ISDA

Deposition Date 2009-02-24

Release Date 2009-05-05

Last Version Date 2023-09-06

Entry Detail

PDB ID:

3GDX

Keywords:

TRANSFERASE/DNA

Title:

Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.20 Å

R-Value Free:

0.26

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA polymerase beta
Gene (Uniprot):POLB
Chain IDs:A
Chain Length:326
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P06746 Pfam ID:PF14716, PF10391, PF14792, PF14791 EC:2.7.7.7

Ligand Molecules

4BD

Primary Citation

Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function

Upton, T.G, Kashemirov, B.A, McKenna, C.E, Goodman, M.F, Prakash, G.K, Kultyshev, R, Batra, V.K, Shock, D.D, Pedersen, L.C, Beard, W.A, Wilson, S.H.Show

Org.Lett. 11 1883 1886 (2009)

PMID: 19351147 DOI: 10.1021/ol701755k

Abstact

Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates (dNTPs, N = A or C) are advantageously obtained via phosphorylation of corresponding dNDP analogues using catalytic ATP, PEP, nucleoside diphosphate kinase, and pyruvate kinase. DNA pol beta K(d) values for the alpha,beta-CF(2) and unmodified dNTPs, alpha,beta-NH dUTP, and the alpha,beta-CH(2) analogues of dATP and dGTP are discussed in relation to the conformations of alpha,beta-CF(2) dTTP versus alpha,beta-NH dUTP bound into the enzyme active site.

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Primary Citation of related structures