PDBsum entry 4j2e

Transferase/DNA

PDB id: 4j2e

Contents

Protein chain

901 a.a.

DNA/RNA

Ligands

ATP

Metals

_CA ×6

Waters ×502

PDB id:

4j2e

Name:

Transferase/DNA

Title:

Rb69 DNA polymerase l415m ternary complex

Structure:

DNA polymerase. Chain: a. Fragment: rb69 DNA polymerase. Synonym: gp43. Engineered: yes. Mutation: yes. DNA (5'- d( Tp Cp Gp Tp Cp Tp Ap Ap Gp Cp Ap Gp Tp Cp Cp Gp Cp G)-3'). Chain: t.

Source:

Enterobacteria phage rb69. Organism_taxid: 12353. Gene: 43. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes

Resolution:

2.02Å R-factor: 0.180 R-free: 0.213

Authors:

S.Xia,J.Wang,W.H.Konigsberg

Key ref:

S.Xia et al. (2013). Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics. Nucleic Acids Res, 41, 9077-9089. PubMed id: 23921641 DOI: 10.1093/nar/gkt674

Date:

04-Feb-13 Release date: 19-Feb-14

Protein chain

Q38087  (DPOL_BPR69) -  DNA-directed DNA polymerase from Escherichia phage RB69

Seq: 903 a.a.

Struc: 901 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

T-C-G-T-C-T-A-A-G-C-A-G-T-C-C-G-C-G 18 bases

G-C-G-G-A-C-T-G-C-T-T-A-G 13 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.3.1.11.- - ?????

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: 10.1093/nar/gkt674

Nucleic Acids Res 41:9077-9089 (2013)

PubMed id: 23921641

Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics.

S.Xia, M.Wood, M.J.Bradley, E.M.De La Cruz, W.H.Konigsberg.

ABSTRACT

Internal cavities are a common feature of many proteins, often having profound effects on the dynamics of their interactions with substrate and binding partners. RB69 DNA polymerase (pol) has a hydrophobic cavity right below the nucleotide binding pocket at the tip of highly conserved L415 side chain. Replacement of this residue with Gly or Met in other B family pols resulted in higher mutation rates. When similar substitutions for L415 were introduced into RB69pol, only L415A and L415G had dramatic effects on pre-steady-state kinetic parameters, reducing base selectivity by several hundred fold. On the other hand, the L415M variant behaved like the wild-type. Using a novel tC(o)-tCnitro Förster Resonance Energy Transfer (FRET) assay, we were able to show that the partition of the primer terminus between pol and exonuclease (exo) domains was compromised with the L415A and L415G mutants, but not with the L415M variant. These results could be rationalized by changes in their structures as determined by high resolution X-ray crystallography.