6DMV

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Soaked for 40 s in 2 mM Mg2+ and 200 mM K+ at 21 C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cation trafficking propels RNA hydrolysis.

Samara, N.L.Yang, W.

(2018) Nat Struct Mol Biol 25: 715-721

  • DOI: 10.1038/s41594-018-0099-4
  • Primary Citation of Related Structures:  
    6DMN, 6DMV, 6DO8, 6DO9, 6DOA, 6DOB, 6DOC, 6DOD, 6DOE, 6DOF, 6DOG, 6DOH, 6DOI, 6DOJ, 6DOK, 6DOL, 6DOM, 6DON, 6DOO, 6DOP, 6DOQ, 6DOR, 6DOS, 6DOT, 6DOU, 6DOV, 6DOW, 6DOX, 6DOY, 6DOZ, 6DP0, 6DP1, 6DP2, 6DP3, 6DP4, 6DP5, 6DP6, 6DP7, 6DP8, 6DP9, 6DPA, 6DPB, 6DPC, 6DPD, 6DPE, 6DPF, 6DPG, 6DPH, 6DPI, 6DPJ

  • PubMed Abstract: 
  • Catalysis by members of the RNase H superfamily of enzymes is generally believed to require only two Mg 2+ ions that are coordinated by active-site carboxylates. By examining the catalytic process of Bacillus halodurans RNase H1 in crystallo, however, we found that the two canonical Mg 2+ ions and an additional K + failed to align the nucleophilic water for RNA cleavage ...

    Catalysis by members of the RNase H superfamily of enzymes is generally believed to require only two Mg 2+ ions that are coordinated by active-site carboxylates. By examining the catalytic process of Bacillus halodurans RNase H1 in crystallo, however, we found that the two canonical Mg 2+ ions and an additional K + failed to align the nucleophilic water for RNA cleavage. Substrate alignment and product formation required a second K + and a third Mg 2+ , which replaced the first K + and departed immediately after cleavage. A third transient Mg 2+ has also been observed for DNA synthesis, but in that case it coordinates the leaving group instead of the nucleophile as in the case of the RNase H1 hydrolysis reaction. These transient cations have no contact with the enzymes. Other DNA and RNA enzymes that catalyze consecutive cleavage and strand-transfer reactions in a single active site may similarly require cation trafficking coordinated by the substrate.


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), US National Institutes of Health (NIH), Bethesda, MD, USA. wei.yang@nih.gov.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease HA142Alkalihalobacillus halodurans C-125Mutation(s): 0 
Gene Names: rnhABH0863
EC: 3.1.26.4
UniProt
Find proteins for Q9KEI9 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Explore Q9KEI9 
Go to UniProtKB:  Q9KEI9
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*AP*CP*AP*U)-3')B4Alkalihalobacillus halodurans
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(P*CP*G)-3')C [auth b]2Alkalihalobacillus halodurans
      Protein Feature View
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      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')D [auth C]6Alkalihalobacillus halodurans
        Protein Feature View
        Expand
        • Reference Sequence
        Small Molecules
        Ligands 5 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        IOD
        Query on IOD

        Download Ideal Coordinates CCD File 
        H [auth A], I [auth A], J [auth A], K [auth A]IODIDE ION
        I
        XMBWDFGMSWQBCA-UHFFFAOYSA-M
         Ligand Interaction
        GOL
        Query on GOL

        Download Ideal Coordinates CCD File 
        L [auth A], M [auth A], P [auth A], Q [auth A]GLYCEROL
        C3 H8 O3
        PEDCQBHIVMGVHV-UHFFFAOYSA-N
         Ligand Interaction
        EDO
        Query on EDO

        Download Ideal Coordinates CCD File 
        N [auth A], O [auth A]1,2-ETHANEDIOL
        C2 H6 O2
        LYCAIKOWRPUZTN-UHFFFAOYSA-N
         Ligand Interaction
        K (Subject of Investigation/LOI)
        Query on K

        Download Ideal Coordinates CCD File 
        G [auth A], R [auth C]POTASSIUM ION
        K
        NPYPAHLBTDXSSS-UHFFFAOYSA-N
         Ligand Interaction
        MG (Subject of Investigation/LOI)
        Query on MG

        Download Ideal Coordinates CCD File 
        E [auth A], F [auth A]MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 1.52 Å
        • R-Value Free: 0.182 
        • R-Value Work: 0.161 
        • R-Value Observed: 0.162 
        • Space Group: C 1 2 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 81.422α = 90
        b = 37.803β = 96.31
        c = 61.986γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement
        Aimlessdata scaling
        PDB_EXTRACTdata extraction
        HKL-2000data reduction
        MOLREPphasing

        Structure Validation

        View Full Validation Report




        Entry History 

        Deposition Data

        • Deposited Date: 2018-06-05 
        • Released Date: 2018-08-15 
        • Deposition Author(s): Samara, N.L., Yang, W.
        • This entry supersedes: 6DMN

        Revision History  (Full details and data files)

        • Version 1.0: 2018-08-15
          Type: Initial release
        • Version 1.1: 2019-12-18
          Changes: Database references, Derived calculations