PDBsum entry 3cdf

Immune system

PDB id: 3cdf

Contents

Protein chains

(+ 0 more) 108 a.a. *

Waters ×1056

* Residue conservation analysis

PDB id:

3cdf

Name:

Immune system

Title:

Ki o18/o8 y87h immunoglobulin light chain variable domain

Structure:

Immunoglobulin light chain. Chain: a, b, c, d, e, f. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Organism_taxid: 9606. Gene: ki o18/o8 germline. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.53Å R-factor: 0.191 R-free: 0.231

Authors:

E.M.Baden,E.G.Randles,J.R.Thompson,M.Ramirez-Alvarado

Key ref:

E.M.Baden et al. (2008). Structural insights into the role of mutations in amyloidogenesis. J Biol Chem, 283, 30950-30956. PubMed id: 18768467 DOI: 10.1074/jbc.M804822200

Date:

26-Feb-08 Release date: 02-Sep-08

Protein chains

P01594  (KV133_HUMAN) -  Immunoglobulin kappa variable 1-33 from Homo sapiens

Seq: 117 a.a.

Struc: 108 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1074/jbc.M804822200

J Biol Chem 283:30950-30956 (2008)

PubMed id: 18768467

Structural insights into the role of mutations in amyloidogenesis.

E.M.Baden, E.G.Randles, A.K.Aboagye, J.R.Thompson, M.Ramirez-Alvarado.

ABSTRACT

Mechanisms of amyloidogenesis are not well understood, including potential structural contributions of mutations in the process. Our previous research indicated that the dimer interface of amyloidogenic immunoglobulin light chain protein AL-09 is twisted 90 degrees relative to the protein from its germline sequence, kappaI O18/O8. Here we report a systematic restoration of AL-09 to its germline sequence by mutating the non-conservative somatic mutations located in the light chain dimer interface. Among these mutants, we find a correlation between increased thermodynamic stability and an increase in the lag time for fibril formation. The restorative mutant AL-09 H87Y completes the trifecta and restores the dimer interface observed in kappaI O18/O8, emphasizing the potential importance of the structural integrity of these proteins to protect against amyloidogenicity. We also find that adding amyloidogenic mutations into the germline protein illustrates mutational cooperativity in promoting amyloidogenesis.

Selected figure(s)

Figure 1.
Interface mutations and thermodynamic stability comparison of restorative and reciprocal mutants. a, κI O18/O8 dimer structure with monomers in blue and cyan. Positions of mutations in the dimer interface of AL-09 are shown in green. b, thermal denaturation studies of the restorative mutants indicate that AL-09 H87Y, AL-09 I34N, and the double restorative mutant all increase in thermodynamic stability compared with AL-09. c, thermal denaturation of the single reciprocal mutants shows some destabilizing effects, and the double reciprocal mutant is completely destabilized to the same extent as amyloidogenic AL-09.

Figure 3.
Crystal structures show canonical dimer interface and destabilized loops. a, superposition of κI O18/O8 (blue) and AL-09 H87Y (orange) shows restored dimer interface. b, differences in the loop between Lys-39 and Pro-44 are visible in the global superposition of κI O18/O8 (blue) and κI O18/O8 Y87H (red). c, superposition of κI O18/O8 (blue) and κI O18/O8 N34I/Y87H (green) shows a change in the same loop as observed in b. d, shift of Pro-40 and Gly-41 in the κI O18/O8 Y87H mutant (pink) disrupts an interaction between Tyr-87 and the carbonyl of Gly-41. e, detailed view of Pro-40 and Gly-41 of κI O18/O8 (blue) and κI O18/O8 N34I/Y87H (green) shows same disrupted interaction as observed with the κI O18/O8 Y87H mutant in d. f, hydrogen bonding between the backbone carbonyl of Lys-42 and the OH of Tyr-87 in κI O18/O8 (blue) is lacking with the His-87 mutation in κI O18/O8 Y87H (pink). This is also observed in the κI O18/O8 N34I/Y87H mutant (not pictured).

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 30950-30956) copyright 2008.

Figures were selected by the author.