein folding.
|
| |
Mol Cell,
8,
633-644.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
N.U.Jain,
A.Venot,
K.Umemoto,
H.Leffler,
and
J.H.Prestegard
(2001).
Distance mapping of protein-binding sites using spin-labeled oligosaccharide ligands.
|
| |
Protein Sci,
10,
2393-2400.
|
|
|
|
|
|
|
C.Fradin,
D.Poulain,
and
T.Jouault
(2000).
beta-1,2-linked oligomannosides from Candida albicans bind to a 32-kilodalton macrophage membrane protein homologous to the mammalian lectin galectin-3.
|
| |
Infect Immun,
68,
4391-4398.
|
|
|
|
|
|
|
J.M.Rini,
and
Y.D.Lobsanov
(1999).
New animal lectin structures.
|
| |
Curr Opin Struct Biol,
9,
578-584.
|
|
|
|
|
|
|
M.M.Prabu,
K.Suguna,
and
M.Vijayan
(1999).
Variability in quaternary association of proteins with the same tertiary fold: a case study and rationalization involving legume lectins.
|
| |
Proteins,
35,
58-69.
|
|
|
|
|
|
|
M.Vijayan,
and
N.Chandra
(1999).
Lectins.
|
| |
Curr Opin Struct Biol,
9,
707-714.
|
|
|
|
|
|
|
R.C.Hughes
(1999).
Secretion of the galectin family of mammalian carbohydrate-binding proteins.
|
| |
Biochim Biophys Acta,
1473,
172-185.
|
|
|
|
|
|
|
R.P.Menon,
and
R.C.Hughes
(1999).
Determinants in the N-terminal domains of galectin-3 for secretion by a novel pathway circumventing the endoplasmic reticulum-Golgi complex.
|
| |
Eur J Biochem,
264,
569-576.
|
|
|
|
|
|
|
T.Shirai,
C.Mitsuyama,
Y.Niwa,
Y.Matsui,
H.Hotta,
T.Yamane,
H.Kamiya,
C.Ishii,
T.Ogawa,
and
K.Muramoto
(1999).
High-resolution structure of the conger eel galectin, congerin I, in lactose-liganded and ligand-free forms: emergence of a new structure class by accelerated evolution.
|
| |
Structure,
7,
1223-1233.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.D.Leonidas,
E.H.Vatzaki,
H.Vorum,
J.E.Celis,
P.Madsen,
and
K.R.Acharya
(1998).
Structural basis for the recognition of carbohydrates by human galectin-7.
|
| |
Biochemistry,
37,
13930-13940.
|
|
|
PDB codes:
|
|
|
|
|
|
|
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
code is
shown on the right.
|
|
Links
