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PDBsum entry 1afb
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protein ligands metals Protein-protein interface(s) links
Lectin PDB id
1afb

 

 

 

 

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Contents
Protein chains
154 a.a. *
Ligands
NGA ×3
Metals
_CL ×2
_CA ×9
Waters ×371
* Residue conservation analysis
PDB id:
1afb
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
Biol. unit: Trimer (from PQS)
Resolution:
1.90Å     R-factor:   0.217     R-free:   0.261
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
Date:
03-Nov-95     Release date:   03-Apr-96    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19999  (MBL1_RAT) -  Mannose-binding protein A from Rattus norvegicus
Seq:
Struc: 		238 a.a.
154 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 

 
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
21112966 R.T.Lee, T.L.Hsu, S.K.Huang, S.L.Hsieh, C.H.Wong, and Y.C.Lee (2011).
Survey of immune-related, mannose/fucose-binding C-type lectin receptors reveals widely divergent sugar-binding specificities.
  Glycobiology, 21, 512-520.  
20447075 L.R.Forbes, and A.Haczku (2010).
SP-D and regulation of the pulmonary innate immune system in allergic airway changes.
  Clin Exp Allergy, 40, 547-562.  
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.  
16226313 A.Haczku (2006).
Role and regulation of lung collectins in allergic airway sensitization.
  Pharmacol Ther, 110, 14-34.  
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.  
  16508080 R.Mikeska, R.Wacker, R.Arni, T.P.Singh, A.Mikhailov, A.Gabdoulkhakov, W.Voelter, and C.Betzel (2005).
Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 17-25.
PDB codes: 1pum 1puu
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.  
11785767 H.Kogelberg, and T.Feizi (2001).
New structural insights into lectin-type proteins of the immune system.
  Curr Opin Struct Biol, 11, 635-643.  
  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
10469567 A.Loukas, N.P.Mullin, K.K.Tetteh, L.Moens, and R.M.Maizels (1999).
A novel C-type lectin secreted by a tissue-dwelling parasitic nematode.
  Curr Biol, 9, 825-828.  
10508765 K.Drickamer (1999).
C-type lectin-like domains.
  Curr Opin Struct Biol, 9, 585-590.  
10524194 P.J.Neame, H.Tapp, and D.R.Grimm (1999).
The cartilage-derived, C-type lectin (CLECSF1): structure of the gene and chromosomal location.
  Biochim Biophys Acta, 1446, 193-202.  
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.  
9115445 K.Drickamer (1997).
Making a fitting choice: common aspects of sugar-binding sites in plant and animal lectins.
  Structure, 5, 465-468.  
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
9433125 S.Elgavish, and B.Shaanan (1997).
Lectin-carbohydrate interactions: different folds, common recognition principles.
  Trends Biochem Sci, 22, 462-467.  
9345619 W.I.Weis (1997).
Cell-surface carbohydrate recognition by animal and viral lectins.
  Curr Opin Struct Biol, 7, 624-630.  
8913692 P.R.Crocker, and T.Feizi (1996).
Carbohydrate recognition systems: functional triads in cell-cell interactions.
  Curr Opin Struct Biol, 6, 679-691.  
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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