6OE7

Crystal structure of HMCES cross-linked to DNA abasic site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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This is version 1.3 of the entry. See complete history


Literature

Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.

Halabelian, L.Ravichandran, M.Li, Y.Zeng, H.Rao, A.Aravind, L.Arrowsmith, C.H.

(2019) Nat Struct Mol Biol 26: 607-612

  • DOI: 10.1038/s41594-019-0246-6
  • Primary Citation of Related Structures:  
    5KO9, 6OE7, 6OEA, 6OEB

  • PubMed Abstract: 
  • Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein (HMCES) can covalently cross-link to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the human HMCES SOS response-associated peptidase (SRAP) domain in complex with DNA-damage substrates, including HMCES cross-linked with an abasic site within a 3' overhang DNA ...

    Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein (HMCES) can covalently cross-link to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the human HMCES SOS response-associated peptidase (SRAP) domain in complex with DNA-damage substrates, including HMCES cross-linked with an abasic site within a 3' overhang DNA. HMCES interacts with both single-strand and duplex segments of DNA, with two independent duplex DNA interaction sites identified in the SRAP domain. The HMCES DNA-protein cross-link structure provides structural insights into a novel thiazolidine covalent interaction between the DNA abasic site and conserved Cys 2 of HMCES. Collectively, our structures demonstrate the capacity for the SRAP domain to interact with a variety of single-strand- and double-strand-containing DNA structures found in DNA-damage sites, including 5' and 3' overhang DNAs and gapped DNAs with short single-strand segments.


    Organizational Affiliation

    Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. cheryl.arrowsmith@uhnresearch.ca.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Embryonic stem cell-specific 5-hydroxymethylcytosine-binding proteinA276Homo sapiensMutation(s): 0 
Gene Names: HMCESC3orf37DC12SRAPD1
EC: 3.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96FZ2 (Homo sapiens)
Explore Q96FZ2 
Go to UniProtKB:  Q96FZ2
PHAROS:  Q96FZ2
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')B [auth C]6synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*(DRZ)P*GP*TP*T)-3')C [auth B]12synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.509α = 90
b = 51.534β = 92.72
c = 149.72γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection, Database references