PDBsum entry 2fms

Transferase/DNA

PDB id: 2fms

Contents

Protein chain

326 a.a. *

DNA/RNA

Ligands

DUP

Metals

_MG ×2

_NA ×2

_CL ×4

Waters ×331

* Residue conservation analysis

PDB id:

2fms

Name:

Transferase/DNA

Title:

DNA polymerase beta with a gapped DNA substrate and dumpnpp with magnesium in the catalytic site

Structure:

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. 5'-d(p Gp Tp Cp Gp G)-3'. Chain: d. Engineered: yes.

Source:

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

Biol. unit:

Tetramer (from PQS)

Resolution:

2.00Å R-factor: 0.196 R-free: 0.244

Authors:

V.K.Batra,W.A.Beard,D.D.Shock,J.M.Krahn,L.C.Pedersen,S.H.Wilson

Key ref:

V.K.Batra et al. (2006). Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Structure, 14, 757-766. PubMed id: 16615916 DOI: 10.1016/j.str.2006.01.011

Date:

09-Jan-06 Release date: 25-Apr-06

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

DOI no: 10.1016/j.str.2006.01.011

Structure 14:757-766 (2006)

PubMed id: 16615916

Magnesium-induced assembly of a complete DNA polymerase catalytic complex.

V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, S.H.Wilson.

ABSTRACT

The molecular details of the nucleotidyl transferase reaction have remained speculative, as strategies to trap catalytic intermediates for structure determination utilize substrates lacking the primer terminus 3'-OH and catalytic Mg2+, resulting in an incomplete and distorted active site geometry. Since the geometric arrangement of these essential atoms will impact chemistry, structural insight into fidelity strategies has been hampered. Here, we present a crystal structure of a precatalytic complex of a DNA polymerase with bound substrates that include the primer 3'-OH and catalytic Mg2+. This catalytic intermediate was trapped with a nonhydrolyzable deoxynucleotide analog. Comparison with two new structures of DNA polymerase beta lacking the 3'-OH or catalytic Mg2+ is described. These structures provide direct evidence that both atoms are required to achieve a proper geometry necessary for an in-line nucleophilic attack of O3' on the alphaP of the incoming nucleotide.

Selected figure(s)

Figure 7.
Figure 7. Stereoview of the Pol b Active Site
Superimposed structures of pol b with either Na^+ (light blue) or Mg2+ (yellow) in the catalytic metal site A. Residues that hydrogen bond (green) to the triphosphate moiety of the incoming nucleotide and the active site aspartates are shown. When Na^+ occupies the catalytic metal site, O3' of the primer terminus is 3.5 and 4.7 Å from the catalytic metal and aP of the incoming nucleotide, respectively. In contrast, with Mg2+ in the catalytic metal site, an altered sugar pucker positions O3' of the primer terminus 2.2 and 3.4 Å from the catalytic metal and Pa of the incoming nucleotide, respectively.

The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 757-766) copyright 2006.

Figure was selected by the author.