PDBsum entry 1qqc

Transferase

PDB id: 1qqc

Contents

Protein chain

740 a.a. *

Ligands

SO4 ×4

Metals

_MG ×2

Waters ×116

* Residue conservation analysis

PDB id:

1qqc

Name:

Transferase

Title:

Crystal structure of an archaebacterial DNA polymerase d.Tok

Structure:

DNA polymerase ii. Chain: a. Engineered: yes

Source:

Desulfurococcus sp. Tok. Organism_taxid: 108142. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.60Å R-factor: 0.244 R-free: 0.296

Authors:

Y.Zhao,D.Jeruzalmi,L.Leighton,R.Lasken,J.Kuriyan

Key ref:

Y.Zhao et al. (1999). Crystal structure of an archaebacterial DNA polymerase. Structure Fold Des, 7, 1189-1199. PubMed id: 10545321 DOI: 10.1016/S0969-2126(00)80053-2

Date:

02-Jun-99 Release date: 14-Oct-99

Protein chain

Q7SIG7  (DPOL_DESST) -  DNA polymerase from Desulfurococcus sp. (strain Tok)

Seq: 773 a.a.

Struc: 740 a.a.

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/S0969-2126(00)80053-2

Structure Fold Des 7:1189-1199 (1999)

PubMed id: 10545321

Crystal structure of an archaebacterial DNA polymerase.

Y.Zhao, D.Jeruzalmi, I.Moarefi, L.Leighton, R.Lasken, J.Kuriyan.

ABSTRACT

BACKGROUND: Members of the Pol II family of DNA polymerases are responsible for chromosomal replication in eukaryotes, and carry out highly processive DNA replication when attached to ring-shaped processivity clamps. The sequences of Pol II polymerases are distinct from those of members of the well-studied Pol I family of DNA polymerases. The DNA polymerase from the archaebacterium Desulfurococcus strain Tok (D. Tok Pol) is a member of the Pol II family that retains catalytic activity at elevated temperatures. RESULTS: The crystal structure of D. Tok Pol has been determined at 2.4 A resolution. The architecture of this Pol II type DNA polymerase resembles that of the DNA polymerase from the bacteriophage RB69, with which it shares less than approximately 20% sequence identity. As in RB69, the central catalytic region of the DNA polymerase is located within the 'palm' subdomain and is strikingly similar in structure to the corresponding regions of Pol I type DNA polymerases. The structural scaffold that surrounds the catalytic core in D. Tok Pol is unrelated in structure to that of Pol I type polymerases. The 3'-5' proofreading exonuclease domain of D. Tok Pol resembles the corresponding domains of RB69 Pol and Pol I type DNA polymerases. The exonuclease domain in D. Tok Pol is located in the same position relative to the polymerase domain as seen in RB69, and on the opposite side of the palm subdomain compared to its location in Pol I type polymerases. The N-terminal domain of D. Tok Pol has structural similarity to RNA-binding domains. Sequence alignments suggest that this domain is conserved in the eukaryotic DNA polymerases delta and epsilon. CONCLUSIONS: The structure of D. Tok Pol confirms that the modes of binding of the template and extrusion of newly synthesized duplex DNA are likely to be similar in both Pol II and Pol I type DNA polymerases. However, the mechanism by which the newly synthesized product transits in and out of the proofreading exonuclease domain has to be quite different. The discovery of a domain that seems to be an RNA-binding module raises the possibility that Pol II family members interact with RNA.

Selected figure(s)

Figure 6.
Figure 6. Comparison of surface charges in D. Tok Pol and RB69 Pol. Accessible-surface representation of (a) D. Tok Pol and (b) RB69 Pol in the same orientation after superposition of their palm subdomains. Surface regions corresponding to the terminal oxygen atoms of aspartate and glutamate are colored red, whereas surface regions contributed by the sidechain nitrogen of lysines and arginines are colored blue. D. Tok Pol has a striking pairing of oppositely charged residues not seen in RB69 pol. A representation of D. Tok Pol as a worm is included for orientation.

The above figure is reprinted by permission from Cell Press: Structure Fold Des (1999, 7, 1189-1199) copyright 1999.

Figure was selected by an automated process.