PDBsum entry: 2wgc

Lectin (agglutinin)

PDB-id

2wgc

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


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Description

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Protein chains

Ligands

SIA-GAL-BGC ×2

Waters ×235

* Residue conservation analysis

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PDB id:

2wgc

Name:

Lectin (agglutinin)

Title:

2.2 angstroms resolution structure analysis of two refined n-acetylneuraminyllactose-wheat germ agglutinin isolectin complexes

Structure:

Wheat germ lectin. Chain: a, b. Engineered: yes

Source:

Triticum aestivum. Common wheat. Organism_taxid: 4565

Biological unit:

Dimer (from PQS)

UniProt:

Chains A, B: P02876 (AGI2_WHEAT)

Seq:

213 a.a.

Struc:

171 a.a.*

Key:		PfamA domain
		Secondary structure			CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Resolution:

2.20Å

R-factor:

0.153

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

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Key reference

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

19593815 J.A.Garnett, Y.Liu, E.Leon, S.A.Allman, N.Friedrich, S.Saouros, S.Curry, D.Soldati-Favre, B.G.Davis, T.Feizi, and S.Matthews (2009).
Detailed insights from microarray and crystallographic studies into carbohydrate recognition by microneme protein 1 (MIC1) of Toxoplasma gondii.

Protein Sci, 18, 1935-1947.

PDB codes: 3f53 3f5a 3f5e

19629717 W.Ubhayasekera, R.Rawat, S.W.Ho, M.Wiweger, S.Von Arnold, M.L.Chye, and S.L.Mowbray (2009).
The first crystal structures of a family 19 class IV chitinase: the enzyme from Norway spruce.

Plant Mol Biol, 71, 277-289.

PDB codes: 3hbd 3hbe 3hbh

18353982 U.Neu, K.Woellner, G.Gauglitz, and T.Stehle (2008).
Structural basis of GM1 ganglioside recognition by simian virus 40.

Proc Natl Acad Sci U S A, 105, 5219-5224.

PDB codes: 3bwq 3bwr

16759379 R.P.Saha, R.P.Bahadur, A.Pal, S.Mandal, and P.Chakrabarti (2006).
ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces.

BMC Struct Biol, 6, 11.

15229884 E.S.Shih, and M.J.Hwang (2004).
Alternative alignments from comparison of protein structures.

Proteins, 56, 519-527.

14769793 H.A.van den Burg, C.A.Spronk, S.Boeren, M.A.Kennedy, J.P.Vissers, G.W.Vuister, P.J.de Wit, and J.Vervoort (2004).
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.

J Biol Chem, 279, 41573-41579.

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.

J Virol, 75, 11392-11400.

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.

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

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.

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.

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.

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.

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.