PDBsum entry 3d9a

Hydrolase/immune system

PDB id: 3d9a

Contents

Protein chains

129 a.a. *

213 a.a. *

210 a.a. *

Waters ×683

* Residue conservation analysis

PDB id:

3d9a

Name:

Hydrolase/immune system

Title:

High resolution crystal structure structure of hyhel10 fab complexed to hen egg lysozyme

Structure:

LysozymE C. Chain: c. Synonym: 1,4-beta-n-acetylmuramidasE C, allergen gal d 4, allergen gal d iv. Light chain of hyhel10 antibody fragment (fab). Chain: l. Engineered: yes. Heavy chain of hyhel10 antibody fragment (fab). Chain: h.

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Other_details: egg white. Mus musculus. Mouse. Expressed in: escherichia coli.

Resolution:

1.20Å R-factor: 0.191 R-free: 0.205

Authors:

M.E.Desantis,M.Li,A.Shanmuganathan,M.Acchione,R.Walter,A.Wlodawer, S.Smith-Gill

Key ref:

M.Acchione et al. (2009). Light chain somatic mutations change thermodynamics of binding and water coordination in the HyHEL-10 family of antibodies. Mol Immunol, 47, 457-464. PubMed id: 19781789

Date:

27-May-08 Release date: 10-Jun-08

Protein chain

P00698  (LYSC_CHICK) -  Lysozyme C from Gallus gallus

Seq: 147 a.a.

Struc: 129 a.a.

Protein chain

No UniProt id for this chain

Struc: 213 a.a.

Protein chain

No UniProt id for this chain

Struc: 210 a.a.

Enzyme reactions

• Enzyme class: Chain C: 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.

Mol Immunol 47:457-464 (2009)

PubMed id: 19781789

Light chain somatic mutations change thermodynamics of binding and water coordination in the HyHEL-10 family of antibodies.

M.Acchione, C.A.Lipschultz, M.E.DeSantis, A.Shanmuganathan, M.Li, A.Wlodawer, S.Tarasov, S.J.Smith-Gill.

ABSTRACT

Thermodynamic and structural studies addressed the increased affinity due to L-chain somatic mutations in the HyHEL-10 family of affinity matured IgG antibodies, using ITC, SPR with van't Hoff analysis, and X-ray crystallography. When compared to the parental antibody H26L26, the H26L10 and H26L8 chimeras binding to lysozyme showed an increase in favorable DeltaG(o) of -1.2+/-0.1 kcal mol(-1) and -1.3+/-0.1 kcal mol(-1), respectively. Increase in affinity of the H26L10 chimera was due to a net increase in favorable enthalpy change with little difference in change in entropy compared to H26L26. The H26L8 chimera exhibited the greatest increase in favorable enthalpy but also showed an increase in unfavorable entropy change, with the result being that the affinities of both chimeras were essentially equivalent. Site-directed L-chain mutants identified the shared somatic mutation S30G as the dominant contributor to increasing affinity to lysozyme. This mutation was not influenced by H-chain somatic mutations. Residue 30L is at the periphery of the binding interface and S30G effects an increase in hydrophobicity and decrease in H-bonding ability and size, but does not make any new energetically important antigen contacts. A new 1.2-A structure of the H10L10-HEL complex showed changes in the pattern of both inter- and intra-molecular water bridging with no other significant structural alterations near the binding interface compared to the H26L26-HEL complex. These results highlight the necessity for investigating both the structure and the thermodynamics associated with introduced mutations, in order to better assess and understand their impact on binding. Furthermore, it provides an important example of how backbone flexibility and water-bridging may favorably influence the thermodynamics of an antibody-antigen interaction.