3SI8

Human DNA polymerase eta - DNA ternary complex with the 5'T of a CPD in the active site (TT2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report



Literature

Structure and mechanism of human DNA polymerase eta.

Biertumpfel, C.Zhao, Y.Kondo, Y.Ramon-Maiques, S.Gregory, M.Lee, J.Y.Masutani, C.Lehmann, A.R.Hanaoka, F.Yang, W.

(2010) Nature 465: 1044-1048

  • DOI: 10.1038/nature09196
  • Primary Citation of Related Structures:  
    3MR2, 3MR3, 3MR5, 3MR6, 3SI8

  • PubMed Abstract: 
  • The variant form of the human syndrome xeroderma pigmentosum (XPV) is caused by a deficiency in DNA polymerase eta (Poleta), a DNA polymerase that enables replication through ultraviolet-induced pyrimidine dimers. Here we report high-resolution crystal s ...

    The variant form of the human syndrome xeroderma pigmentosum (XPV) is caused by a deficiency in DNA polymerase eta (Poleta), a DNA polymerase that enables replication through ultraviolet-induced pyrimidine dimers. Here we report high-resolution crystal structures of human Poleta at four consecutive steps during DNA synthesis through cis-syn cyclobutane thymine dimers. Poleta acts like a 'molecular splint' to stabilize damaged DNA in a normal B-form conformation. An enlarged active site accommodates the thymine dimer with excellent stereochemistry for two-metal ion catalysis. Two residues conserved among Poleta orthologues form specific hydrogen bonds with the lesion and the incoming nucleotide to assist translesion synthesis. On the basis of the structures, eight Poleta missense mutations causing XPV can be rationalized as undermining the molecular splint or perturbing the active-site alignment. The structures also provide an insight into the role of Poleta in replicating through D loop and DNA fragile sites.


    Organizational Affiliation

    Laboratory of Molecular Biology, NIDDK, NIH, 9000 Rockville Pike, Building 5, Room B103, Bethesda, Maryland 20892, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase eta A435Homo sapiensMutation(s): 0 
Gene Names: POLHRAD30RAD30AXPV
EC: 2.7.7.7
Find proteins for Q9Y253 (Homo sapiens)
Explore Q9Y253 
Go to UniProtKB:  Q9Y253
NIH Common Fund Data Resources
PHAROS:  Q9Y253
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*A*AP*CP*(TTD)P*AP*TP*GP*AP*CP*GP*C)-3')T12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*GP*CP*GP*TP*CP*AP*TP*A)-3')P9N/A
      Small Molecules
      Ligands 7 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DZ4
      Query on DZ4

      Download Ideal Coordinates CCD File 
      A
      2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
      C10 H17 N6 O11 P3
      WKIPJDSLGCBQCU-RRKCRQDMSA-N
       Ligand Interaction
      3D1
      Query on 3D1

      Download Ideal Coordinates CCD File 
      A
      (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol
      C10 H13 N5 O3
      OLXZPDWKRNYJJZ-RRKCRQDMSA-N
       Ligand Interaction
      DTT
      Query on DTT

      Download Ideal Coordinates CCD File 
      A
      2,3-DIHYDROXY-1,4-DITHIOBUTANE
      C4 H10 O2 S2
      VHJLVAABSRFDPM-IMJSIDKUSA-N
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      A
      GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      EDO
      Query on EDO

      Download Ideal Coordinates CCD File 
      A
      1,2-ETHANEDIOL
      C2 H6 O2
      LYCAIKOWRPUZTN-UHFFFAOYSA-N
       Ligand Interaction
      CO
      Query on CO

      Download Ideal Coordinates CCD File 
      A
      COBALT (II) ION
      Co
      XLJKHNWPARRRJB-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

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      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.15 Å
      • R-Value Free: 0.258 
      • R-Value Work: 0.241 
      • R-Value Observed: 0.241 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 61.236α = 90
      b = 80.259β = 90
      c = 139.759γ = 90
      Software Package:
      Software NamePurpose
      MAR345dtbdata collection
      CNSrefinement
      HKL-2000data reduction
      SCALEPACKdata scaling
      CNSphasing

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2011-08-03
        Type: Initial release