6DPB

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 8 mM Mn2+ and 200 mM K+ for 40 s at 21 C

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.0 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: https://doi.org/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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease H136Halalkalibacterium halodurans C-125Mutation(s): 0 
Gene Names: rnhA, BH0863
EC: 3.1.26.4
UniProt
Find proteins for Q9KEI9 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Explore Q9KEI9 
Go to UniProtKB:  Q9KEI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KEI9
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*AP*CP*AP*U)-3') portion of cleaved RNA4synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*CP*G)-3') portion of cleaved RNAC [auth b]2synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')D [auth C]6synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD
Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A]		IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
GOL
Query on GOL
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M [auth A],
N [auth A],
O [auth A],
R [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
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P [auth A],
Q [auth A],
S [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MN (Subject of Investigation/LOI)
Query on MN
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E [auth A],
F [auth A],
G [auth A],
U [auth b]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
K (Subject of Investigation/LOI)
Query on K
Download Ideal Coordinates CCD File 
H [auth A],
T [auth A],
V [auth C]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.546α = 90
b = 37.318β = 96.85
c = 62.154γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release