PDBsum entry 2van

Transferase

PDB id: 2van

Contents

Protein chain

240 a.a. *

Waters ×128

* Residue conservation analysis

PDB id:

2van

Name:

Transferase

Title:

Nucleotidyl transfer mechanism of mismatched dntp incorporation by DNA polymerase b by structural and kinetic analyses

Structure:

DNA polymerse beta. Chain: a. Fragment: 31k domain, residues 90-334. Engineered: yes. Mutation: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.10Å R-factor: 0.217 R-free: 0.249

Authors:

H.Chan,C.Chou,K.Tang,M.Niebuhr,C.Tung,M.Tsai

Key ref:

K.H.Tang et al. (2008). Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways. Nucleic Acids Res, 36, 2948-2957. PubMed id: 18385153

Date:

03-Sep-07 Release date: 15-Apr-08

Protein chain

P06766  (DPOLB_RAT) -  DNA polymerase beta from Rattus norvegicus

Seq: 335 a.a.

Struc: 240 a.a.*

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

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

Nucleic Acids Res 36:2948-2957 (2008)

PubMed id: 18385153

Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways.

K.H.Tang, M.Niebuhr, C.S.Tung, H.C.Chan, C.C.Chou, M.D.Tsai.

ABSTRACT

Understanding how DNA polymerases control fidelity requires elucidation of the mechanisms of matched and mismatched dNTP incorporations. Little is known about the latter because mismatched complexes do not crystallize readily. In this report, we employed small-angle X-ray scattering (SAXS) and structural modeling to probe the conformations of different intermediate states of mammalian DNA polymerase beta (Pol beta) in its wild-type and an error-prone variant, I260Q. Our structural results indicate that the mismatched ternary complex lies in-between the open and the closed forms, but more closely resembles the open form for WT and the closed form for I260Q. On the basis of molecular modeling, this over-stabilization of mismatched ternary complex of I260Q is likely caused by formation of a hydrogen bonding network between the side chains of Gln(260), Tyr(296), Glu(295) and Arg(258), freeing up Asp(192) to coordinate MgdNTP. These results argue against recent reports suggesting that mismatched dNTP incorporations follow a conformational path distinctly different from that of matched dNTP incorporation, or that its conformational closing is a major contributor to fidelity.