PDBsum entry: 1afa

Lectin

PDB-id

1afa


	Biological unit* = asymmetric unit, as shown (as deduced by PQS*)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

154 a.a. *

Ligands

MBG ×3

Metal ions

_CA ×9

_CL ×2

Waters ×391

* Residue conservation analysis

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PDB id:

1afa

Name:

Lectin

Title:

Structural basis of galactose recognition in c-type animal lectins

Structure:

Mannose-binding protein-a. Chain: 1, 2, 3. Fragment: clostripain fragment (residues 73 - 226). Synonym: cl-qpdwg. Engineered: yes. Mutation: yes. Other_details: ph 8.0, data collected at 100k, 20% 2- methyl,2-4 pentanediol (cryoprotectant)

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: the bacterially expressed material is digested with clostripain to produce the protein used in the crystal structure analysis

Biological unit:

Trimer (from PQS)

UniProt:

Chains 1, 2, 3: P19999 (MBL1_RAT)

Seq:

238 a.a.

Struc:

154 a.a.*

Key:		PfamA domain
		Secondary structure			CATH domain

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Resolution:

2.00Å

R-factor:

0.221

R-free:

0.268

Authors:

A.R.Kolatkar,W.I.Weis

Key ref:

A.R.Kolatkar and W.I.Weis (1996). Structural basis of galactose recognition by C-type animal lectins.. J Biol Chem, 271, 6679-6685. [PubMed id: 8636086] [DOI: 10.1074/jbc.271.12.6679]

Date:

03-Nov-95

Release date:

03-Apr-96

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Key reference

DOI no: 10.1074/jbc.271.12.6679 J Biol Chem 271:6679-6685 (1996)

PubMed id: 8636086

Structural basis of galactose recognition by C-type animal lectins.

A.R.Kolatkar, W.I.Weis.

ABSTRACT

The asialoglycoprotein receptors and many other C-type (Ca2+-dependent) animal lectins specifically recognize galactose- or N-acetylgalactosamine-terminated oligosaccharides. Analogous binding specificity can be engineered into the homologous rat mannose-binding protein A by changing three amino acids and inserting a glycine-rich loop (Iobst, S. T., and Drickamer, K. (1994) J. Biol. Chem. 269, 15512-15519). Crystal structures of this mutant complexed with beta-methyl galactoside and N-acetylgalactosamine (GalNAc) reveal that as with wild-type mannose-binding proteins, the 3- and 4-OH groups of the sugar directly coordinate Ca2+ and form hydrogen bonds with amino acids that also serve as Ca2+ ligands. The different stereochemistry of the 3- and 4-OH groups in mannose and galactose, combined with a fixed Ca2+ coordination geometry, leads to different pyranose ring locations in the two cases. The glycine-rich loop provides selectivity against mannose by holding a critical tryptophan in a position optimal for packing with the apolar face of galactose but incompatible with mannose binding. The 2-acetamido substituent of GalNAc is in the vicinity of amino acid positions identified by site-directed mutagenesis (Iobst, S. T., and Drickamer, K. (1996) J. Biol. Chem. 271, 6686-6693) as being important for the formation of a GalNAc-selective binding site.

Literature references that cite this PDB file's key reference

PubMed id Reference

19433864 A.S.Powlesland, P.G.Hitchen, S.Parry, S.A.Graham, M.M.Barrio, M.T.Elola, J.Mordoh, A.Dell, K.Drickamer, and M.E.Taylor (2009).
Targeted glycoproteomic identification of cancer cell glycosylation.

Glycobiology, 19, 899-909.

18720336 E.J.Cocinero, E.C.Stanca-Kaposta, E.M.Scanlan, D.P.Gamblin, B.G.Davis, and J.P.Simons (2008).
Conformational choice and selectivity in singly and multiply hydrated monosaccharides in the gas phase.

Chemistry, 14, 8947-8955.

18790731 M.Sakakura, S.Oo-Puthinan, C.Moriyama, T.Kimura, J.Moriya, T.Irimura, and I.Shimada (2008).
Carbohydrate binding mechanism of the macrophage galactose-type C-type lectin 1 revealed by saturation transfer experiments.

J Biol Chem, 283, 33665-33673.

17724729 B.Mertz, A.D.Hill, C.Mulakala, and P.J.Reilly (2007).
Automated docking to explore subsite binding by glycoside hydrolase family 6 cellobiohydrolases and endoglucanases.

Biopolymers, 87, 249-260.

16734974 K.L.White, T.Rades, R.H.Furneaux, P.C.Tyler, and S.Hook (2006).
Mannosylated liposomes as antigen delivery vehicles for targeting to dendritic cells.

J Pharm Pharmacol, 58, 729-737.

16691507 M.Patra, S.Majumder, and C.Mandal (2006).
Structural studies on mannose-selective glycoprotein receptors using molecular modeling techniques.

Glycoconj J, 23, 241-249.

16336259 A.N.Zelensky, and J.E.Gready (2005).
The C-type lectin-like domain superfamily.

FEBS J, 272, 6179-6217.

15030473 J.K.van de Wetering, L.M.van Golde, and J.J.Batenburg (2004).
Collectins: players of the innate immune system.

Eur J Biochem, 271, 1229-1249.

15490154 K.H.Soanes, K.Figuereido, R.C.Richards, N.R.Mattatall, and K.V.Ewart (2004).
Sequence and expression of C-type lectin receptors in Atlantic salmon (Salmo salar).

Immunogenetics, 56, 572-584.

14997539 M.S.Sujatha, and P.V.Balaji (2004).
Identification of common structural features of binding sites in galactose-specific proteins.

Proteins, 55, 44-65.

11866098 T.Hatakeyama, N.Matsuo, K.Shiba, S.Nishinohara, N.Yamasaki, H.Sugawara, and H.Aoyagi (2002).
Amino acid sequence and carbohydrate-binding analysis of the N-acetyl-D-galactosamine-specific C-type lectin, CEL-I, from the Holothuroidea, Cucumaria echinata.

Biosci Biotechnol Biochem, 66, 157-163.

11045608 K.Håkansson, and K.B.Reid (2000).
Collectin structure: a review.

Protein Sci, 9, 1607-1617.

10931211 K.Mann, I.M.Weiss, S.André, H.J.Gabius, and M.Fritz (2000).
The amino-acid sequence of the abalone (Haliotis laevigata) nacre protein perlucin. Detection of a functional C-type lectin domain with galactose/mannose specificity.

Eur J Biochem, 267, 5257-5264.

10748229 Y.Liu, A.J.Chirino, Z.Misulovin, C.Leteux, T.Feizi, M.C.Nussenzweig, and P.J.Bjorkman (2000).
Crystal structure of the cysteine-rich domain of mannose receptor complexed with a sulfated carbohydrate ligand.

J Exp Med, 191, 1105-1116.

PDB codes: 1dqg 1dqo

9922165 K.K.Ng, S.Park-Snyder, and W.I.Weis (1998).
Ca2+-dependent structural changes in C-type mannose-binding proteins.

Biochemistry, 37, 17965-17976.

PDB codes: 1buu 1bv4

9922166 K.K.Ng, and W.I.Weis (1998).
Coupling of prolyl peptide bond isomerization and Ca2+ binding in a C-type mannose-binding protein.

Biochemistry, 37, 17977-17989.

9521729 K.V.Ewart, Z.Li, D.S.Yang, G.L.Fletcher, and C.L.Hew (1998).
The ice-binding site of Atlantic herring antifreeze protein corresponds to the carbohydrate-binding site of C-type lectins.

Biochemistry, 37, 4080-4085.

9700499 W.I.Weis, M.E.Taylor, and K.Drickamer (1998).
The C-type lectin superfamily in the immune system.

Immunol Rev, 163, 19-34.

9057819 H.J.Gabius (1997).
Animal lectins.

Eur J Biochem, 243, 543-576.

9033386 K.K.Ng, and W.I.Weis (1997).
Structure of a selectin-like mutant of mannose-binding protein complexed with sialylated and sulfated Lewis(x) oligosaccharides.

Biochemistry, 36, 979-988.

PDB codes: 1kmb 2kmb 3kmb 4kmb

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.