PDBsum entry 3lk9

Lyase,transferase/DNA

PDB id: 3lk9

Contents

Protein chain

326 a.a.

DNA/RNA

Ligands

TFF

Metals

_CL ×3

_MG ×2

_NA ×2

Waters ×158

PDB id:

3lk9

Name:

Lyase,transferase/DNA

Title:

DNA polymerase beta with a gapped DNA substrate and dtmp(cf2)p(cf2)p

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. DNA (5'-d( Cp Cp Gp Ap Cp Ap Gp Cp Gp Cp Ap Tp Cp Ap Gp C)- 3'). Chain: t. Engineered: yes. DNA (5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp C)-3'). Chain: p.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: chemically synthesized oligonucleotide. Other_details: chemically synthesized oligonucleotide

Resolution:

2.50Å R-factor: 0.198 R-free: 0.281

Authors:

M.Zibinsky,G.K.Surya Prakash,T.G.Upton,B.A.Kashemirov,C.E.Mckenna, K.Oertell,M.F.Goodman,V.K.Batra,L.C.Pedersen,W.A.Beard,S.H.Wilson

Key ref:

G.K.Surya Prakash et al. (2010). Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid. Proc Natl Acad Sci U S A, 107, 15693-15698. PubMed id: 20724659

Date:

27-Jan-10 Release date: 12-Jan-11

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 326 a.a.

DNA/RNA chains

C-C-G-A-C-A-G-C-G-C-A-T-C-A-G-C 16 bases

G-C-T-G-A-T-G-C-G-C 10 bases

G-T-C-G-G 5 bases

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 2: E.C.4.2.99.- - ?????
• Enzyme class 3: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Proc Natl Acad Sci U S A 107:15693-15698 (2010)

PubMed id: 20724659

Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid.

G.K.Surya Prakash, M.Zibinsky, T.G.Upton, B.A.Kashemirov, C.E.McKenna, K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, D.D.Shock, S.H.Wilson, G.A.Olah.

ABSTRACT

It is difficult to overestimate the importance of nucleoside triphosphates in cellular chemistry: They are the building blocks for DNA and RNA and important sources of energy. Modifications of biologically important organic molecules with fluorine are of great interest to chemists and biologists because the size and electronegativity of the fluorine atom can be used to make defined structural alterations to biologically important molecules. Although the concept of nonhydrolyzable nucleotides has been around for some time, the progress in the area of modified triphosphates was limited by the lack of synthetic methods allowing to access bisCF(2)-substituted nucleotide analogs-one of the most interesting classes of nonhydrolyzable nucleotides. These compounds have "correct" polarity and the smallest possible steric perturbation compared to natural nucleotides. No other known nucleotides have these advantages, making bisCF(2)-substituted analogs unique. Herein, we report a concise route for the preparation of hitherto unknown highly acidic and polybasic bis(difluoromethylene)triphosphoric acid 1 using a phosphorous(III)/phosphorous(V) interconversion approach. The analog 1 compared to triphosphoric acid is enzymatically nonhydrolyzable due to substitution of two bridging oxygen atoms with CF(2) groups, maintaining minimal perturbations in steric bulkiness and overall polarity of the triphosphate polyanion. The fluorinated triphosphoric acid 1 was used for the preparation of the corresponding fluorinated deoxynucleotides (dNTPs). One of these dNTP analogs (dT) was demonstrated to fit into DNA polymerase beta (DNA pol beta) binding pocket by obtaining a 2.5 A resolution crystal structure of a ternary complex with the enzyme. Unexpected dominating effect of triphosphate/Mg(2+) interaction over Watson-Crick hydrogen bonding was found and discussed.