4E5Z

Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair.

Yeh, J.I., Levine, A.S., Du, S., Chinte, U., Ghodke, H., Wang, H., Shi, H., Hsieh, C.L., Conway, J.F., Van Houten, B., Rapic-Otrin, V.

(2012) Proc.Natl.Acad.Sci.USA 109: E2737-E2746

  • DOI: 10.1073/pnas.1110067109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • UV light-induced photoproducts are recognized and removed by the nucleotide-excision repair (NER) pathway. In humans, the UV-damaged DNA-binding protein (UV-DDB) is part of a ubiquitin E3 ligase complex (DDB1-CUL4A(DDB2)) that initiates NER by recogn ...

    UV light-induced photoproducts are recognized and removed by the nucleotide-excision repair (NER) pathway. In humans, the UV-damaged DNA-binding protein (UV-DDB) is part of a ubiquitin E3 ligase complex (DDB1-CUL4A(DDB2)) that initiates NER by recognizing damaged chromatin with concomitant ubiquitination of core histones at the lesion. We report the X-ray crystal structure of the human UV-DDB in a complex with damaged DNA and show that the N-terminal domain of DDB2 makes critical contacts with two molecules of DNA, driving N-terminal-domain folding and promoting UV-DDB dimerization. The functional significance of the dimeric UV-DDB [(DDB1-DDB2)(2)], in a complex with damaged DNA, is validated by electron microscopy, atomic force microscopy, solution biophysical, and functional analyses. We propose that the binding of UV-damaged DNA results in conformational changes in the N-terminal domain of DDB2, inducing helical folding in the context of the bound DNA and inducing dimerization as a function of nucleotide binding. The temporal and spatial interplay between domain ordering and dimerization provides an elegant molecular rationale for the unprecedented binding affinities and selectivities exhibited by UV-DDB for UV-damaged DNA. Modeling the DDB1-CUL4A(DDB2) complex according to the dimeric UV-DDB-AP24 architecture results in a mechanistically consistent alignment of the E3 ligase bound to a nucleosome harboring damaged DNA. Our findings provide unique structural and conformational insights into the molecular architecture of the DDB1-CUL4A(DDB2) E3 ligase, with significant implications for the regulation and overall organization of the proteins responsible for initiation of NER in the context of chromatin and for the consequent maintenance of genomic integrity.

    Organizational Affiliation: 

    Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA. jiyeh@pitt.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA damage-binding protein 1
A
1150Homo sapiensMutation(s): 0 
Gene Names: DDB1 (XAP1)
Find proteins for Q16531 (Homo sapiens)
Go to Gene View: DDB1
Go to UniProtKB:  Q16531
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA damage-binding protein 2
B
436Homo sapiensMutation(s): 0 
Gene Names: DDB2
Find proteins for Q92466 (Homo sapiens)
Go to Gene View: DDB2
Go to UniProtKB:  Q92466
Entity ID: 3
MoleculeChainsLengthOrganism
AP24 DNA strandF24N/A
Entity ID: 4
MoleculeChainsLengthOrganism
AP24 DNA complementary strandG24N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
G
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.228 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 72.418α = 90.00
b = 76.504β = 90.00
c = 389.738γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SOLVEphasing
SCALEPACKdata scaling
ADSCdata collection
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-03-15 
  • Released Date: 2012-08-22 
  • Deposition Author(s): Yeh, J.I., Du, S.

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-10-24
    Type: Database references
  • Version 1.2: 2019-07-17
    Type: Data collection, Derived calculations, Refinement description