PDBsum entry 1qht

Transferase

PDB id: 1qht

Contents

Protein chain

710 a.a. *

Waters ×109

* Residue conservation analysis

PDB id:

1qht

Name:

Transferase

Title:

DNA polymerase from thermococcus sp. 9on-7 archaeon

Structure:

Protein (DNA polymerase). Chain: a. Engineered: yes. Mutation: yes

Source:

Thermococcus sp.. Organism_taxid: 103799. Strain: 9on-7. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.10Å R-factor: 0.245 R-free: 0.312

Authors:

H.-W.Park,A.C.Rodriguez,L.S.Beese

Key ref:

A.C.Rodriguez et al. (2000). Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7. J Mol Biol, 299, 447-462. PubMed id: 10860752 DOI: 10.1006/jmbi.2000.3728

Date:

26-May-99 Release date: 26-May-00

Protein chain

Q56366  (DPOL_THES9) -  DNA polymerase from Thermococcus sp. (strain 9oN-7)

Seq: 775 a.a.

Struc: 710 a.a.*

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

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: 10.1006/jmbi.2000.3728

J Mol Biol 299:447-462 (2000)

PubMed id: 10860752

Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7.

A.C.Rodriguez, H.W.Park, C.Mao, L.S.Beese.

ABSTRACT

The 2.25 A resolution crystal structure of a pol alpha family (family B) DNA polymerase from the hyperthermophilic marine archaeon Thermococcus sp. 9 degrees N-7 (9 degrees N-7 pol) provides new insight into the mechanism of pol alpha family polymerases that include essentially all of the eukaryotic replicative and viral DNA polymerases. The structure is folded into NH(2)- terminal, editing 3'-5' exonuclease, and polymerase domains that are topologically similar to the two other known pol alpha family structures (bacteriophage RB69 and the recently determined Thermococcus gorgonarius), but differ in their relative orientation and conformation.The 9 degrees N-7 polymerase domain structure is reminiscent of the "closed" conformation characteristic of ternary complexes of the pol I polymerase family obtained in the presence of their dNTP and DNA substrates. In the apo-9 degrees N-7 structure, this conformation appears to be stabilized by an ion pair. Thus far, the other apo-pol alpha structures that have been determined adopt open conformations. These results therefore suggest that the pol alpha polymerases undergo a series of conformational transitions during the catalytic cycle similar to those proposed for the pol I family. Furthermore, comparison of the orientations of the fingers and exonuclease (sub)domains relative to the palm subdomain that contains the pol active site suggests that the exonuclease domain and the fingers subdomain of the polymerase can move as a unit and may do so as part of the catalytic cycle. This provides a possible structural explanation for the interdependence of polymerization and editing exonuclease activities unique to pol alpha family polymerases.We suggest that the NH(2)-terminal domain of 9 degrees N-7 pol may be structurally related to an RNA-binding motif, which appears to be conserved among archaeal polymerases. The presence of such a putative RNA- binding domain suggests a mechanism for the observed autoregulation of bacteriophage T4 DNA polymerase synthesis by binding to its own mRNA. Furthermore, conservation of this domain could indicate that such regulation of pol expression may be a characteristic of archaea. Comparion of the 9 degrees N-7 pol structure to its mesostable homolog from bacteriophage RB69 suggests that thermostability is achieved by shortening loops, forming two disulfide bridges, and increasing electrostatic interactions at subdomain interfaces.

Selected figure(s)

Figure 4.
Figure 4. Comparisons of 9°N-7 and RB69 pols in different (sub)domains to indicate loop segments that are shorter in 9°N-7 pol. Least-squares C^a superposition was performed over the region in blue, and the domains were separated for side-by-side comparison. Loop regions are shown in magenta and their residue endpoints are labeled. (a) Comparison of the exonuclease domains. Indicated with purple asterisks are the active site carboxylates (mutated to Ala in the case of the 9°N-7exo - pol used in this study). (b) Comparison of the palm domains. The three active-site carboxylate groups are depicted with side-chains.

Figure 5.
Figure 5. Least-squares C^a superpositions of 9°N-7 and RB69 pols in the (a) palm subdomain or (b) exonuclease domain. The 9°N-7 pol backbone is shown in yellow, and its active-site carboxylate groups in gold. The RB69 pol backbone is drawn in green, and its active-site residues in magenta. The central b-sheet of the exonuclease domain is light blue (9°N-7 pol) or dark blue (RB69 pol) to allow tracking of the domain motion. The precise regions used in the palm and exonuclease superpositions are shown in Figure 4. The NH[2]-terminal domain has been omitted for clarity. Arrows in (a) indicate the direction of fingers and exonuclease movement when moving from (a) to (b).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 299, 447-462) copyright 2000.

Figures were selected by an automated process.