ISDA: 3SYZ

Deposition Date 2011-07-18

Release Date 2012-06-06

Last Version Date 2023-09-13

Entry Detail

PDB ID:

3SYZ

Keywords:

TRANSFERASE/DNA

Title:

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase

Biological Source:

Source Organism:

Thermus aquaticus (Taxon ID: 271)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.95 Å

R-Value Free:

0.20

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 31 2 1

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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*(BMN)P*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

GOL

Primary Citation

KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.

Betz, K, Malyshev, D.A, Lavergne, T, Welte, W, Diederichs, K, Dwyer, T.J, Ordoukhanian, P, Romesberg, F.E, Marx, A.Show

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.

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Primary Citation of related structures