6O8E

Crystal structure of UvrB bound to duplex DNA with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System.

Lee, S.J.Sung, R.J.Verdine, G.L.

(2019) Res 2019: 5641746-5641746

  • DOI: 10.34133/2019/5641746
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nucleotide excision repair (NER) is an essential DNA repair system distinguished from other such systems by its extraordinary versatility. NER removes a wide variety of structurally dissimilar lesions having only their bulkiness in common. NER can al ...

    Nucleotide excision repair (NER) is an essential DNA repair system distinguished from other such systems by its extraordinary versatility. NER removes a wide variety of structurally dissimilar lesions having only their bulkiness in common. NER can also repair several less bulky nucleobase lesions, such as 8-oxoguanine. Thus, how a single DNA repair system distinguishes such a diverse array of structurally divergent lesions from undamaged DNA has been one of the great unsolved mysteries in the field of genome maintenance. Here we employ a synthetic crystallography approach to obtain crystal structures of the pivotal NER enzyme UvrB in complex with duplex DNA, trapped at the stage of lesion-recognition. These structures coupled with biochemical studies suggest that UvrB integrates the ATPase-dependent helicase/translocase and lesion-recognition activities. Our work also conclusively establishes the identity of the lesion-containing strand and provides a compelling insight to how UvrB recognizes a diverse array of DNA lesions.


    Organizational Affiliation

    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UvrABC system protein B
A, B
593Bacillus caldotenaxMutation(s): 0 
Gene Names: uvrB
Find proteins for P56981 (Bacillus caldotenax)
Go to UniProtKB:  P56981
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*TP*CP*TP*AP*GP*AP*TP*TP*TP*TP*CP*AP*TP*AP*CP*GP*GP*C)-3')C,E20synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*GP*TP*AP*TP*GP*CP*CP*AP*AP*TP*CP*TP*AP*GP*AP*GP*C)-3')D,F20synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.269α = 90.00
b = 115.719β = 90.00
c = 266.795γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA100742

Revision History 

  • Version 1.0: 2020-01-22
    Type: Initial release