PDBsum entry 2g4c

Transferase

PDB id: 2g4c

Contents

Protein chains

397 a.a. *

Waters ×31

* Residue conservation analysis

PDB id:

2g4c

Name:

Transferase

Title:

Crystal structure of human DNA polymerase gamma accessory subunit

Structure:

DNA polymerase gamma subunit 2. Chain: a, b, c, d. Synonym: mitochondrial DNA polymerase accessory subunit, polg-beta, mtpolb, DNA polymerase gamma accessory 55 kda subunit, p55. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polg2, mtpolb. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

3.15Å R-factor: 0.232 R-free: 0.285

Authors:

L.Fan,C.L.Farr,L.S.Kaguni,J.A.Tainer

Key ref:

L.Fan et al. (2006). A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase. J Mol Biol, 358, 1229-1243. PubMed id: 16574152 DOI: 10.1016/j.jmb.2006.02.073

Date:

22-Feb-06 Release date: 18-Apr-06

Protein chains

Q9UHN1  (DPOG2_HUMAN) -  DNA polymerase subunit gamma-2, mitochondrial from Homo sapiens

Seq: 485 a.a.

Struc: 397 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: 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: 10.1016/j.jmb.2006.02.073

J Mol Biol 358:1229-1243 (2006)

PubMed id: 16574152

A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase.

L.Fan, S.Kim, C.L.Farr, K.T.Schaefer, K.M.Randolph, J.A.Tainer, L.S.Kaguni.

ABSTRACT

Mitochondrial DNA polymerase (pol gamma) is the sole DNA polymerase responsible for replication and repair of animal mitochondrial DNA. Here, we address the molecular mechanism by which the human holoenzyme achieves high processivity in nucleotide polymerization. We have determined the crystal structure of human pol gamma-beta, the accessory subunit that binds with high affinity to the catalytic core, pol gamma-alpha, to stimulate its activity and enhance holoenzyme processivity. We find that human pol gamma-beta shares a high level of structural similarity to class IIa aminoacyl tRNA synthetases, and forms a dimer in the crystal. A human pol gamma/DNA complex model was developed using the structures of the pol gamma-beta dimer and the bacteriophage T7 DNA polymerase ternary complex, which suggests multiple regions of subunit interaction between pol gamma-beta and the human catalytic core that allow it to encircle the newly synthesized double-stranded DNA, and thereby enhance DNA binding affinity and holoenzyme processivity. Biochemical properties of a novel set of human pol gamma-beta mutants are explained by and test the model, and elucidate the role of the accessory subunit as a novel type of processivity factor in stimulating pol gamma activity and in enhancing processivity.

Selected figure(s)

Figure 1.
Figure 1. Human pol g-b shares structural homology with E. coli threonyl tRNA synthetase (ThrRS). (a) Ribbon display of the human pol g-b structure. The N and C-terminal domains and HLH-b3 domain of monomer A are colored light green, green, and cyan, respectively. Monomer B is in gray. (b) Superposition of the N-terminal (upper panel) and C-terminal (lower panel) domains of human pol g-b (blue) on the catalytic and anticodon binding domains of ThrRS,44 respectively. (c) RNA operator (yellow, PDB code 1KOG),12 tRNA (green, PDB code 1QF6),11 and DNA (orange, PDB code 1T7P),13 were docked onto the electrostatic surface of the pol g-b dimer. (d) The electrostatic surface of the ThrRS dimer with bound tRNA (green) and RNA operator (yellow). Surfaces in (c) and (d) are colored according to electrostatic potential (red, -7.5kT/e^ - to blue, +7.5kT/e^ -).

Figure 5.
Figure 5. Structural details of human pol g-b mutants. (a) Mutant residues in the N-terminal domain of pol g-b. (b) Local environment around residues E105 and G103 of pol g-b. (c) Mutant residues in the C-terminal domain of pol g-b. (d) Local charge balance at residue D433 in pol g-b. Mutant residues are shown in color (see Figure 2 and Table 2): class I, black; class II, magenta; class III, yellow (D433); class IV, blue; and class V, red.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 1229-1243) copyright 2006.

Figures were selected by an automated process.