Brand  (β version)

PDB ID: 6US5

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Ligands
Code Name Style Show Link
XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine PoSSuM
MN Manganese (II) ion PoSSuM
SO4 Sulfate ion PoSSuM
Non-standard Residues
Code Name Show
C42 3'-amino-2'-deoxy-cytidine-5'-monophosphate
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 6US5   PDBj   RCSB PDB   PDBe
Header : REPLICATION/DNA
Title : DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, 3'-amino primer, dGpNHpp analog, and Mn2+
Release Data : 2020-03-18
Compound :
mol_id molecule chains
1 DNA polymerase I A,D
ec: 2.7.7.7
mutation: D598A/F710Y
mol_id molecule chains
2 DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42))-3') B,E
mol_id molecule chains
3 DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3') C,F
Source :
mol_id organism_scientific expression_system
1 Geobacillus stearothermophilus  (taxid:1422) Escherichia coli  (taxid:562)
strain: Strain X
gene: DPO1, polA
mol_id organism_scientific
2 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
3 Synthetic construct  (taxid:32630)
synthetic: yes
Authors : Zhang, W., Lelyveld, V.S., Szostak, J.W.
Keywords : DNA polymerase, 3'-amino terminal primer, GpNHpp, Mn2+, REPLICATION-DNA complex
Exp. method : X-RAY DIFFRACTION ( 2.2500 Å )
Citation :

Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase.

Lelyveld, V.S.,Zhang, W.,Szostak, J.W.
(2020)  Proc.Natl.Acad.Sci.USA  117 : 7276 - 7283

PubMed: 32188786
DOI: 10.1073/pnas.1922400117

Reaction

Chain : A, D
UniProt : D9N168 (D9N168_GEOSE)
Reaction: EC: Evidence:
Physiological Direction:
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 2.7.7.7 ARBA:ARBA00024632, RuleBase:RU004460
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