PDBsum entry 2dqi

Immune system/hydrolase

PDB id: 2dqi

Contents

Protein chains

107 a.a. *

114 a.a. *

129 a.a. *

Waters ×365

* Residue conservation analysis

PDB id:

2dqi

Name:

Immune system/hydrolase

Title:

Crystal structure of hyhel-10 fv mutant (ly50a) complexed with hen egg lysozyme

Structure:

Lysozyme binding ig kappa chain v23-j2 region. Chain: l. Synonym: light chain of lysozyme antibody hyhel-10. Engineered: yes. Mutation: yes. Ig vh,anti-lysozyme. Chain: h. Synonym: heavy chain of lysozyme antibody hyhel-10. Engineered: yes.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gallus gallus. Chicken. Organism_taxid: 9031. Tissue: egg white

Resolution:

2.00Å R-factor: 0.218 R-free: 0.257

Authors:

M.Shiroishi,H.Kondo,K.Tsumoto,I.Kumagai

Key ref:

M.Shiroishi et al. (2007). Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL. J Biol Chem, 282, 6783-6791. PubMed id: 17166830 DOI: 10.1074/jbc.M605197200

Date:

26-May-06 Release date: 23-Jan-07

Protein chain

No UniProt id for this chain

Struc: 107 a.a.

Protein chain

No UniProt id for this chain

Struc: 114 a.a.

Protein chain

P00698  (LYSC_CHICK) -  Lysozyme C from Gallus gallus

Seq: 147 a.a.

Struc: 129 a.a.

Enzyme reactions

• Enzyme class: Chain Y: E.C.3.2.1.17 - lysozyme.
• Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.

DOI no: 10.1074/jbc.M605197200

J Biol Chem 282:6783-6791 (2007)

PubMed id: 17166830

Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL.

M.Shiroishi, K.Tsumoto, Y.Tanaka, A.Yokota, T.Nakanishi, H.Kondo, I.Kumagai.

ABSTRACT

Tyrosine is an important amino acid in protein-protein interaction hot spots. In particular, many Tyr residues are located in the antigen-binding sites of antibodies and endow high affinity and high specificity to these antibodies. To investigate the role of interfacial Tyr residues in protein-protein interactions, we performed crystallographic studies and thermodynamic analyses of the interaction between hen egg lysozyme (HEL) and the anti-HEL antibody HyHEL-10 Fv fragment. HyHEL-10 has six Tyr residues in its antigen-binding site, which were systematically mutated to Phe and Ala using site-directed mutagenesis. The crystal structures revealed several critical roles for these Tyr residues in the interaction between HEL and HyHEL-10 as follows: 1) the aromatic ring of Tyr-50 in the light chain (LTyr-50) was important for the correct ternary structure of variable regions of the immunoglobulin light chain and heavy chain and of HEL; 2) deletion of the hydroxyl group of Tyr-50 in the heavy chain (HTyr-50) resulted in structural changes in the antigen-antibody interface; and 3) the side chains of HTyr-33 and HTyr-53 may help induce fitting of the antibody to the antigen. Hot spot Tyr residues may contribute to the high affinity and high specificity of the antigen-antibody interaction through a diverse set of structural and thermodynamic interactions.

Selected figure(s)

Figure 1.
FIGURE 1. Tyr residues participating in the interaction of HyHEL10 and HEL. a, overall structure of the wild-type HyHEL-10 Fv-HEL complex. C- traces of VL, VH, and HEL are drawn in green, cyan, and pink, respectively. Tyr residues contacting HEL are represented by orange sticks. Interfacial water molecules bridging Fv and HEL are represented by red balls. b, space-filling model of the wild-type HyHEL-10 Fv fragment from the direction of the antigen-binding site. The contacting residues in VL and VH are shown in green and cyan, respectively. Tyr residues are shown in orange. Interfacial water molecules are shown in red. c, space-filling model of HEL. The residues contacting the six Tyr residues of HyHEL-10 are shown in orange, and the other contacting residues are shown in pink.

Figure 3.
FIGURE 3. Comparison of local structures (at the mutation site) between mutant and wild-type Fv-HEL complexes. a, LY50A-HEL; b, HY33F-HEL; c, HY50F-HEL; d, HY58A-HEL; and e, HY53A-HEL. C- atoms of all polypeptide chains of each mutant complex are superimposed on those of the wild-type complex. Wild-type complex is shown in gray. Residues of VL, VH, and HEL of the mutant complexes are shown in green, cyan, and pink, respectively. Water molecules are shown as red balls. Hydrogen bonds in the mutant complexes and wild-type complexes are depicted as red dotted lines and gray dotted lines, respectively. The amino-aromatic (cation- ) interaction is represented as a gray thick dashed line.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 6783-6791) copyright 2007.

Figures were selected by an automated process.