1Q9X

Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Lesion (in)tolerance reveals insights into DNA replication fidelity.

Freisinger, E.Grollman, A.P.Miller, H.Kisker, C.

(2004) EMBO J 23: 1494-1505

  • DOI: 10.1038/sj.emboj.7600158
  • Primary Citation of Related Structures:  
    1Q9X, 1Q9Y

  • PubMed Abstract: 
  • The initial encounter of an unrepaired DNA lesion is likely to be with a replicative DNA polymerase, and the outcome of this event determines whether an error-prone or error-free damage avoidance pathway is taken. To understand the atomic details of this critical encounter, we have determined the crystal structures of the pol alpha family RB69 DNA polymerase with DNA containing the two most prevalent, spontaneously generated premutagenic lesions, an abasic site and 2'-deoxy-7,8-dihydro-8-oxoguanosine (8-oxodG) ...

    The initial encounter of an unrepaired DNA lesion is likely to be with a replicative DNA polymerase, and the outcome of this event determines whether an error-prone or error-free damage avoidance pathway is taken. To understand the atomic details of this critical encounter, we have determined the crystal structures of the pol alpha family RB69 DNA polymerase with DNA containing the two most prevalent, spontaneously generated premutagenic lesions, an abasic site and 2'-deoxy-7,8-dihydro-8-oxoguanosine (8-oxodG). Identification of the interactions between these damaged nucleotides and the active site provides insight into the capacity of the polymerase to incorporate a base opposite the lesion. A novel open, catalytically inactive conformation of the DNA polymerase has been identified in the complex with a primed abasic site template. This structure provides the first molecular characterization of the DNA synthesis barrier caused by an abasic site and suggests a general mechanism for polymerase fidelity. In contrast, the structure of the ternary 8-oxodG:dCTP complex is almost identical to the replicating complex containing unmodified DNA, explaining the relative ease and fidelity by which this lesion is bypassed.


    Organizational Affiliation

    Department of Pharmacological Sciences, Center for Structural Biology, SUNY at Stony Brook, Stony Brook, NY, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseI [auth A],
J [auth B],
K [auth C],
L [auth D]
903Escherichia phage RB69Mutation(s): 2 
Gene Names: 43
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for Q38087 (Escherichia phage RB69)
Explore Q38087 
Go to UniProtKB:  Q38087
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38087
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-GCGGACTGCTTAC(dideoxycytidine)-3'A [auth E],
C [auth F],
E [auth G],
G [auth H]
18N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-AC(tetrahydrofuran)GGTAAGCAGTCCGCGG-3'B [auth I],
D [auth J],
F [auth K],
H [auth L]
13N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGP
Query on DGP

Download Ideal Coordinates CCD File 
O [auth F],
R [auth G],
S [auth G],
U [auth K],
W [auth H],
O [auth F],
R [auth G],
S [auth G],
U [auth K],
W [auth H],
Y [auth L]
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
LTFMZDNNPPEQNG-KVQBGUIXSA-N
 Ligand Interaction
DOC
Query on DOC

Download Ideal Coordinates CCD File 
N [auth I],
Q [auth J],
V [auth K],
Z [auth L]
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O6 P
RAJMXAZJKUGYGW-POYBYMJQSA-N
 Ligand Interaction
3DR
Query on 3DR

Download Ideal Coordinates CCD File 
M [auth E],
P [auth F],
T [auth G],
X [auth H]
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
C5 H11 O6 P
BVOBPNSQIRMLCA-CRCLSJGQSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
CA [auth B],
DA [auth B],
EA [auth C],
AA [auth A],
BA [auth A],
CA [auth B],
DA [auth B],
EA [auth C],
FA [auth C],
GA [auth D],
HA [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.948α = 90
b = 122.237β = 96.85
c = 165.358γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Advisory, Data collection, Database references, Derived calculations