ISDA

Entry Detail

PDB ID:

4DFK

Keywords:

Title:

large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentinyl)-2-dUTP

Biological Source:

Source Organism:

Thermus aquaticus,

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2012-01-24

Release Date:

2012-05-16

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.65 Å

R-Value Free:

0.19

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 31 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA polymerase I, thermostable
Chain IDs:A
Chain Length:540
Number of Molecules:1
Biological Source:Thermus aquaticus

UniProt ID:P19821 Pfam ID:PF09281, PF00476 EC:2.7.7.7

Polymer Type:polydeoxyribonucleotide
Description:5'-d(GACCACGGCGC DOC)-3'
Chain IDs:B
Chain Length:12
Number of Molecules:1
Biological Source:

Polymer Type:polydeoxyribonucleotide
Description:5'-d(AAAAGGCGCCGTGGTC)-3'
Chain IDs:C
Chain Length:16
Number of Molecules:1
Biological Source:

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
DOC	B	DC	2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE

Ligand Molecules

0L5

EDO

FMT

Primary Citation

Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates.

Bergen, K, Steck, A.L, Strutt, S, Baccaro, A, Welte, W, Diederichs, K, Marx, A.Show

J.Am.Chem.Soc. 134 11840 11843 (2012)

PMID: 22475415 DOI: 10.1021/ja3017889

Abstact

The capability of DNA polymerases to accept chemically modified nucleotides is of paramount importance for many biotechnological applications. Although these analogues are widely used, the structural basis for the acceptance of the unnatural nucleotide surrogates has been only sparsely explored. Here we present in total six crystal structures of modified 2'-deoxynucleoside-5'-O-triphosphates (dNTPs) carrying modifications at the C5 positions of pyrimidines or C7 positions of 7-deazapurines in complex with a DNA polymerase and a primer/template complex. The modified dNTPs are in positions poised for catalysis leading to incorporation. These structural data provide insight into the mechanism of incorporation and acceptance of modified dNTPs. Our results open the door for rational design of modified nucleotides, which should offer great opportunities for future applications.

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Primary Citation of related structures