PDBsum entry 1ig9

Transferase/DNA

PDB id: 1ig9

Contents

Protein chain

901 a.a. *

DNA/RNA

Ligands

TTP

Metals

_CA ×4

Waters ×356

* Residue conservation analysis

PDB id:

1ig9

Name:

Transferase/DNA

Title:

Structure of the replicating complex of a pol alpha family DNA polymerase

Structure:

5'-d( Ap Cp Ap Gp Gp Tp Ap Ap Gp Cp Ap Gp Tp Cp Cp Gp Cp G) -3'. Chain: t. Engineered: yes. Other_details: substrate DNA, template strand. 5'-d( Gp Cp Gp Gp Ap Cp Tp Gp Cp Tp Tp Ap Cp (Doc))-3'. Chain: p. Engineered: yes. Other_details: substrate DNA, primer strand (dideoxy-terminated).

Source:

Synthetic: yes. Enterobacteria phage rb69. Organism_taxid: 12353. Gene: gp43. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Trimer (from PQS)

Resolution:

2.60Å R-factor: 0.197 R-free: 0.258

Authors:

M.C.Franklin,J.Wang,T.A.Steitz

Key ref:

M.C.Franklin et al. (2001). Structure of the replicating complex of a pol alpha family DNA polymerase. Cell, 105, 657-667. PubMed id: 11389835 DOI: 10.1016/S0092-8674(01)00367-1

Date:

17-Apr-01 Release date: 11-Jun-01

Protein chain

Q38087  (DPOL_BPR69) -  DNA-directed DNA polymerase from Escherichia phage RB69

Seq: 903 a.a.

Struc: 901 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

A-C-A-G-G-T-A-A-G-C-A-G-T-C-C-G-C-G 18 bases

G-C-G-G-A-C-T-G-C-T-T-A-C-DOC 14 bases

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 2: E.C.3.1.11.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1016/S0092-8674(01)00367-1

Cell 105:657-667 (2001)

PubMed id: 11389835

Structure of the replicating complex of a pol alpha family DNA polymerase.

M.C.Franklin, J.Wang, T.A.Steitz.

ABSTRACT

We describe the 2.6 A resolution crystal structure of RB69 DNA polymerase with primer-template DNA and dTTP, capturing the step just before primer extension. This ternary complex structure in the human DNA polymerase alpha family shows a 60 degrees rotation of the fingers domain relative to the apo-protein structure, similar to the fingers movement in pol I family polymerases. Minor groove interactions near the primer 3' terminus suggest a common fidelity mechanism for pol I and pol alpha family polymerases. The duplex product DNA orientation differs by 40 degrees between the polymerizing mode and editing mode structures. The role of the thumb in this DNA motion provides a model for editing in the pol alpha family.

Selected figure(s)

Figure 2.
Figure 2. The Polymerase Active Site(A) The backbones of the polymerase palm and fingers domains are shown as magenta and blue ribbons. The carbon atoms of the polymerase side chains shown in stick form are white, while those of the DNA template are dark gray, and those of the primer DNA and dTTP are gold. The bound calcium atoms are shown as light blue mesh spheres, labeled A and B according to their catalytic function. Hydrogen bonds are shown as green lines, while interactions with the metal ions are blue lines. This view looks down the length of the fingers, roughly 180° away from the orientation of Figure 1A.(B) The KKRY motif (residues 705–708) interacts with the primer-template duplex next to the polymerase active site. Residues 703–708 are shown; Thr 703 and Gly 704 are not conserved in the pol α family. Asp 621 from Figure 2A is shown as an isolated side chain. Only the last two bases of the primer strand are shown for clarity. The orientation of this figure can be related to that of Figure 2A by comparing the primer-template DNA

Figure 4.
Figure 4. A Tunnel into the Polymerase Active SiteThe molecular surface of RB69 pol in its polymerizing mode is colored by domain according to the scheme of Figure 1A. The dTTP and associated metal ions are at the center of the image, with the primer-template DNA, shown semitransparently behind the surface, extending off to the left. The terminal amine of Lys 560 protrudes into the tunnel, as indicated. This view is roughly the same as that of Figure 2 and Figure 3

The above figures are reprinted by permission from Cell Press: Cell (2001, 105, 657-667) copyright 2001.

Figures were selected by an automated process.