5SWM | pdb_00005swm

BACILLUS HALODURANS RNASE H MUTANT D132N IN COMPLEX WITH 12-MER FRNA/DNA HYBRID

• PDB DOI: https://doi.org/10.2210/pdb5SWM/pdb
• NAKB: 5SWM

• Classification: HYDROLASE/RNA/DNA
• Organism(s): Halalkalibacterium halodurans, synthetic construct
• Expression System: Halalkalibacterium halodurans
• Mutation(s): Yes 


• Deposited: 2016-08-08 Released: 2016-09-21 
• Deposition Author(s): Pallan, P.S., Egli, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.185 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Limits of RNA 2'-OH Mimicry by Fluorine: Crystal Structure of Bacillus halodurans RNase H Bound to a 2'-FRNA:DNA Hybrid.

Pallan, P.S., Prakash, T.P., de Leon, A.R., Egli, M.

(2016) Biochemistry 55: 5321-5325

• PubMed: 27611889 
• DOI: https://doi.org/10.1021/acs.biochem.6b00849
• Primary Citation Related Structures: 
  5SWM


• PubMed Abstract: 
  

  RNase H1 cleaves the RNA strand of RNA:DNA hybrids. Replacement of RNA 2'-hydroxyls by fluorine (FRNA) is commonly used to stabilize aptamers and siRNAs. However, FRNA:DNA hybrids fail to elicit RNase H activity. The underlying reasons are unclear, as 2'-OH groups are not directly involved in cleavage. We determined the crystal structure of Bacillus halodurans RNase H bound to a FRNA:DNA hybrid. The structure points to dynamic (slippage of the FRNA:DNA hybrid relative to the enzyme), geometric (different curvatures of FRNA:DNA and RNA:DNA hybrids), and electronic reasons (Mg(2+) absent from the active site of the FRNA:DNA complex) for the loss of RNaseH activity.

---

Organizational Affiliation: 
• Department of Biochemistry, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States.
Department of Medicinal Chemistry, Ionis Pharmaceuticals Inc. , Carlsbad, California 92010, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.48 kDa 
• Atom Count: 3,908 
• Modeled Residue Count: 288 
• Deposited Residue Count: 308 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease H	A, B	142	Halalkalibacterium halodurans	Mutation(s): 1  Gene Names: rnhA 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 ID: 2
Molecule	Chains	Length	Organism	Image
RNA (12-MER)	C	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (12-MER)	D	12	synthetic construct

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	H [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.185 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.474	α = 84.42
b = 44.5	β = 89.9
c = 62.174	γ = 65.1

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Pallan, P.S., Egli, M.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM055237

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2016-10-12
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description