Structure of the virulence-associated protein VapD from the intracellular pathogen Rhodococcus equi

Whittingham, J.L.; Blagova, E.V.; Finn, C.E.; Luo, H.; Miranda-CasoLuengo, R.; Turkenburg, J.P.; Leech, A.P.; Walton, P.H.; Murzin, A.G.; Meijer, W.G.; Wilkinson, A.J.

doi:10.1107/S1399004714012632

Acta Crystallographica Section D
Acta Crystallographica
Section D BIOLOGICAL CRYSTALLOGRAPHY

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Figure 4
Core and conserved residues. (a) Stereoview of the VapD chain represented as a green worm highlighting the side chains of residues (which are labelled) in the protein core, defined here as residues with <10 Å² of accessible surface area. The C^α atoms and side chains of these residues are shown in cylinder format coloured by atom: carbon, grey; oxygen, red; nitrogen, blue. Side chain–side chain hydrogen bonds are indicated by dashed lines. (b) Local hydrogen-bonding networks in the otherwise apolar core of VapD: left, interactions of the side chains of Ser35, Gln40, Thr65 and Tyr93; right, the role of Asp70 in organizing the β7–β8 loop through side-chain carboxylate–main-chain amide interactions with Ala120, Gly121, Thr122 and Val123. Also shown is the interaction of Asp70 with one of three buried water molecules. (c) View of the VapD chain as in (a) depicting the 30 invariant residues from the alignment of Vap proteins shown in Fig. 1

. The C^α atoms of the invariant glycine residues are shown as spheres.

BIOLOGICAL
CRYSTALLOGRAPHY

ISSN: 1399-0047

Volume 70| Part 8| July 2014| Pages 2139-2151

doi:10.1107/S1399004714012632

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