PDBsum entry 1p69

Viral protein/receptor

PDB id: 1p69

Contents

Protein chains

185 a.a. *

124 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural basis for variation in adenovirus affinity for the cellular coxsackievirus and adenovirus receptor.

Authors

J.Howitt, M.C.Bewley, V.Graziano, J.M.Flanagan, P.Freimuth.

Ref.

J Biol Chem, 2003, 278, 26208-26215. [DOI no: 10.1074/jbc.M301492200]

PubMed id

12716886

Abstract

The majority of adenovirus serotypes can bind to the coxsackievirus and adenovirus receptor (CAR) on human cells despite only limited conservation of the amino acid residues that comprise the receptor-binding sites of these viruses. Using a fluorescence anisotropy-based assay, we determined that the recombinant knob domain of the fiber protein from adenovirus serotype (Ad) 2 binds the soluble, N-terminal domain (domain 1 (D1)) of CAR with 8-fold greater affinity than does the recombinant knob domain from Ad12. Homology modeling predicted that the increased affinity of Ad2 knob for CAR D1 could result from additional contacts within the binding interface contributed by two residues, Ser408 and Tyr477, which are not conserved in the Ad12 knob. Consistent with this structural model, substitution of serine and tyrosine for the corresponding residues in the Ad12 knob (P417S and S489Y) increased the binding affinity by 4- and 8-fold, respectively, whereas the double mutation increased binding affinity 10-fold. X-ray structure analysis of Ad12 knob mutants P417S and S489Y indicated that both substituted residues potentially could form additional hydrogen bonds across the knob-CAR interface. Structural changes resulting from these mutations were highly localized, implying that the high tolerance for surface variation conferred by the stable knob scaffold can minimize the impact of antigenic drift on binding specificity and affinity during evolution of virus serotypes. Our results suggest that the interaction of knob domains from different adenovirus serotypes with CAR D1 can be accurately modeled using the Ad12 knob-CAR D1 crystal structure as a template.

Figure 3.
FIG. 3. Homology model of Ad2 knob bound to CAR D1. The x-ray structure of Ad2 knob was overlaid onto Ad12 knob in the x-ray structure of the Ad12 knob-CAR D1 complex. For simplicity, only one monomer of the knob trimer is shown. The surface of CAR D1 (space-filling model on left) is colored blue. Superimposed ribbon structures of Ad2 knob and Ad12 knob are colored cyan and green, respectively. Side chain residues of Ad12 knob contacting CAR D1 are shown in gray except for side chains of Ser489 and Pro417, which are shown in red. Ad2 knob Ser408 and Tyr477 side chains are colored yellow.

Figure 5.
FIG. 5. Comparison of crystal structures of wild type Ad12 knob-CAR D1 and Ad12 knob P417S-CAR D1. a, stereo figure showing part of the wild type Ad12 knob-CAR D1 interface including CAR D1 residues I55-E56-W57 (cyan) and Ad12 knob residues P416-P417-P418 (yellow); no hydrogen bonds are formed at this interface. b, stereo figure of same view of the interface between Ad12 knob mutant P417S (blue) and CAR D1 (red); note the novel hydrogen bond formed between Ser417 of knob and Glu56 of CAR D1.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 26208-26215) copyright 2003.

Secondary reference #1

Title

Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, Car.

Authors

M.C.Bewley, K.Springer, Y.B.Zhang, P.Freimuth, J.M.Flanagan.

Ref.

Science, 1999, 286, 1579-1583. [DOI no: 10.1126/science.286.5444.1579]

PubMed id

10567268

Figure 2.
Fig. 2. A molecular surface representation of the interface in the Ad12 knob-CAR D1 complex. (A) Sequence conservation surface diagram of two knob monomers viewed at the CAR interface. The molecules are colored on a sliding scale from white (conserved) to red (nonconserved). Conservation analysis was based on an alignment of all human Ad knob sequences available in GenBank. A white strip of conservation transects the surface of the molecule. Upon binding, the CAR D1 molecule occludes the conserved strip on Ad12 knob. (B) Surface diagram of two adjacent Ad12 knob monomers shown in the same view as (A). The molecules are colored on a sliding scale from yellow (contact) to red (no contact). Atoms in contact with CAR D1 are shared between monomers. (C) Surface diagram of CAR D1. The molecules are colored on a sliding scale from magenta (contact) to cyan (no contact). This figure was generated with GRASP (30).

Figure 3.
Fig. 3. CPK model of the region around the cavity. The three consecutive proline residues in Ad12 knob partially shape the cavity, which is colored magenta. The AB loop, whose carbon atoms are colored yellow, lines one side of the cavity. The carbon atoms from the remainder of the monomer are colored red, those of the second knob monomer, green, and those of CAR D1, cyan. All oxygen and nitrogen atoms are colored light red and blue, respectively. The cavity is lined with atoms from residues , (backbone), (side), V448 (side), (backbone), V450, L455 (side), Q535 (side), P573 (side), and S575 (side) from one Ad12 knob; S514 (backbone), A515 (backbone), (side), N520 (side), A524 (main), E523, K525, and S526 (side) from the other Ad12 knob; and L39 (side), K47 (backbone), V48 (backbone), D49, Q50, V51, and K102 (side) from CAR. The underlined residues are conserved or similar in all CAR-binding Ad serotypes.

The above figures are reproduced from the cited reference with permission from the AAAs

Secondary reference #2

Title

Coxsackievirus and adenovirus receptor amino-Terminal immunoglobulin v-Related domain binds adenovirus type 2 and fiber knob from adenovirus type 12.

Authors

P.Freimuth, K.Springer, C.Berard, J.Hainfeld, M.Bewley, J.Flanagan.

Ref.

J Virol, 1999, 73, 1392-1398.

PubMed id

9882344