PDBsum entry 5ktq

Transferase

PDB id: 5ktq

Contents

Protein chain

534 a.a. *

Ligands

DCP

* Residue conservation analysis

PDB id:

5ktq

Name:

Transferase

Title:

Large fragment of taq DNA polymerase bound to dctp

Structure:

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

Source:

Thermus aquaticus. Organism_taxid: 271. Strain: x7029. Gene: taq. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.217 R-free: 0.280

Authors:

Y.Li,Y.Kong,S.Korolev,G.Waksman

Key ref:

Y.Li et al. (1998). Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates. Protein Sci, 7, 1116-1123. PubMed id: 9605316 DOI: 10.1002/pro.5560070505

Date:

22-Sep-98 Release date: 30-Sep-98

Protein chain

P19821  (DPO1_THEAQ) -  DNA polymerase I, thermostable from Thermus aquaticus

Seq: 832 a.a.

Struc: 534 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: 10.1002/pro.5560070505

Protein Sci 7:1116-1123 (1998)

PubMed id: 9605316

Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates.

Y.Li, Y.Kong, S.Korolev, G.Waksman.

ABSTRACT

The crystal structures of the Klenow fragment of the Thermus aquaticus DNA polymerase I (Klentaq1) complexed with four deoxyribonucleoside triphosphates (dNTP) have been determined to 2.5 A resolution. The dNTPs bind adjacent to the O helix of Klentaq1. The triphosphate moieties are at nearly identical positions in all four complexes and are anchored by three positively charged residues, Arg659, Lys663, and Arg587, and by two polar residues, His639 and Gln613. The configuration of the base moieties in the Klentaq1/dNTP complexes demonstrates variability suggesting that dNTP binding is primarily determined by recognition and binding of the phosphate moiety. However, when superimposed on the Taq polymerase/blunt end DNA complex structure (Eom et al., 1996), two of the dNTP/Klentaq1 structures demonstrate appropriate stacking of the nucleotide base with the 3' end of the DNA primer strand, suggesting that at least in these two binary complexes, the observed dNTP conformations are functionally relevant.

Selected figure(s)

Figure 2.
Fig. 2. A: Schematic representation of the secondary structure of Klentaql bound with dAW. The small vestigial 3â-5â exonuclease domain is shown in yellow and the polymerase domaiins shown in green. The secondarys tructure elements are labeled according to the notation of Ollise t al. (1985). The helix 0 is shown in blue and tdhAeT P molecule in red. The side chains of the three carboxylates, Asp610, Asp785, Asp786, which form the catalytic core are shown in purple. This figure was prepared using MOLSCRIPT and RASTER3D (Merritt 8c Murphy, 1994; Kraulis, 1991). B: Superimposition of the binary complex of Klentaql bound to dCTP (this work; in purple) with the binary complex of E. coli Klenow Pol I bound to dCTP ((Beese et al., 1993); in pink). C Superimposition of d N T P s in the four Klentaql/dNTP binary complexes. The binary complexoefs Klentaql with dATP (green), dTTP (yellow), dCTP (magenta), dGTP (cyan) were superimposed. The positions of the triphosphaotef st he dNTP in the four complexa re nearly identical, while those for the sugar and base differ. The orientation of the side chain of Qr671 also differs in the four binary complexes. D: Superimposition of the Klentaql/dCTP binary complex structure (in purple) with the Taq/DNA complex structure of Eom et al. (1996) (in yellow for the protein, and white and blue for the template/primer DNA strands, respectively). The dCTP base is seen in a stacking arrangement with the 3â end base of the primer strand, suggesting that this complex is functionally relevant. (Figure continues on facing page.)

Figure 3.
Fig. 3. Distances bwteen the nucleotides and interacting protein side chains. Only potential H-bonds are shown. A: Klentaql with dATP. B: Klentaql with dCTP. C: Klentaql with dGTP. D: Klentaql with dTTP.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1998, 7, 1116-1123) copyright 1998.

Figures were selected by an automated process.