PDBsum entry 1g5h

DNA binding protein

PDB id: 1g5h

Contents

Protein chains

405 a.a. *

Ligands

GOL ×2

Metals

_NA ×4

Waters ×872

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure and deletion analysis show that the accessory subunit of mammalian DNA polymerase gamma, Pol gamma b, Functions as a homodimer.

Authors

J.A.Carrodeguas, K.Theis, D.F.Bogenhagen, C.Kisker.

Ref.

Mol Cell, 2001, 7, 43-54. [DOI no: 10.1016/S1097-2765(01)00153-8]

PubMed id

11172710

Abstract

Polymerase gamma, which replicates and repairs mitochondrial DNA, requires the Pol gamma B subunit for processivity. We determined the crystal structure of mouse Pol gamma B, a core component of the mitochondrial replication machinery. Pol gamma B shows high similarity to glycyl-tRNA synthetase and dimerizes through an unusual intermolecular four-helix bundle. A human Pol gamma B mutant lacking the four-helix bundle failed to dimerize in solution or to stimulate the catalytic subunit Pol gamma A, but retained the ability to bind with Pol gamma A to a primer-template construct, indicating that the functional holoenzyme contains two Pol gamma B molecules. Other mutants retained stimulatory activity but lost the ability to bind folded ssDNA. These results suggest that the Pol gamma B dimer contains distinct sites for Pol gamma A binding, dimerization, and DNA binding.

Figure 3.
Figure 3. Interface of the PolγB Homodimer(A) Dimer interface of PolγB. Left, oriented as in Figure 1B; right, rotated by 120° around the y axis to show the interface in domain 2. Red, atoms that become solvent inaccessible upon dimer formation; yellow, atoms whose accessibility decreases upon dimer formation; blue, waters that are in van der Waals distance to both monomers in the dimer; green, metal bound to main chain carbonyls at the dimer interface. Figure 3A and Figure 5 were prepared with Grasp ( [32]).(B) 2F[o] − F[c] electron density map of the metal binding site. The octahedral coordination sphere of the metal is indicated with dotted lines.(C) Comparison of the dimerization domain of CheA (blue and red subunits, PDB code 1B3Q) with domain 2 of PolγB (green and gray monomers). Helices are shown as cylinders and strands in ball-and-stick with hydrogen bonds as dotted lines. N and C termini are indicated.

Figure 5.
Figure 5. Surface Features of PolγB(A) Conserved residues in PolγB from human, mouse, and Xenopus laevis. Residues of mouse PolγB strictly conserved in human and at least type-conserved in Xenopus are colored green (noncarbon atoms) or yellow (carbon atoms). Residues of mouse PolγB deleted in Xenopus PolγB are colored in magenta.(B) Surface potential of the PolγB dimer calculated at neutral pH, ionic strength 100 mM, contoured at ± 10 kT (blue, positive; red, negative). The surface potential of human PolγB (homology model, not shown) is similar. Top, front view as in Figure 1B; bottom, view of the C-terminal regions of PolγB. The arrows indicate the pocket in domain 1.

The above figures are reprinted by permission from Cell Press: Mol Cell (2001, 7, 43-54) copyright 2001.

Secondary reference #1

Title

Protein sequences conserved in prokaryotic aminoacyl-Trna synthetases are important for the activity of the processivity factor of human mitochondrial DNA polymerase.

Authors

J.A.Carrodeguas, D.F.Bogenhagen.

Ref.

Nucleic Acids Res, 2000, 28, 1237-1244. [DOI no: 10.1093/nar/28.5.1237]

PubMed id

10666468