Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.44 kDa 
• Atom Count: 877 
• Modelled Residue Count: 104 
• Deposited Residue Count: 104 
• Unique protein chains: 1

1LOV

X-ray structure of the E58A mutant of Ribonuclease T1 complexed with 3'-guanosine monophosphate

• PDB DOI: 10.2210/pdb1LOV/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus oryzae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-05-07 Released: 2002-08-21 
• Deposition Author(s): Mignon, P., Steyaert, J., Loris, R., Geerlings, P., Loverix, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.199 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Literature

A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study

Mignon, P., Steyaert, J., Loris, R., Geerlings, P., Loverix, S.

(2002) J Biol Chem 277: 36770-36774

• PubMed: 12122018 
• DOI: 10.1074/jbc.M206461200
• Primary Citation of Related Structures:  
  1LOV, 1LOW, 1LOY


• PubMed Abstract: 
  

Ribonucleases (RNases) catalyze the cleavage of the phosphodiester bond in RNA up to 10(15)-fold, as compared with the uncatalyzed reaction. High resolution crystal structures of these enzymes in complex with 3'-mononucleotide substrates demonstrate the accommodation of the nucleophilic 2'-OH group in a binding pocket comprising the catalytic base (glutamate or histidine) and a charged hydrogen bond donor (lysine or histidine). Ab initio quantum chemical calculations performed on such Michaelis complexes of the mammalian RNase A (EC ) and the microbial RNase T(1) (EC ) show negative charge build up on the 2'-oxygen upon substrate binding. The increased nucleophilicity results from stronger hydrogen bonding to the catalytic base, which is mediated by a hydrogen bond from the charged donor. This hitherto unrecognized catalytic dyad in ribonucleases constitutes a general mechanism for nucleophile activation in both enzymic and RNA-catalyzed phosphoryl transfer reactions.

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Organizational Affiliation: 

Eenheid Algemene Chemie (ALGC), Faculteit Wetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanyl-specific ribonuclease T1	A	104	Aspergillus oryzae	Mutation(s): 1  EC: 3.1.27.3 (PDB Primary Data), 4.6.1.24 (UniProt)
UniProt
Find proteins for P00651 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore P00651  Go to UniProtKB:  P00651

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3GP	C [auth A]	GUANOSINE-3'-MONOPHOSPHATE C10 H14 N5 O8 P ZDPUTNZENXVHJC-UUOKFMHZSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.199 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.631	α = 90
b = 48.126	β = 90
c = 53.172	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-05-07 
• Released Date: 2002-08-21 
Deposition Author(s): Mignon, P., Steyaert, J., Loris, R., Geerlings, P., Loverix, S.

Revision History  

• Version 1.0: 2002-08-21
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations