PDBsum entry 8scm

Replication/DNA

PDB id: 8scm

Contents

Protein chains

579 a.a.

DNA/RNA

Ligands

DPO-DGT ×2

SO4 ×4

Metals

_CA ×2

Waters ×217

PDB id:

8scm

Name:

Replication/DNA

Title:

Bst DNA polymerase i large fragment mutant f710y/d598a with 3'-amino primer, dgtp, and calcium time-resolved 8h

Structure:

DNA polymerase i. Chain: a, d. Engineered: yes. DNA primer/product. Chain: b, e. Engineered: yes. DNA template. Chain: c, f. Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: dpo1, pola. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

2.30Å R-factor: 0.196 R-free: 0.250

Authors:

Z.Fang,V.S.Lelyveld,J.W.Szostak

Key ref:

V.S.Lelyveld et al. Trivalent rare earth metal cofactors confer rapid np- Polymerase activity. Science, . PubMed id: 37883544

Date:

05-Apr-23 Release date: 25-Oct-23

Protein chains

D9N168  (D9N168_GEOSE) -  DNA polymerase I from Geobacillus stearothermophilus

Seq: 579 a.a.

Struc: 579 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

G-C-G-A-T-C-A-G-C42-G 10 bases

C-A-C-G-C-T-G-A-T-C-G-C-A 13 bases

G-C-G-A-T-C-A-G-C42-G 10 bases

C-A-C-G-C-T-G-A-T-C-G-C-A 13 bases

Enzyme reactions

• Enzyme class: 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 = DPO) corresponds exactly) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site