4F4W

Y-family DNA polymerase chimera Dbh-Dpo4-Dpo4 #1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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


Literature

Y-family polymerase conformation is a major determinant of fidelity and translesion specificity.

Wilson, R.C., Jackson, M.A., Pata, J.D.

(2013) Structure 21: 20-31

  • DOI: 10.1016/j.str.2012.11.005
  • Primary Citation of Related Structures:  
    4F4W, 4F4X, 4F4Y, 4F4Z, 4F50, 4HYK

  • PubMed Abstract: 

    • Y-family polymerases help cells tolerate DNA damage by performing translesion synthesis opposite damaged DNA bases, yet they also have a high intrinsic error rate. We constructed chimeras of two closely related Y-family polymerases that display distinctly different activity profiles and found that the polypeptide linker that tethers the catalytic polymerase domain to the C-terminal DNA-binding domain is a major determinant of overall polymerase activity, nucleotide incorporation fidelity, and abasic site-bypass ability ...

    Y-family polymerases help cells tolerate DNA damage by performing translesion synthesis opposite damaged DNA bases, yet they also have a high intrinsic error rate. We constructed chimeras of two closely related Y-family polymerases that display distinctly different activity profiles and found that the polypeptide linker that tethers the catalytic polymerase domain to the C-terminal DNA-binding domain is a major determinant of overall polymerase activity, nucleotide incorporation fidelity, and abasic site-bypass ability. Exchanging just 3 out of the 15 linker residues is sufficient to interconvert the polymerase activities tested. Crystal structures of four chimeras show that the conformation of the protein correlates with the identity of the interdomain linker sequence. Thus, residues that are more than 15 Å away from the active site are able to influence many aspects of polymerase activity by altering the relative orientations of the catalytic and DNA-binding domains.

    Organizational Affiliation: 

    Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA; Department of Biomedical Sciences, University at Albany, Albany, NY 12201-0509, USA. Electronic address: jpata@wadsworth.org.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVA,
D [auth B]		361Sulfolobus acidocaldarius DSM 639, Saccharolobus solfataricus P2
This entity is chimeric		Mutation(s): 0 
Gene Names: dbh, dpo4, Dpo4 (S. solfataricus) and Dbh (S. acidocaldarius), Saci_0554, SSO24 48
EC: 2.7.7.7
UniProt
Find proteins for Q4JB80 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Explore Q4JB80 
Go to UniProtKB:  Q4JB80
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97W02 
Go to UniProtKB:  Q97W02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ4JB80Q97W02
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*C)-3')E,
B [auth P]		13N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*TP*AP*CP*GP*GP*CP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3')F,
C [auth T]		18N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.82α = 90
b = 99.655β = 90.16
c = 101.625γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2013-02-13
    Changes: Database references
  • Version 1.2: 2014-01-29
    Changes: Source and taxonomy
  • Version 1.3: 2014-02-12
    Changes: Source and taxonomy
  • Version 1.4: 2017-08-16
    Changes: Refinement description, Source and taxonomy