1BGX

TAQ POLYMERASE IN COMPLEX WITH TP7, AN INHIBITORY FAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.

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

(1998) Proc.Natl.Acad.Sci.USA 95: 12562-12567


  • PubMed 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 co ...

    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.


    Related Citations: 
    • Structural Studies on an Inhibitory Antibody Against Thermus Aquaticus DNA Polymerase Suggest Mode of Inhibition
      Murali, R.,Helmer-Citterich, M.,Sharkey, D.J.,Scalice, E.R.,Daiss, J.L.,Sullivan, M.A.,Krishna Murthy, H.M.
      (1998) Protein Eng. 11: 79


    Organizational Affiliation

    Department of Pathology, University of Pennsylvania, Philadelphia, PA, 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TAQ DNA POLYMERASE
T
832Thermus aquaticusMutation(s): 0 
Gene Names: polA (pol1)
EC: 2.7.7.7
Find proteins for P19821 (Thermus aquaticus)
Go to UniProtKB:  P19821
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TP7 MAB
L
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
TP7 MAB
H
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.189 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 76.600α = 100.70
b = 89.100β = 115.30
c = 89.300γ = 95.30
Software Package:
Software NamePurpose
XDSdata reduction
X-PLORrefinement
XDSdata scaling
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-07
    Type: Data collection