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PDBsum entry 1byf

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protein ligands metals Protein-protein interface(s) links
Sugar binding protein PDB id
1byf
Jmol
Contents
Protein chains
123 a.a. *
Ligands
ACT ×4
GOL ×2
Metals
_CA ×4
_ZN ×7
Waters ×279
* Residue conservation analysis
PDB id:
1byf
Name: Sugar binding protein
Title: Structure of tc14; a c-type lectin from the tunicate polyand misakiensis
Structure: Protein (polyandrocarpa lectin). Chain: a, b. Synonym: tc14. Engineered: yes
Source: Polyandrocarpa misakiensis. Organism_taxid: 7723. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: c41. Other_details: synthetic gene
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.207     R-free:   0.250
Authors: S.F.Poget,G.B.Legge,M.Bycroft,R.L.Williams
Key ref:
S.F.Poget et al. (1999). The structure of a tunicate C-type lectin from Polyandrocarpa misakiensis complexed with D -galactose. J Mol Biol, 290, 867-879. PubMed id: 10398588 DOI: 10.1006/jmbi.1999.2910
Date:
14-Oct-98     Release date:   23-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P16108  (LECC_POLMI) -  Lectin
Seq:
Struc:
125 a.a.
123 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     carbohydrate binding     1 term  

 

 
DOI no: 10.1006/jmbi.1999.2910 J Mol Biol 290:867-879 (1999)
PubMed id: 10398588  
 
 
The structure of a tunicate C-type lectin from Polyandrocarpa misakiensis complexed with D -galactose.
S.F.Poget, G.B.Legge, M.R.Proctor, P.J.Butler, M.Bycroft, R.L.Williams.
 
  ABSTRACT  
 
C-type lectins are calcium-dependent carbohydrate-recognising proteins. Isothermal titration calorimetry of the C-type Polyandrocarpa lectin (TC14) from the tunicate Polyandrocarpa misakiensis revealed the presence of a single calcium atom per monomer with a dissociation constant of 2.6 microM, and confirmed the specificity of TC14 for D -galactose and related monosaccharides. We have determined the 2.2 A X-ray crystal structure of Polyandrocarpa lectin complexed with D -galactose. Analytical ultracentrifugation revealed that TC14 behaves as a dimer in solution. This is reflected by the presence of two molecules in the asymmetric unit with the dimeric interface formed by antiparallel pairing of the two N-terminal beta-strands and hydrophobic interactions. TC14 adopts a typical C-type lectin fold with differences in structure from other C-type lectins mainly in the diverse loop regions and in the second alpha-helix, which is involved in the formation of the dimeric interface. The D -galactose is bound through coordination of the 3 and 4-hydroxyl oxygen atoms with a bound calcium atom. Additional hydrogen bonds are formed directly between serine, aspartate and glutamate side-chains of the protein and the sugar 3 and 4-hydroxyl groups. Comparison of the galactose binding by TC14 with the mannose binding by rat mannose-binding protein reveals how monosaccharide specificity is achieved in this lectin. A tryptophan side-chain close to the binding site and the distribution of hydrogen-bond acceptors and donors around the 3 and 4-hydroxyl groups of the sugar are essential determinants of specificity. These elements are, however, arranged in a very different way than in an engineered galactose-specific mutant of MBPA. Possible biological functions can more easily be understood from the fact that TC14 is a dimer under physiological conditions.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Ribbon diagram of the TC14 dimer. All elements of secondary structure are labelled in the upper molecule, and labelling is repeated for some elements in the lower molecule to improve clarity. The sugar-binding calcium ions are shown as grey spheres and the galactose molecules in a ball-and-stick representation.
Figure 6.
Figure 6. Representation of the hydrophobic interactions at the dimeric interface. The phenylalanine residues involved in hydrophobic contacts are shown in ball-and-stick representations. Molecule A is shown in light grey and molecule B in dark grey.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 290, 867-879) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18687680 J.P.Gourdine, G.Cioci, L.Miguet, C.Unverzagt, D.V.Silva, A.Varrot, C.Gautier, E.J.Smith-Ravin, and A.Imberty (2008).
High affinity interaction between a bivalve C-type lectin and a biantennary complex-type N-glycan revealed by crystallography and microcalorimetry.
  J Biol Chem, 283, 30112-30120.
PDB codes: 2vuv 2vuz
17986261 K.Kawamura, Y.Sugino, T.Sunanaga, and S.Fujiwara (2008).
Multipotent epithelial cells in the process of regeneration and asexual reproduction in colonial tunicates.
  Dev Growth Differ, 50, 1.  
17912404 S.E.Kiehna, Z.R.Laughrey, and M.L.Waters (2007).
Evaluation of a carbohydrate-pi interaction in a peptide model system.
  Chem Commun (Camb), (), 4026-4028.  
17437137 V.Pletnev, R.Huether, L.Habegger, W.Schultz, and W.Duax (2007).
Rational proteomics of PKD1. I. Modeling the three dimensional structure and ligand specificity of the C_lectin binding domain of Polycystin-1.
  J Mol Model, 13, 891-896.  
16765898 B.A.Wurzburg, S.S.Tarchevskaya, and T.S.Jardetzky (2006).
Structural changes in the lectin domain of CD23, the low-affinity IgE receptor, upon calcium binding.
  Structure, 14, 1049-1058.
PDB codes: 2h2r 2h2t
16336259 A.N.Zelensky, and J.E.Gready (2005).
The C-type lectin-like domain superfamily.
  FEBS J, 272, 6179-6217.  
15687495 J.M.Mancheño, H.Tateno, I.J.Goldstein, M.Martínez-Ripoll, and J.A.Hermoso (2005).
Structural analysis of the Laetiporus sulphureus hemolytic pore-forming lectin in complex with sugars.
  J Biol Chem, 280, 17251-17259.
PDB codes: 1w3a 1w3f 1w3g
15465324 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.  
15319425 H.Sugawara, M.Kusunoki, G.Kurisu, T.Fujimoto, H.Aoyagi, and T.Hatakeyama (2004).
Characteristic recognition of N-acetylgalactosamine by an invertebrate C-type Lectin, CEL-I, revealed by X-ray crystallographic analysis.
  J Biol Chem, 279, 45219-45225.
PDB codes: 1wmy 1wmz
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.  
15194688 T.Uchida, T.Yamasaki, S.Eto, H.Sugawara, G.Kurisu, A.Nakagawa, M.Kusunoki, and T.Hatakeyama (2004).
Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata: implications of domain structure for its membrane pore-formation mechanism.
  J Biol Chem, 279, 37133-37141.
PDB code: 1vcl
12923175 R.Zhang, H.Y.Cho, H.S.Kim, Y.G.Ma, T.Osaki, S.Kawabata, K.Söderhäll, and B.L.Lee (2003).
Characterization and properties of a 1,3-beta-D-glucan pattern recognition protein of Tenebrio molitor larvae that is specifically degraded by serine protease during prophenoloxidase activation.
  J Biol Chem, 278, 42072-42079.  
11856355 J.C.Achenbach, and K.V.Ewart (2002).
Structural and functional characterization of a C-type lectin-like antifreeze protein from rainbow smelt (Osmerus mordax).
  Eur J Biochem, 269, 1219-1226.  
11861620 K.Natarajan, N.Dimasi, J.Wang, R.A.Mariuzza, and D.H.Margulies (2002).
Structure and function of natural killer cell receptors: multiple molecular solutions to self, nonself discrimination.
  Annu Rev Immunol, 20, 853-885.  
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.  
11248071 M.M.Altamirano, A.Woolfson, A.Donda, A.Shamshiev, L.Briseño-Roa, N.W.Foster, D.B.Veprintsev, G.De Libero, A.R.Fersht, and C.Milstein (2001).
Ligand-independent assembly of recombinant human CD1 by using oxidative refolding chromatography.
  Proc Natl Acad Sci U S A, 98, 3288-3293.  
11264583 W.K.Wang, M.Bycroft, N.W.Foster, A.M.Buckle, A.R.Fersht, and Y.W.Chen (2001).
Structure of the C-terminal sterile alpha-motif (SAM) domain of human p73 alpha.
  Acta Crystallogr D Biol Crystallogr, 57, 545-551.
PDB code: 1dxs
  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.  
10508765 K.Drickamer (1999).
C-type lectin-like domains.
  Curr Opin Struct Biol, 9, 585-590.  
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.