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828 a.a.
210 a.a.
209 a.a.
 N deoxynucleoside triphosphate |
= |
 N diphosphate |
+ |
{DNA}(N) |
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Key reference
DOI no: 10.1073/pnas.95.21.12562 Proc Natl Acad Sci U S A 95:12562-12567 (1998) PubMed id: 9770525
Crystal structure of Taq DNA polymerase in complex with an inhibitory Fab: the Fab is directed against an intermediate in the helix-coil dynamics of the enzyme. R.Murali, D.J.Sharkey, J.L.Daiss, H.M.Murthy. ABSTRACT
We report the crystal structure of Thermus aquaticus DNA polymerase I in complex with an inhibitory Fab, TP7, directed against the native enzyme. Some of the residues present in a helical conformation in the native enzyme have adopted a gamma turn conformation in the complex. Taken together, structural information that describes alteration of helical structure and solution studies that demonstrate the ability of TP7 to inhibit 100% of the polymerase activity of the enzyme suggest that the change in conformation is probably caused by trapping of an intermediate in the helix-coil dynamics of this helix by the Fab. Antibodies directed against modified helices in proteins have long been anticipated. The present structure provides direct crystallographic evidence. The Fab binds within the DNA binding cleft of the polymerase domain, interacting with several residues that are used by the enzyme in binding the primer:template complex. This result unequivocally corroborates inferences drawn from binding experiments and modeling calculations that the inhibitory activity of this Fab is directly attributable to its interference with DNA binding by the polymerase domain of the enzyme. The combination of interactions made by the Fab residues in both the polymerase and the vestigial editing nuclease domain of the enzyme reveal the structural basis of its preference for binding to DNA polymerases of the Thermus species. The orientation of the structure-specific nuclease domain with respect to the polymerase domain is significantly different from that seen in other structures of this polymerase. This reorientation does not appear to be antibody-induced and implies remarkably high relative mobility between these two domains.
Selected figure(s)
Figure 1.
Fig. 1. Electron density map with refined model superimposed. Shown is a stereo representation of a 2F[o]F[c] map, contoured at 1.1
. Phases were generated by removing residues 520-560 in TaqP and refining the structure for 40 cycles with tight geometric restraints. Final refined model for residues 540-550 in TaqP is superimposed. All residues are labeled. The figure was made by using SETOR (47).
Figure 3.
Fig. 3. Overall View of the complex. Cribbon drawings of the pol domain (magenta), with the V-edit subdomain colored orange, and light (green) and heavy chains (cyan) are shown. Residues 540-550 in the helix are colored yellow. The figure was made with GRASP (48).
Figures were selected by the author.
Literature references that cite this PDB file's key reference
PubMed id Reference
18318449 D.Sutlovic, S.Gamulin, M.Definis-Gojanovic, D.Gugic, and S.Andjelinovic (2008).
Interaction of humic acids with human DNA: proposed mechanisms and kinetics.Electrophoresis, 29, 1467-1472.
14973201 Y.Wang, D.E.Prosen, L.Mei, J.C.Sullivan, M.Finney, and P.B.Vander Horn (2004).
A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro.Nucleic Acids Res, 32, 1197-1207.
12447903 P.Rezacova, J.Brynda, M.Fabry, M.Horejsi, R.Stouracova, J.Lescar, V.Chitarra, M.M.Riottot, J.Sedlacek, and G.A.Bentley (2002).
Inhibition of HIV protease by monoclonal antibodies.J Mol Recognit, 15, 272-276.
10570132 J.M.van Den Elsen, D.A.Kuntz, F.J.Hoedemaeker, and D.R.Rose (1999).
Antibody C219 recognizes an alpha-helical epitope on P-glycoprotein.Proc Natl Acad Sci U S A, 96, 13679-13684.
PDB code: 2ap2
10339555 V.Lyamichev, M.A.Brow, V.E.Varvel, and J.E.Dahlberg (1999).
Comparison of the 5' nuclease activities of taq DNA polymerase and its isolated nuclease domain.Proc Natl Acad Sci U S A, 96, 6143-6148. The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.
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