7NMS

InlB392_T332E: T332E variant of Listeria monocytogenes InlB (internalin B) residues 36-392

Summary for 7NMS

• Entry DOI: 10.2210/pdb7nms/pdb
• Related: 1D0B 1H6T 1M9S 2Y5P 2Y5Q 7pv8 7pv9
• Descriptor: Internalin B, SULFATE ION, GLYCEROL, ... (5 entities in total)
• Functional Keywords: leucine rich repeat, protein binding, pathogenicity, virulence factor, cell invasion
• Biological source: Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
• Total number of polymer chains: 1
• Total formula weight: 41028.30

Authors

Geerds, C.,Niemann, H.H. (deposition date: 2021-02-23, release date: 2022-01-26, Last modification date: 2024-01-31)

Primary citation

Geerds, C.,Bleymuller, W.M.,Meyer, T.,Widmann, C.,Niemann, H.H.
A recurring packing contact in crystals of InlB pinpoints functional binding sites in the internalin domain and the B repeat.
Acta Crystallogr D Struct Biol, 78:310-320, 2022

PubMed Abstract: InlB, a bacterial agonist of the human receptor tyrosine kinase MET, consists of an N-terminal internalin domain, a central B repeat and three C-terminal GW domains. In all previous structures of full-length InlB or an InlB construct lacking the GW domains (InlB), there was no interpretable electron density for the B repeat. Here, three InlB crystal structures in which the B repeat is resolved are described. These are the first structures to reveal the relative orientation of the internalin domain and the B repeat. A wild-type structure and two structures of the T332E variant together contain five crystallographically independent molecules. Surprisingly, the threonine-to-glutamate substitution in the B repeat substantially improved the crystallization propensity and crystal quality of the T332E variant. The internalin domain and B repeat are quite rigid internally, but are flexibly linked to each other. The new structures show that inter-domain flexibility is the most likely cause of the missing electron density for the B repeat in previous InlB structures. A potential binding groove between B-repeat strand β2 and an adjacent loop forms an important crystal contact in all five crystallographically independent chains. This region may represent a hydrophobic `sticky patch' that supports protein-protein interactions. This assumption agrees with the previous finding that all known inactivating point mutations in the B repeat lie within strand β2. The groove formed by strand β2 and the adjacent loop may thus represent a functionally important protein-protein interaction site in the B repeat.

PubMed: 35234145
DOI: 10.1107/S2059798322000432

Experimental method

X-RAY DIFFRACTION (1.8 Å)