3W5W | pdb_00003w5w

Mn2+-GMP complex of nanoRNase (Nrn) from Bacteroides fragilis

• PDB DOI: https://doi.org/10.2210/pdb3W5W/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides fragilis YCH46
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-07 Released: 2013-07-10 
• Deposition Author(s): Uemura, Y., Nakagawa, N., Wakamatsu, T., Montelione, G.T., Hunt, J.F., Masui, R., Kuramitsu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.270 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Crystal structure of the ligand-binding form of nanoRNase from Bacteroides fragilis, a member of the DHH/DHHA1 phosphoesterase family of proteins.

Uemura, Y., Nakagawa, N., Wakamatsu, T., Kim, K., Montelione, G.T., Hunt, J.F., Kuramitsu, S., Masui, R.

(2013) FEBS Lett 587: 2669-2674

• PubMed: 23851074 
• DOI: https://doi.org/10.1016/j.febslet.2013.06.053
• Primary Citation of Related Structures:  
  3W5W


• PubMed Abstract: 
  

  NanoRNase (Nrn) specifically degrades nucleoside 3',5'-bisphosphate and the very short RNA, nanoRNA, during the final step of mRNA degradation. The crystal structure of Nrn in complex with a reaction product GMP was determined. The overall structure consists of two domains that are interconnected by a flexible loop and form a cleft. Two Mn²⁺ ions are coordinated by conserved residues in the DHH motif of the N-terminal domain. GMP binds near the DHHA1 motif region in the C-terminal domain. Our structure enables us to predict the substrate-bound form of Nrn as well as other DHH/DHHA1 phosphoesterase family proteins.

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Organizational Affiliation: 

Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.75 kDa 
• Atom Count: 2,794 
• Modelled Residue Count: 340 
• Deposited Residue Count: 351 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative exopolyphosphatase-related protein	A	351	Bacteroides fragilis YCH46	Mutation(s): 0  Gene Names: BF3900
UniProt
Find proteins for Q64PD9 (Bacteroides fragilis (strain YCH46)) Explore Q64PD9  Go to UniProtKB:  Q64PD9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	B [auth A]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N
MN	C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.270 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.210 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.828	α = 90
b = 90.828	β = 90
c = 107.878	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-10 
Deposition Author(s): Uemura, Y., Nakagawa, N., Wakamatsu, T., Montelione, G.T., Hunt, J.F., Masui, R., Kuramitsu, S.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Refinement description