4XZF

Crystal structure of HIRAN domain of human HLTF in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a Novel DNA-binding Domain of Helicase-like Transcription Factor (HLTF) and Its Functional Implication in DNA Damage Tolerance

Hishiki, A.Hara, K.Ikegaya, Y.Yokoyama, H.Shimizu, T.Sato, M.Hashimoto, H.

(2015) J Biol Chem 290: 13215-13223

  • DOI: 10.1074/jbc.M115.643643
  • Primary Citation of Related Structures:  
    4XZF, 4XZG

  • PubMed Abstract: 
  • HLTF (helicase-like transcription factor) is a yeast RAD5 homolog found in mammals. HLTF has E3 ubiquitin ligase and DNA helicase activities, and plays a pivotal role in the template-switching pathway of DNA damage tolerance. HLTF has an N-terminal domain that has been designated the HIRAN (HIP116 and RAD5 N-terminal) domain ...

    HLTF (helicase-like transcription factor) is a yeast RAD5 homolog found in mammals. HLTF has E3 ubiquitin ligase and DNA helicase activities, and plays a pivotal role in the template-switching pathway of DNA damage tolerance. HLTF has an N-terminal domain that has been designated the HIRAN (HIP116 and RAD5 N-terminal) domain. The HIRAN domain has been hypothesized to play a role in DNA binding; however, the structural basis of, and functional evidence for, the HIRAN domain in DNA binding has remained unclear. Here we show for the first time the crystal structure of the HIRAN domain of human HLTF in complex with DNA. The HIRAN domain is composed of six β-strands and two α-helices, forming an OB-fold structure frequently found in ssDNA-binding proteins, including in replication factor A (RPA). Interestingly, this study reveals that the HIRAN domain interacts with not only with a single-stranded DNA but also with a duplex DNA. Furthermore, the structure unexpectedly clarifies that the HIRAN domain specifically recognizes the 3'-end of DNA. These results suggest that the HIRAN domain functions as a sensor to the 3'-end of the primer strand at the stalled replication fork and that the domain facilitates fork regression. HLTF is recruited to a damaged site through the HIRAN domain at the stalled replication fork. Furthermore, our results have implications for the mechanism of template switching.


    Organizational Affiliation

    From the School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan, the Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan hash@u-shizuoka-ken.ac.jp.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Helicase-like transcription factorB [auth A]122Homo sapiensMutation(s): 0 
Gene Names: HLTFHIP116ARNF80SMARCA3SNF2L3ZBU1
EC: 3.6.4 (PDB Primary Data), 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14527 (Homo sapiens)
Explore Q14527 
Go to UniProtKB:  Q14527
PHAROS:  Q14527
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    (DA)(DC)(DC)(DG)(DC)(DC)(DG)(DG)(DG)(DT)(DG)(DC)(DC)A [auth B]13synthetic construct
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.38 Å
    • R-Value Free: 0.207 
    • R-Value Work: 0.165 
    • R-Value Observed: 0.167 
    • Space Group: P 21 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 147.399α = 90
    b = 33.418β = 90
    c = 36.797γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    HKL-2000data reduction
    SCALEPACKdata scaling
    SOLVEphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2015-04-15
      Type: Initial release
    • Version 1.1: 2015-04-22
      Changes: Database references
    • Version 1.2: 2015-06-03
      Changes: Database references
    • Version 1.3: 2020-02-05
      Changes: Data collection, Database references, Derived calculations, Source and taxonomy