PDBsum entry 1bgx

Complex (polymerase/inhibitor)

PDB id: 1bgx

Contents

Protein chains

828 a.a. *

210 a.a. *

209 a.a. *

Waters ×262

* Residue conservation analysis

PDB id:

1bgx

Name:

Complex (polymerase/inhibitor)

Title:

Taq polymerase in complex with tp7, an inhibitory fab

Structure:

Taq DNA polymerase. Chain: t. Engineered: yes. Tp7 mab. Chain: l. Fragment: fab. Engineered: yes. Tp7 mab. Chain: h.

Source:

Thermus aquaticus. Organism_taxid: 271. Gene: taq. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: mus musculus.

Biol. unit:

Monomer (from PDB file)

Resolution:

2.30Å R-factor: 0.189 R-free: 0.253

Authors:

R.Murali,D.J.Sharkey,J.L.Daiss,H.M.Krishna Murthy

Key ref:

R.Murali et al. (1998). 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. Proc Natl Acad Sci U S A, 95, 12562-12567. PubMed id: 9770525 DOI: 10.1073/pnas.95.21.12562

Date:

02-Jun-98 Release date: 14-Oct-98

Protein chain

P19821  (DPO1_THEAQ) -  DNA polymerase I, thermostable from Thermus aquaticus

Seq: 832 a.a.

Struc: 828 a.a.

Protein chain

No UniProt id for this chain

Struc: 210 a.a.

Protein chain

No UniProt id for this chain

Struc: 209 a.a.

Enzyme reactions

• Enzyme class: Chain T: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added 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. C ribbon 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 an automated process.