PDBsum entry 3v72

DNA binding protein/DNA

PDB id: 3v72

Contents

Protein chain

327 a.a.

DNA/RNA

Metals

_CL ×2

_NA ×2

Waters ×83

PDB id:

3v72

Name:

DNA binding protein/DNA

Title:

Crystal structure of rat DNA polymerase beta mutator e295k: enzyme- dsdna

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. Mutation: yes. DNA 5'-d(p Ap Tp Gp Tp Gp Ap Gp T)-3'. Chain: p. Engineered: yes. Other_details: primer strand of DNA. DNA 5'-d(p Ap Ap Ap Cp Tp Cp Ap Cp Ap T)-3'.

Source:

Rattus norvegicus. Rat. Organism_taxid: 10116. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: DNA primer strand. Other_details: DNA template strand

Resolution:

2.49Å R-factor: 0.223 R-free: 0.291

Authors:

C.L.Gridley,J.Jaeger

Key ref:

Y.Li et al. (2012). Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway. J Am Chem Soc, 134, 9999-10010. PubMed id: 22651551

Date:

20-Dec-11 Release date: 04-Jul-12

Protein chain

P06766  (DPOLB_RAT) -  DNA polymerase beta from Rattus norvegicus

Seq: 335 a.a.

Struc: 327 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

A-T-G-T-G-A-G-T 8 bases

A-A-A-C-T-C-A-C-A-T 10 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 134:9999-10010 (2012)

PubMed id: 22651551

Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway.

Y.Li, C.L.Gridley, J.Jaeger, J.B.Sweasy, T.Schlick.

ABSTRACT

No abstract given.