PDBsum entry 4doc

Transferase/DNA

PDB id: 4doc

Contents

Protein chain

326 a.a.

DNA/RNA

Ligands

G1C

Metals

_MG

_NA ×3

_CL ×5

Waters ×435

PDB id:

4doc

Name:

Transferase/DNA

Title:

Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of s-isomer

Structure:

DNA polymerase beta. Chain: a. Fragment: DNA polymerase beta. Engineered: yes. C c g a c c g c g c a t c a g c. Chain: t. Engineered: yes. G c t g a t g c g (doc). 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:

1.95Å R-factor: 0.203 R-free: 0.249

Authors:

V.K.Batra

Key ref:

Y.Wu et al. (2012). β,γ-CHF- and β,γ-CHCl-dGTP diastereomers: synthesis, discrete 31P NMR signatures, and absolute configurations of new stereochemical probes for DNA polymerases. J Am Chem Soc, 134, 8734-8737. PubMed id: 22397499

Date:

09-Feb-12 Release date: 13-Jun-12

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

G-C-T-G-A-T-G-C-G-DOC 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

J Am Chem Soc 134:8734-8737 (2012)

PubMed id: 22397499

β,γ-CHF- and β,γ-CHCl-dGTP diastereomers: synthesis, discrete 31P NMR signatures, and absolute configurations of new stereochemical probes for DNA polymerases.

Y.Wu, V.M.Zakharova, B.A.Kashemirov, M.F.Goodman, V.K.Batra, S.H.Wilson, C.E.McKenna.

ABSTRACT

No abstract given.