PDBsum entry 4j2d

Transferase/DNA

PDB id: 4j2d

Contents

Protein chain

901 a.a.

DNA/RNA

Ligands

TTP

Metals

_CA ×9

Waters ×962

PDB id:

4j2d

Name:

Transferase/DNA

Title:

Rb69 DNA polymerase l415k ternary complex

Structure:

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

Source:

Enterobacteria phage rb69. Organism_taxid: 12353. Gene: 43. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: oligo was synthesized at keck facility.. Other_details: oligo was synthesized at keck facility.

Resolution:

1.76Å R-factor: 0.172 R-free: 0.197

Authors:

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

Key ref:

S.Xia et al. Role of l415 in the replication of rb69 DNA polymeras. To be published, .

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-A-G-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-T 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