PDBsum entry 1rum

Immune system

PDB id: 1rum

Contents

Protein chains

219 a.a. *

222 a.a. *

Ligands

BEZ

GOL ×3

Waters ×625

* Residue conservation analysis

PDB id:

1rum

Name:

Immune system

Title:

Crystal structure (f) of h2o2-soaked cationic cyclization antibody 4c6 fab at ph 8.5 with a data set collected at ssrl beamline 9-1.

Structure:

Immunoglobulin igg2a, light chain. Chain: l. Fragment: fab. Immunoglobulin igg2a, heavy chain. Chain: h. Fragment: fab

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Strain: 129g1x+. Strain: 129g1x+

Biol. unit:

Dimer (from PQS)

Resolution:

1.48Å R-factor: 0.175 R-free: 0.245

Authors:

X.Zhu,P.Wentworth Jr.,A.D.Wentworth,A.Eschenmoser,R.A.Lerner, I.A.Wilson

Key ref:

X.Zhu et al. (2004). Probing the antibody-catalyzed water-oxidation pathway at atomic resolution. Proc Natl Acad Sci U S A, 101, 2247-2252. PubMed id: 14982995 DOI: 10.1073/pnas.0307311101

Date:

11-Dec-03 Release date: 02-Mar-04

Protein chain

Q58EU8  (Q58EU8_MOUSE) -  Igk protein from Mus musculus

Seq: 239 a.a.

Struc: 219 a.a.*

Protein chain

P01865  (GCAM_MOUSE) -  Immunoglobulin heavy constant gamma 2A from Mus musculus

Seq: 398 a.a.

Struc: 222 a.a.

* PDB and UniProt seqs differ at 15 residue positions (black crosses)

DOI no: 10.1073/pnas.0307311101

Proc Natl Acad Sci U S A 101:2247-2252 (2004)

PubMed id: 14982995

Probing the antibody-catalyzed water-oxidation pathway at atomic resolution.

X.Zhu, P.Wentworth, A.D.Wentworth, A.Eschenmoser, R.A.Lerner, I.A.Wilson.

ABSTRACT

Antibodies can catalyze the generation of hydrogen peroxide (H2O2) from singlet dioxygen (1O2*) and water via the postulated intermediacy of dihydrogen trioxide (H2O3) and other trioxygen species. Nine different crystal structures were determined to elucidate the chemical consequences to the antibody molecule itself of exposure to such reactive intermediates and to provide insights into the location on the antibody where these species could be generated. Herein, we report structural evidence for modifications of two specific antibody residues within the interfacial region of the variable and constant domains of different murine antibody antigen-binding fragments (Fabs) by reactive species generated during the antibody-catalyzed water oxidation process. Crystal structure analyses of murine Fabs 4C6 and 13G5 after UV-irradiation revealed complex oxidative modifications to tryptophan L163 and, in 4C6, hydroxylation of the Cgamma of glutamine H6. These discrete modifications of specific residues add further support for the "active site" of the water-oxidation pathway being located within the interfacial region of the constant and variable domains and highlight the general resistance of the antibody molecule to oxidation by reactive oxygen species generated during the water-oxidation process.

Selected figure(s)

Figure 1.
Fig. 1. Stereoview of the crystal structure of 4C6 Fab, with the C^ trace of the light (L) and heavy (H) chains colored in light and dark gray, respectively. The modified tryptophan TrpL163 is highlighted in red, and other tryptophan residues (such as TrpH97) are colored green. The modified glutamine residue GlnH6 is also colored red. All of the figures were generated in BOBSCRIPT (12) and rendered in RASTER3D (13).

Figure 4.
Fig. 4. Fourier electron density maps showing TrpL163 in 13G5 Fab for UV-irradiated data set H and native control data set I. For a and b, the tryptophan residue was refined as tryptophan, whereas for control (c and d), the tryptophan residue was refined as alanine to avoid model bias. (a) 2F[o] - F[c] maps (blue), contoured at 1.0 .(b) F[o] - F[c] maps, contoured at 3.0 (green) and -3.0 (red). (c)2F[o] - F[c] maps (blue), contoured at 0.8 .(d) F[o] - F[c] maps, contoured at 3.0 (green).

Figures were selected by an automated process.