PDBsum entry 7rbh

Transferase/DNA

PDB id: 7rbh

Contents

Protein chain

326 a.a.

DNA/RNA

Ligands

QPJ

DCP ×2

Metals

_CA ×3

Waters ×288

PDB id:

7rbh

Name:

Transferase/DNA

Title:

Human DNA polymerase beta crosslinked ternary complex 2

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. DNA (5'-d( Gp Tp Cp Gp G)-3'). Chain: d. Engineered: yes. DNA (5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp C)-3'). Chain: p. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

1.75Å R-factor: 0.182 R-free: 0.225

Authors:

A.Kumar

Key ref:

A.Kumar et al. (2022). Interlocking activities of DNA polymerase beta in the excision repair pathway. Proc natl acad sci usa, 119, . PubMed id: 35238634

Date:

06-Jul-21 Release date: 09-Mar-22

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 326 a.a.

DNA/RNA chains

G-T-C-G-G 5 bases

G-C-T-G-A-T-G-C-G-C 10 bases

C-C-G-A-C-G-G-C-G-C-A-T-C-A-G-C 16 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

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate (Bound ligand (Het Group name = QPJ) matches with 45.45% similarity) = 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