PDBsum entry 1p7k

Immune system

PDB id: 1p7k

Contents

Protein chains

213 a.a. *

220 a.a. *

Ligands

SO4 ×9

EPE ×2

1PE ×4

PEG ×2

GOL ×16

Waters ×771

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structure of an anti-Dna FAB complexed with a non-Dna ligand provides insights into cross-Reactivity and molecular mimicry.

Authors

J.P.Schuermann, M.T.Henzl, S.L.Deutscher, J.J.Tanner.

Ref.

Proteins, 2004, 57, 269-278. [DOI no: 10.1002/prot.20200]

PubMed id

15340914

Abstract

Antibodies that recognize DNA (anti-DNA) are part of the autoimmune response underlying systemic lupus erythematosus. To better understand molecular recognition by anti-DNA antibodies, crystallographic studies have been performed using an anti-ssDNA antigen-binding fragment (Fab) known as DNA-1. The previously determined structure of a DNA-1/dT5 complex revealed that thymine bases insert into a narrow groove, and that ligand recognition primarily involves the bases of DNA. We now report the 1.75-A resolution structure of DNA-1 complexed with the biological buffer HEPES (4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid). All three light chain complementarity-determining regions (CDRs) and HCDR3 contribute to binding. The HEPES sulfonate hydrogen bonds to His L91, Asn L50, and to the backbone of Tyr H100 and Tyr H100A. The Tyr side-chains of L32, L92, H100, and H100A form nonpolar contacts with the HEPES ethylene and piperazine groups. Comparison to the DNA-1/dT5 structure reveals that the dual recognition of dT5 and HEPES requires a 13-A movement of HCDR3. This dramatic structural change converts the combining site from a narrow groove, appropriate for the edge-on insertion of thymine bases, to one sufficiently wide to accommodate the HEPES sulfonate and piperazine. Isothermal titration calorimetry verified the association of HEPES with DNA-1 under conditions similar those used for crystallization (2 M ammonium sulfate). Interestingly, the presence of 2 M ammonium sulfate increases the affinities of DNA-1 for both HEPES and dT5, suggesting that non-polar Fab-ligand interactions are important for molecular recognition in highly ionic solvent conditions. The structural and thermodynamic data suggest a molecular mimicry mechanism based on structural plasticity and hydrophobic interactions.

Figure 3.
Figure 3. Stereo-view of the DNA-1/HEPES binding site highlighting Fab-ligand interactions. The HEPES and sulfate ligands appear in yellow and green; protein side-chains are colored white. The dotted lines denote hydrogen bonds and ion pairs. The orientation of the protein depicted in this figure is identical to those of Figures 1 and 4.

Figure 4.
Figure 4. Stereo-view of Fab-DNA interactions from DNA-1/dT[5] structure (PDB code 1I8M).[16] DNA appears in yellow, while protein side-chains are colored white. The dotted lines denote hydrogen bonds. The orientation of the protein depicted in this figure is identical to those of Figures 1 and 3.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 57, 269-278) copyright 2004.

Secondary reference #1

Title

Crystal structure of an antigen-Binding fragment bound to single-Stranded DNA.

Authors

J.J.Tanner, A.A.Komissarov, S.L.Deutscher.

Ref.

J Mol Biol, 2001, 314, 807-822. [DOI no: 10.1006/jmbi.2001.5178]

PubMed id

11733999

Figure 1.
Figure 1. Ribbon drawing of the asymmetric unit of the DNA-1/dT[5] structure. The light chains are colored purple and the heavy chains are colored cyan. The DNA appears in ball-and-stick mode in yellow. This Figure was prepared with Molscript [73] and Raster3D. [74]

Figure 3.
Figure 3. Space filling models of the two Fabs in the asymmetric unit of DNA-1/dT[5]. (a) A view looking into the combining site of Fab 1. (b) A view looking into the combining site of Fab 2. The two molecules have been rotated to a common orientation to facilitate their comparison. The DNA appears in ball-and-stick mode in yellow, and the CDRs are color coded as follows: L1, red; L2, green; L3, purple; H1, yellow; H2, blue; and H3, cyan. This Figure was prepared with MOLSCRIPT[73] and Raster3D. [74]

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

Secondary reference #2

Title

Crystallization and molecular-Replacement studies of a recombinant antigen-Binding fragment complexed with single-Stranded DNA.

Authors

S.P.Prewitt, A.A.Komissarov, S.L.Deutscher, J.J.Tanner.

Ref.

Acta Crystallogr D Biol Crystallogr, 2000, 56, 1007-1011. [DOI no: 10.1107/S0907444900008222]

PubMed id

10944338

Figure 1.
Figure 1 Crystal forms of DNA-1 grown in the presence of dT[5]. The scales indicate 0.1 mm.

The above figure is reproduced from the cited reference with permission from the IUCr