5ZMN

Sulfur binding domain and SRA domain of ScoMcrA complexed with phosphorothioated DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the recognition of sulfur in phosphorothioated DNA.

Liu, G.Fu, W.Zhang, Z.He, Y.Yu, H.Wang, Y.Wang, X.Zhao, Y.Deng, Z.Wu, G.He, X.

(2018) Nat Commun 9: 4689-4689

  • DOI: 10.1038/s41467-018-07093-1
  • Primary Citation of Related Structures:  
    5ZMM, 5ZMO, 5ZMN

  • PubMed Abstract: 
  • There have been very few reports on protein domains that specifically recognize sulfur. Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. SBD cont ...

    There have been very few reports on protein domains that specifically recognize sulfur. Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. SBD contains a hydrophobic surface cavity that is formed by the aromatic ring of Y164, the pyrolidine ring of P165, and the non-polar side chains of four other residues that serve as lid, base, and wall of the cavity. The SBD and PT-DNA undergo conformational changes upon binding. The S 187 RGRR 191 loop inserts into the DNA major groove to make contacts with the bases of the G PS GCC core sequence. Mutating key residues of SBD impairs PT-DNA association. More than 1000 sequenced microbial species from fourteen phyla contain SBD homologs. We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. These results show that SBD-like PT-DNA readers exist widely in prokaryotes.


    Organizational Affiliation

    State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, The Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, 200240, Shanghai, China. xyhe@sjtu.edu.cn.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein McrAA354Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: SCO4631
Find proteins for Q9L0M9 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9L0M9 
Go to UniProtKB:  Q9L0M9
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*CP*GP*(GS)P*CP*CP*GP*GP*G)-3')B, C10Streptomyces lividans
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SO4
    Query on SO4

    Download CCD File 
    A
    SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.29 Å
    • R-Value Free: 0.288 
    • R-Value Work: 0.251 
    • R-Value Observed: 0.253 
    • Space Group: I 41 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 122.34α = 90
    b = 122.34β = 90
    c = 313.691γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data scaling
    REFMACrefinement
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Science Foundation (China)China31670034
    National Science Foundation (China)China31470223
    National Science Foundation (China)China31670106
    National Science Foundation (China)China31130068

    Revision History 

    • Version 1.0: 2018-09-26
      Type: Initial release
    • Version 1.1: 2018-11-28
      Changes: Data collection, Database references