3SV4 image
Deposition Date 2011-07-12
Release Date 2012-06-06
Last Version Date 2023-09-13
Entry Detail
PDB ID:
3SV4
Keywords:
TRANSFERASE/DNA
Title:
Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dT as templating nucleobase
Biological Source:
Source Organism:
Thermus aquaticus (Taxon ID: 271)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.99 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.18
Space Group:
P 31 2 1
3SV4 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:(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:
Polymer Type:polydeoxyribonucleotide
Molecule:(5'-D(*AP*AP*AP*TP*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:
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
DOC B DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
Ligand Molecules
FMT
MG
Primary Citation
KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
Nat.Chem.Biol. 8 612 614 (2012)
PMID: 22660438 DOI: 10.1038/nchembio.966

Abstact

Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
4KTQ
3SV3
3SYZ
3SZ2