PDBsum entry 3gdx

Transferase/DNA

PDB id: 3gdx

Contents

Protein chain

326 a.a. *

DNA/RNA

Ligands

4BD

Metals

_CL ×2

_MG ×2

_NA ×2

Waters ×277

* Residue conservation analysis

PDB id:

3gdx

Name:

Transferase/DNA

Title:

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

Structure:

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

Source:

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

Resolution:

2.20Å R-factor: 0.208 R-free: 0.266

Authors:

S.H.Wilson,V.K.Batra,L.C.Pedersen

Key ref:

T.G.Upton et al. (2009). Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function. Org Lett, 11, 1883-1886. PubMed id: 19351147

Date:

24-Feb-09 Release date: 05-May-09

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

Org Lett 11:1883-1886 (2009)

PubMed id: 19351147

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

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

ABSTRACT

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.