4X6A

Crystal structure of yeast RNA polymerase II encountering oxidative Cyclopurine DNA lesions

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.96 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions.

Walmacq, C., Wang, L., Chong, J., Scibelli, K., Lubkowska, L., Gnatt, A., Brooks, P.J., Wang, D., Kashlev, M.

(2015) Proc Natl Acad Sci U S A 112: E410-E419

  • DOI: 10.1073/pnas.1415186112
  • Primary Citation of Related Structures:  
    4X67, 4X6A

  • PubMed Abstract: 

    • In human cells, the oxidative DNA lesion 8,5'-cyclo-2'-deoxyadenosine (CydA) induces prolonged stalling of RNA polymerase II (Pol II) followed by transcriptional bypass, generating both error-free and mutant transcripts with AMP misincorporated immediately downstream from the lesion ...

    In human cells, the oxidative DNA lesion 8,5'-cyclo-2'-deoxyadenosine (CydA) induces prolonged stalling of RNA polymerase II (Pol II) followed by transcriptional bypass, generating both error-free and mutant transcripts with AMP misincorporated immediately downstream from the lesion. Here, we present biochemical and crystallographic evidence for the mechanism of CydA recognition. Pol II stalling results from impaired loading of the template base (5') next to CydA into the active site, leading to preferential AMP misincorporation. Such predominant AMP insertion, which also occurs at an abasic site, is unaffected by the identity of the 5'-templating base, indicating that it derives from nontemplated synthesis according to an A rule known for DNA polymerases and recently identified for Pol II bypass of pyrimidine dimers. Subsequent to AMP misincorporation, Pol II encounters a major translocation block that is slowly overcome. Thus, the translocation block combined with the poor extension of the dA.rA mispair reduce transcriptional mutagenesis. Moreover, increasing the active-site flexibility by mutation in the trigger loop, which increases the ability of Pol II to accommodate the bulky lesion, and addition of transacting factor TFIIF facilitate CydA bypass. Thus, blocking lesion entry to the active site, translesion A rule synthesis, and translocation block are common features of transcription across different bulky DNA lesions.

    Organizational Affiliation: 

    Center for Cancer Research, National Cancer Institute, Frederick, MD 21702; dongwang@ucsd.edu kashlevm@mail.nih.gov.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1A1,733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150
EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2B1,224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB2
EC: 2.7.7.6
UniProt
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Entity ID: 3
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DNA-directed RNA polymerase II subunit RPB3C318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB3, YIL021W
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1D [auth E]215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5, RPA7, RPC9, YBR154C, YBR1204
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2E [auth F]155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26, RPB6, YPR187W, P9677.8
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3F [auth H]146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8, YOR224C, YOR50-14
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9G [auth I]122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB9, YGL070C
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5H [auth J]70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10, YOR210W
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Entity ID: 9
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DNA-directed RNA polymerase II subunit RPB11I [auth K]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB11, YOL005C
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4J [auth L]70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10, RPB12, YHR143W-A, YHR143BW
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Entity ID: 11
MoleculeChainsLengthOrganismImage
RNA_9 merK [auth R]9synthetic construct
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Entity ID: 12
MoleculeChainsLengthOrganismImage
Template DNA _29 merL [auth T]29synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.96 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.55α = 90
b = 220.334β = 97
c = 191.563γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXrefinement
Cootmodel building

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM085136 and GM102362
Sidney Kimmel Foundation for Cancer ResearchUnited Statesthe Kimmel Scholar Award
Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSDUnited Statesstart-up funds

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.3: 2017-10-04
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence