PDBsum entry 4mfa

Transferase/DNA

PDB id: 4mfa

Contents

Protein chain

321 a.a.

DNA/RNA

Ligands

PO4

Metals

_MG ×2

_NA ×2

Waters ×81

PDB id:

4mfa

Name:

Transferase/DNA

Title:

Structure of human DNA polymerase beta complexed with nicked DNA containing a mismatched template o6mg and incoming ttp

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. Template. Chain: t. Engineered: yes. Up primer. Chain: p. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic template. Other_details: synthetic up primer.

Resolution:

2.27Å R-factor: 0.216 R-free: 0.283

Authors:

M.C.Koag,K.Min,A.F.Monzingo,S.Lee

Key ref:

M.C.Koag et al. Structures of human DNA polymerase beta inserting bas opposite templating o6mg. To be published, .

Date:

27-Aug-13 Release date: 27-Aug-14

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 321 a.a.

DNA/RNA chains

C-C-G-A-C-6OG-T-C-G-C-A-T-C-A-G-C 16 bases

G-C-T-G-A-T-G-C-G-A-T 11 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

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + 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