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Lectin (agglutinin) PDB id
1wgc
Jmol
Contents
Protein chains
171 a.a. *
Ligands
SIA-GAL-BGC ×2
Waters ×214
* Residue conservation analysis
PDB id:
1wgc
Name: Lectin (agglutinin)
Title: 2.2 angstroms resolution structure analysis of two refined n acetylneuraminyllactose-wheat germ agglutinin isolectin com
Structure: Wheat germ lectin. Chain: a, b. Engineered: yes
Source: Triticum aestivum. Bread wheat. Organism_taxid: 4565
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.172    
Authors: C.S.Wright
Key ref: C.S.Wright (1990). 2.2 A resolution structure analysis of two refined N-acetylneuraminyl-lactose--wheat germ agglutinin isolectin complexes. J Mol Biol, 215, 635-651. PubMed id: 2231724 DOI: 10.1016/S0022-2836(05)80174-3
Date:
03-Apr-90     Release date:   15-Oct-90    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P10968  (AGI1_WHEAT) -  Agglutinin isolectin 1
Seq:
Struc: 		212 a.a.
171 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     sugar binding     2 terms  

 

 
DOI no: 10.1016/S0022-2836(05)80174-3 J Mol Biol 215:635-651 (1990)
PubMed id: 2231724  
 
 
2.2 A resolution structure analysis of two refined N-acetylneuraminyl-lactose--wheat germ agglutinin isolectin complexes.
C.S.Wright.
 
  ABSTRACT  
 
The crystal structures of complexes of isolectins 1 and 2 of wheat germ agglutinin (WGA1 and WGA2) with N-acetylneuraminyl-lactose (NeuNAc-alpha(2-3)-Gal-beta(1-4)-Glc) have been refined on the basis of data in the 8 to 2.2 A resolution range to final crystallographic R-factors of 17.2% and 15.3% (Fo greater than 1 sigma), respectively. Specific binding interactions and water association, as well as changes in conformation and mobility of the structure upon ligand binding, were compared in the two complexes. The temperature factors (B = 16.3 A2 and 18.4 A2) were found to be much lower compared with those of their respective native structures (19 to 22 A2). Residues involved in sugar binding, dimerization and in lattice contacts exhibit the largest decreases in B-value, suggesting that sugar binding reduces the overall mobility of the protein molecules in the crystal lattice. The binding mode of this sialyl-trisaccharide, an important cell receptor analogue, has been compared in the two isolectins. Only one of the two unique binding sites (4 per dimer), located in the subunit/subunit interface, is occupied in the crystals. This site, termed the "primary" binding site, contains one of the five amino acid substitutions that differentiate WGA1 and WGA2. Superposition of the refined models in each of the independent crystallographic environments indicates a close match only of the terminal non-reducing NeuNAc residue (root-mean-square delta r of 0.5 to 0.6 A). The Gal-Glc portion was found to superimpose poorly, lack electron density, and possess high atomic thermal factors. In both complexes NeuNAc is stabilized through contact with six amino acid side-chains (Ser114 and Glu115 of subunit 1 and Ser62, Tyr64, Tyr(His)66 and Tyr73 of subunit 2), involving all NeuNAc ring substituents. Refinement has allowed accurate assessment of the contact distances for four hydrogen bonds, a strong buried non-polar contact with the acetamido CH3 group and a large number of van der Waals' interactions with the three aromatic side-chains. The higher affinity of N-acetylneuraminyl-lactose observed by nuclear magnetic resonance studies for WGA1 can be explained by the more favorable binding interactions that occur when residue 66 is a Tyr. The tyrosyl side-chain provides a larger surface for van der Waals' stacking against the NeuNAc pyranose ring than His66 and a hydrogen bond contact with Gal (C2-OH), not possible in WGA2.(ABSTRACT TRUNCATED AT 400 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Structural basis for recognition of phosphodiester-containing lysosomal enzymes by the cation-independent mannose 6-phosphate receptor.
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PDB codes: 2kva 2kvb
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Peptide sugar mimetics prevent HIV type 1 replication in peripheral blood mononuclear cells in the presence of HIV-positive antiserum.
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Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering.
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PDB code: 3iwr
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PDB codes: 3f53 3f5a 3f5e
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PDB codes: 3hbd 3hbe 3hbh
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PDB codes: 3bwq 3bwr
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Binding of the AVR4 elicitor of Cladosporium fulvum to chitotriose units is facilitated by positive allosteric protein-protein interactions: the chitin-binding site of AVR4 represents a novel binding site on the folding scaffold shared between the invertebrate and the plant chitin-binding domain.
  J Biol Chem, 279, 16786-16796.  
15226294 I.Moustafa, H.Connaris, M.Taylor, V.Zaitsev, J.C.Wilson, M.J.Kiefel, M.von Itzstein, and G.Taylor (2004).
Sialic acid recognition by Vibrio cholerae neuraminidase.
  J Biol Chem, 279, 40819-40826.
PDB codes: 1w0o 1w0p
15292169 M.Cavaldesi, M.Caruso, O.Sthandier, P.Amati, and M.I.Garcia (2004).
Conformational changes of murine polyomavirus capsid proteins induced by sialic acid binding.
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15039554 T.Fujii, M.Hayashida, M.Hamasu, M.Ishiguro, and Y.Hata (2004).
Structures of two lectins from the roots of pokeweed (Phytolacca americana).
  Acta Crystallogr D Biol Crystallogr, 60, 665-673.
PDB codes: 1uha 1uln
12676931 H.Hemmi, J.Ishibashi, T.Tomie, and M.Yamakawa (2003).
Structural basis for new pattern of conserved amino acid residues related to chitin-binding in the antifungal peptide from the coconut rhinoceros beetle Oryctes rhinoceros.
  J Biol Chem, 278, 22820-22827.
PDB code: 1iyc
12493725 J.Rao, J.C.Herr, P.P.Reddi, M.J.Wolkowicz, L.A.Bush, N.E.Sherman, M.Black, and C.J.Flickinger (2003).
Cloning and characterization of a novel sperm-associated isoantigen (E-3) with defensin- and lectin-like motifs expressed in rat epididymis.
  Biol Reprod, 68, 290-301.  
11787005 S.V.Vasudevan, and P.V.Balaji (2002).
Molecular dynamics simulations of alpha2 --> 8-linked disialoside: conformational analysis and implications for binding to proteins.
  Biopolymers, 63, 168-180.  
11689620 H.Wedemeyer, E.Mizukoshi, A.R.Davis, J.R.Bennink, and B.Rehermann (2001).
Cross-reactivity between hepatitis C virus and Influenza A virus determinant-specific cytotoxic T cells.
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Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II.
  Structure, 8, 593-603.
PDB codes: 1eis 1en2 1enm
10866795 J.F.Espinosa, J.L.Asensio, J.L.García, J.Laynez, M.Bruix, C.Wright, H.C.Siebert, H.J.Gabius, F.J.Cañada, and J.Jiménez-Barbero (2000).
NMR investigations of protein-carbohydrate interactions binding studies and refined three-dimensional solution structure of the complex between the B domain of wheat germ agglutinin and N,N', N"-triacetylchitotriose.
  Eur J Biochem, 267, 3965-3978.  
10903932 J.L.Asensio, F.J.Cañada, H.C.Siebert, J.Laynez, A.Poveda, P.M.Nieto, U.M.Soedjanaamadja, H.J.Gabius, and J.Jiménez-Barbero (2000).
Structural basis for chitin recognition by defense proteins: GlcNAc residues are bound in a multivalent fashion by extended binding sites in hevein domains.
  Chem Biol, 7, 529-543.  
10842338 J.L.Asensio, H.C.Siebert, C.W.von Der Lieth, J.Laynez, M.Bruix, U.M.Soedjanaamadja, J.J.Beintema, F.J.Cañada, H.J.Gabius, and J.Jiménez-Barbero (2000).
NMR investigations of protein-carbohydrate interactions: studies on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on hevein domains. Determination of the NMR structure of the complex between pseudohevein and N,N',N"-triacetylchitotriose.
  Proteins, 40, 218-236.  
10228146 H.G.Beisel, S.Kawabata, S.Iwanaga, R.Huber, and W.Bode (1999).
Tachylectin-2: crystal structure of a specific GlcNAc/GalNAc-binding lectin involved in the innate immunity host defense of the Japanese horseshoe crab Tachypleus tridentatus.
  EMBO J, 18, 2313-2322.
PDB code: 1tl2
10413474 M.W.Fischer, J.A.Losonczi, J.L.Weaver, and J.H.Prestegard (1999).
Domain orientation and dynamics in multidomain proteins from residual dipolar couplings.
  Biochemistry, 38, 9013-9022.  
10393293 S.D.Wood, L.M.Wright, C.D.Reynolds, P.J.Rizkallah, A.K.Allen, W.J.Peumans, and E.J.Van Damme (1999).
Structure of the native (unligated) mannose-specific bulb lectin from Scilla campanulata (bluebell) at 1.7 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 1264-1272.
PDB code: 1b2p
9660955 A.P.May, R.C.Robinson, M.Vinson, P.R.Crocker, and E.Y.Jones (1998).
Crystal structure of the N-terminal domain of sialoadhesin in complex with 3' sialyllactose at 1.85 A resolution.
  Mol Cell, 1, 719-728.
PDB codes: 1qfo 1qfp
9694833 D.P.Molloy, A.E.Milner, I.K.Yakub, G.Chinnadurai, P.H.Gallimore, and R.J.Grand (1998).
Structural determinants present in the C-terminal binding protein binding site of adenovirus early region 1A proteins.
  J Biol Chem, 273, 20867-20876.  
9305654 T.Stehle, and S.C.Harrison (1997).
High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding.
  EMBO J, 16, 5139-5148.
PDB codes: 1vpn 1vps
  8844838 C.S.Wright, and G.E.Kellogg (1996).
Differences in hydropathic properties of ligand binding at four independent sites in wheat germ agglutinin-oligosaccharide crystal complexes.
  Protein Sci, 5, 1466-1476.  
  8805524 T.Stehle, and S.C.Harrison (1996).
Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments.
  Structure, 4, 183-194.
PDB codes: 1sid 1sie
7588755 H.Nagahora, K.Harata, M.Muraki, and Y.Jigami (1995).
Site-directed mutagenesis and sugar-binding properties of the wheat germ agglutinin mutants Tyr73Phe and Phe116Tyr.
  Eur J Biochem, 233, 27-34.  
7607237 J.L.Asensio, F.J.Canada, M.Bruix, A.Rodriguez-Romero, and J.Jimenez-Barbero (1995).
The interaction of hevein with N-acetylglucosamine-containing oligosaccharides. Solution structure of hevein complexed to chitobiose.
  Eur J Biochem, 230, 621-633.  
  8003954 E.A.Merritt, S.Sarfaty, F.van den Akker, C.L'Hoir, J.A.Martial, and W.G.Hol (1994).
Crystal structure of cholera toxin B-pentamer bound to receptor GM1 pentasaccharide.
  Protein Sci, 3, 166-175.  
  7987217 M.A.Williams, J.M.Goodfellow, and J.M.Thornton (1994).
Buried waters and internal cavities in monomeric proteins.
  Protein Sci, 3, 1224-1235.  
  8075982 P.E.Stein, A.Boodhoo, G.D.Armstrong, S.A.Cockle, M.H.Klein, and R.J.Read (1994).
The crystal structure of pertussis toxin.
  Structure, 2, 45-57.
PDB code: 1prt
  8069624 C.A.Orengo, and J.M.Thornton (1993).
Alpha plus beta folds revisited: some favoured motifs.
  Structure, 1, 105-120.  
8404897 D.Gupta, S.Sabesan, and C.F.Brewer (1993).
Selective inhibition of N-acetylglucosamine and galactose-specific lectins including the 14-kDa vertebrate lectin by novel synthetic biantennary oligosaccharides.
  Eur J Biochem, 216, 789-797.  
8387891 D.W.Banner, A.D'Arcy, W.Janes, R.Gentz, H.J.Schoenfeld, C.Broger, H.Loetscher, and W.Lesslauer (1993).
Crystal structure of the soluble human 55 kd TNF receptor-human TNF beta complex: implications for TNF receptor activation.
  Cell, 73, 431-445.
PDB code: 1tnr
8346557 N.Sharon (1993).
Lectin-carbohydrate complexes of plants and animals: an atomic view.
  Trends Biochem Sci, 18, 221-226.  
8441755 R.Loris, M.H.Thi, J.Lisgarten, and L.Wyns (1993).
Purification, crystallization, and preliminary X-ray studies on the rhizome lectin from stinging nettle and its complex with NN'N"-triacetylchitotriose.
  Proteins, 15, 205-208.  
  8069621 W.P.Burmeister, B.Henrissat, C.Bosso, S.Cusack, and R.W.Ruigrok (1993).
Influenza B virus neuraminidase can synthesize its own inhibitor.
  Structure, 1, 19-26.
PDB codes: 1nsc 1nsd
  1307487 C.von Eichel-Streiber, M.Sauerborn, and H.K.Kuramitsu (1992).
Evidence for a modular structure of the homologous repetitive C-terminal carbohydrate-binding sites of Clostridium difficile toxins and Streptococcus mutans glucosyltransferases.
  J Bacteriol, 174, 6707-6710.  
1483481 H.Nagahora, K.Ishikawa, Y.Niwa, M.Muraki, and Y.Jigami (1992).
Expression and secretion of wheat germ agglutinin by Saccharomyces cerevisiae.
  Eur J Biochem, 210, 989-997.  
  1740114 W.P.Burmeister, R.W.Ruigrok, and S.Cusack (1992).
The 2.2 A resolution crystal structure of influenza B neuraminidase and its complex with sialic acid.
  EMBO J, 11, 49-56.
PDB code: 1nsb
1757999 H.T.Wright, G.Sandrasegaram, and C.S.Wright (1991).
Evolution of a family of N-acetylglucosamine binding proteins containing the disulfide-rich domain of wheat germ agglutinin.
  J Mol Evol, 33, 283-294.  
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.