8QND | pdb_00008qnd

Crystal structure of the ribonucleoside hydrolase C from Lactobacillus reuteri

• PDB DOI: https://doi.org/10.2210/pdb8QND/pdb

• Classification: HYDROLASE
• Organism(s): Limosilactobacillus reuteri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-09-26 Released: 2023-12-20 
• Deposition Author(s): Matyuta, I.O., Minyaev, M.E., Shaposhnikov, L.A., Pometun, A.A., Tishkov, V.I., Popov, V.O., Boyko, K.M.
• Funding Organization(s): Russian Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.201 (Depositor) 
• R-Value Work: 
  0.168 (Depositor) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Structure-Functional Examination of Novel Ribonucleoside Hydrolase C (RihC) from Limosilactobacillus reuteri LR1.

Shaposhnikov, L.A., Chikurova, N.Y., Atroshenko, D.L., Savin, S.S., Kleymenov, S.Y., Chernobrovkina, A.V., Pometun, E.V., Minyaev, M.E., Matyuta, I.O., Hushpulian, D.M., Boyko, K.M., Tishkov, V.I., Pometun, A.A.

(2023) Int J Mol Sci 25

• PubMed: 38203708 
• DOI: https://doi.org/10.3390/ijms25010538
• Primary Citation Related Structures: 
  8QND


• PubMed Abstract: 
  

  Ribonucleoside hydrolase C (RihC, EC 3.2.2.1, 3.2.2.2, 3.2.2.3, 3.2.2.7, 3.2.2.8) belongs to the family of ribonucleoside hydrolases Rih and catalyzes the cleavage of ribonucleosides to nitrogenous bases and ribose. RihC is one of the enzymes that are synthesized by lactobacilli in response to the presence of Klebsiella . To characterize this protein from Limosilactobacillus reuteri LR1, we cloned and expressed it. The activity of the enzyme was studied towards a wide range of substrates, including ribonucleosides, deoxyribonucleosides as well as an arabinoside. It was shown that the enzyme is active only with ribonucleosides and arabinoside, with the best substrate being uridine. The thermal stability of this enzyme was studied, and its crystal structure was obtained, which demonstrated the tetrameric architecture of the enzyme and allowed to shed light on a correlation between its structure and enzymatic activity. Comprehensive comparisons of all known RihC structures, both existing crystal structures and computed model structures from various species, were made, allowing for the identification of structural motifs important for enzyme functioning.

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Organizational Affiliation: 
• Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Avenue, 33/2, Moscow 119071, Russia.
Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, 1-3, Moscow 119991, Russia.
Institute of Medicine, Peoples' Friendship University of Russia Named after Patrice Lumumba, Miklouho-Maklaya, 8, Moscow 117198, Russia.
Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Vavilova, 26, Moscow 119334, Russia.
Department of Analytical, Physical and Colloidal Chemistry, A.P. Nelyubin Institute of Pharmacy, Sechenov First Moscow State Medical University, Trubetskaya St., 8, Building 2, Moscow 119048, Russia.
N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky Avenue, 47, Moscow 119991, Russia.
Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Profsoyuznaya St., 33, Building 4, Moscow 117418, Russia.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 133.92 kDa 
• Atom Count: 9,654 
• Modeled Residue Count: 1,184 
• Deposited Residue Count: 1,232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-uridine nucleoside N-ribohydrolase	A, B, C, D	308	Limosilactobacillus reuteri	Mutation(s): 0  Gene Names: rihC EC: 3.2.2
UniProt
Find proteins for A5JJT3 (Limosilactobacillus reuteri) Explore A5JJT3  Go to UniProtKB:  A5JJT3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.201 (Depositor) 
• R-Value Work:  0.168 (Depositor) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.112	α = 90
b = 81.53	β = 95.76
c = 86.847	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Matyuta, I.O., Minyaev, M.E., Shaposhnikov, L.A., Pometun, A.A., Tishkov, V.I., Popov, V.O., Boyko, K.M.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	23-64-10029

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Database references
• Version 1.3: 2024-10-16
  Changes: Structure summary