PDBsum entry 4i0c

Immune system/hydrolase

PDB id: 4i0c

Contents

Protein chains

130 a.a.

126 a.a.

Ligands

GOL ×2

Metals

_CL ×7

Waters ×373

PDB id:

4i0c

Name:

Immune system/hydrolase

Title:

The structure of the camelid antibody cabhul5 in complex with human lysozyme

Structure:

LysozymE C. Chain: a, b. Synonym: 1,4-beta-n-acetylmuramidasE C. Engineered: yes. Cabhul5 antibody. Chain: c, d. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: lyz, lzm. Expressed in: komagataella pastoris. Expression_system_taxid: 4922. Camelus dromedarius. Organism_taxid: 9838. Expressed in: escherichia coli.

Resolution:

1.95Å R-factor: 0.189 R-free: 0.219

Authors:

E.De Genst,P.H.Chan,E.Pardon,J.R.Kumita,J.Christodoulou,L.Menzer, D.Y.Chirgadze,C.V.Robinson,S.Muyldermans,A.Matagne,L.Wyns, C.M.Dobson,M.Dumoulin

Key ref:

E.De Genst et al. (2013). A nanobody binding to non-amyloidogenic regions of the protein human lysozyme enhances partial unfolding but inhibits amyloid fibril formation. J Phys Chem B, 117, 13245-13258. PubMed id: 23919586 DOI: 10.1021/jp403425z

Date:

16-Nov-12 Release date: 09-Oct-13

Protein chains

P61626  (LYSC_HUMAN) -  Lysozyme C from Homo sapiens

Seq: 148 a.a.

Struc: 130 a.a.

Protein chains

No UniProt id for this chain

Struc: 126 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: 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: 10.1021/jp403425z

J Phys Chem B 117:13245-13258 (2013)

PubMed id: 23919586

A nanobody binding to non-amyloidogenic regions of the protein human lysozyme enhances partial unfolding but inhibits amyloid fibril formation.

E.De Genst, P.H.Chan, E.Pardon, S.T.Hsu, J.R.Kumita, J.Christodoulou, L.Menzer, D.Y.Chirgadze, C.V.Robinson, S.Muyldermans, A.Matagne, L.Wyns, C.M.Dobson, M.Dumoulin.

ABSTRACT

We report the effects of the interaction of two camelid antibody fragments, generally called nanobodies, namely cAb-HuL5 and a stabilized and more aggregation-resistant variant cAb-HuL5G obtained by protein engineering, on the properties of two amyloidogenic variants of human lysozyme, I56T and D67H , whose deposition in vital organs including the liver, kidney, and spleen is associated with a familial non-neuropathic systemic amyloidosis. Both NMR spectroscopy and X-ray crystallographic studies reveal that cAb-HuL5 binds to the α-domain, one of the two lobes of the native lysozyme structure. The binding of cAb-HuL5/cAb-HuL5G strongly inhibits fibril formation by the amyloidogenic variants; it does not, however, suppress the locally transient cooperative unfolding transitions, characteristic of these variants, in which the β-domain and the C-helix unfold and which represents key early intermediate species in the formation of amyloid fibrils. Therefore, unlike two other nanobodies previously described, cAb-HuL5/cAb-HuL5G does not inhibit fibril formation via the restoration of the global cooperativity of the native structure of the lysozyme variants to that characteristic of the wild-type protein. Instead, it inhibits a subsequent step in the assembly of the fibrils, involving the unfolding and structural reorganization of the α-domain. These results show that nanobodies can protect against the formation of pathogenic aggregates at different stages in the structural transition of a protein from the soluble native state into amyloid fibrils, illustrating their value as structural probes to study the molecular mechanisms of amyloid fibril formation. Combined with their amenability to protein engineering techniques to improve their stability and solubility, these findings support the suggestion that nanobodies can potentially be developed as therapeutics to combat protein misfolding diseases.