ISDA

Deposition Date 2010-04-20

Release Date 2010-09-08

Last Version Date 2023-12-20

Entry Detail

PDB ID:

2XC9

Keywords:

TRANSFERASE/DNA

Title:

BINARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE AND 1, N2-ETHENOGUANINE MODIFIED DNA, MAGNESIUM FORM

Biological Source:

Source Organism:

SULFOLOBUS SOLFATARICUS (Taxon ID: 273057)
(Taxon ID: 32630)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.20 Å

R-Value Free:

0.25

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 21 21 2

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA POLYMERASE IV
Gene (Uniprot):dbh
Chain IDs:A
Chain Length:358
Number of Molecules:1
Biological Source:SULFOLOBUS SOLFATARICUS

UniProt ID:Q97W02 Pfam ID:PF00817, PF11798, PF11799 EC:2.7.7.7

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3'
Chain IDs:B (auth: P)
Chain Length:14
Number of Molecules:1
Biological Source:

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*TP*CP*AP*CP*GNEP*GP*AP*AP*TP*CP*CP*TP*TP* CP*CP*CP*CP*C)-3'
Chain IDs:C (auth: T)
Chain Length:18
Number of Molecules:1
Biological Source:

Primary Citation

Metal Ion Dependence of the Active Site Conformation of the Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus Solfataricus

Irimia, A, Loukachevitch, L.V, Eoff, R.L, Guengerich, F.P, Egli, M.Show

Acta Crystallogr.,Sect.F 66 1013 ? (2010)

PMID: 20823515 DOI: 10.1107/S1744309110029374

Abstact

Crystal structures of a binary Mg2+-form Dpo4-DNA complex with 1,N2-etheno-dG in the template strand as well as of ternary Mg2+-form Dpo4-DNA-dCTP/dGTP complexes with 8-oxoG in the template strand have been determined. Comparison of their conformations and active-site geometries with those of the corresponding Ca2+-form complexes revealed that the DNA and polymerase undergo subtle changes as a result of the catalytically more active Mg2+ occupying both the A and B sites.

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Primary Citation of related structures