1NOY

DNA POLYMERASE (E.C.2.7.7.7)/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.222 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions.

Wang, J.Yu, P.Lin, T.C.Konigsberg, W.H.Steitz, T.A.

(1996) Biochemistry 35: 8110-8119

  • DOI: 10.1021/bi960178r
  • Primary Citation of Related Structures:  
    1NOY, 1NOZ

  • PubMed Abstract: 
  • We report the crystal structure of an NH2-terminal 388-residue fragment of T4 DNA polymerase (protein N388) refined at 2.2 A resolution. This fragment contains both the 3'-5' exonuclease active site and part of the autologous mRNA binding site (J. D. Karam, personal communication) ...

    We report the crystal structure of an NH2-terminal 388-residue fragment of T4 DNA polymerase (protein N388) refined at 2.2 A resolution. This fragment contains both the 3'-5' exonuclease active site and part of the autologous mRNA binding site (J. D. Karam, personal communication). The structure of a complex between the apoprotein N388 and a substrate, p(dT)3, has been refined at 2.5 A resolution to a crystallographic R-factor of 18.7%. Two divalent metal ion cofactors, Zn(II) and Mn(II), have been located in crystals of protein N388 which had been soaked in solutions containing Zn(II), Mn(II), or both. The structure of the 3'-5' exonuclease domain of protein N388 closely resembles the corresponding region in the Klenow fragment despite minimal sequence identity. The side chains of four carboxylate residues that serve as ligands for the two metal ions required for catalysis are located in geometrically equivalent positions in both proteins with a rms deviation of 0.87 A. There are two main differences between the 3'-5' exonuclease active site regions of the two proteins: (I) the OH of Tyr-497 in the Klenow fragment interacts with the scissile phosphate in the active site whereas the OH of the equivalent tyrosine (Tyr-320) in protein N388 points away from the active center; (II) different residues form of the binding pocket for the 3'-terminal bases of the substrate. In the protein N388 complex the 3'-terminal base of p(dT)3 is rotated approximately 60 degrees relative to the position that the corresponding base occupies in the p(dT)3 complex with the Klenow fragment. Finally, a separate domain (residues 1-96) of protein N388 may be involved in mRNA binding that results in translational regulation of T4 DNA polymerase (Pavlov & Karam, 1994).


    Related Citations: 
    • Isolation, Characterization, and Kinetic Properties of Truncated Forms of T4 DNA Polymerase that Exhibit 3'-5' Exonuclease Activity
      Lin, T.C., Karam, G., Konigsberg, W.H.
      (1994) J Biol Chem 269: 19286
    • Primary Structure of T4 DNA Polymerase. Evolutionary Relatedness to Eucaryotic and Other Procaryotic DNA Polymerases
      Spicer, E.K., Rush, J., Fung, C., Reha-Krantz, L.J., Karam, J.D., Konigsberg, W.H.
      (1988) J Biol Chem 263: 7478

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8114, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DNA POLYMERASE (E.C.2.7.7.7))B [auth A], C [auth B]388Escherichia virus T4Mutation(s): 0 
Gene Names: 43
EC: 2.7.7.7 (UniProt), 3.1.11 (UniProt)
UniProt
Find proteins for P04415 (Enterobacteria phage T4)
Explore P04415 
Go to UniProtKB:  P04415
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*TP*T)-3')A [auth S]3N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth B]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.222 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.701α = 90
b = 109.656β = 90
c = 70.268γ = 90
Software Package:
Software NamePurpose
DCREDUCEdata collection
SCALEPACKdata scaling
X-PLORrefinement
DCREDUCEdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance