5E41 image
Deposition Date 2015-10-05
Release Date 2016-12-07
Last Version Date 2024-01-10
Entry Detail
PDB ID:
5E41
Keywords:
TRANSFERASE
Title:
Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentenyl)-2'-deoxyuridine-triphosphate
Biological Source:
Source Organism:
Thermus aquaticus (Taxon ID: 271)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.80 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 31 2 1
5E41 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA polymerase I, thermostable
Gene (Uniprot):polA
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
Molecule:DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
Chain IDs:B
Chain Length:12
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
Chain IDs:C
Chain Length:16
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
AUL
GOL
MG
Primary Citation
Structural Basis for the KlenTaq DNA Polymerase Catalysed Incorporation of Alkene- versus Alkyne-Modified Nucleotides.
Chemistry 23 2109 2118 (2017)
PMID: 27901305 DOI: 10.1002/chem.201604515

Abstact

Efficient incorporation of modified nucleotides by DNA polymerases is essential for many cutting-edge biomolecular technologies. The present study compares the acceptance of either alkene- or alkyne-modified nucleotides by KlenTaq DNA polymerase and provides structural insights into how 7-deaza-adenosine and deoxyuridine with attached alkene-modifications are incorporated into the growing DNA strand. Thereby, we identified modified nucleotides that prove to be superior substrates for KlenTaq DNA polymerase compared with their natural analogues. The knowledge can be used to guide future design of functionalized nucleotide building blocks.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
5E41