PDBsum entry 1lov

Hydrolase

PDB id: 1lov

Contents

Protein chain

104 a.a. *

Ligands

3GP

Metals

_CA

Waters ×75

* Residue conservation analysis

PDB id:

1lov

Name:

Hydrolase

Title:

X-ray structure of the e58a mutant of ribonuclease t1 complexed with 3'-guanosine monophosphate

Structure:

Guanyl-specific ribonuclease t1. Chain: a. Synonym: rnase t1. Engineered: yes. Mutation: yes

Source:

Aspergillus oryzae. Organism_taxid: 5062. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.55Å R-factor: 0.187 R-free: 0.199

Authors:

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

Key ref:

P.Mignon et al. (2002). A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study. J Biol Chem, 277, 36770-36774. PubMed id: 12122018 DOI: 10.1074/jbc.M206461200

Date:

07-May-02 Release date: 21-Aug-02

Protein chain

P00651  (RNT1_ASPOR) -  Guanyl-specific ribonuclease T1 from Aspergillus oryzae (strain ATCC 42149 / RIB 40)

Seq: 130 a.a.

Struc: 104 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.6.1.24 - ribonuclease T1.
• Reaction: [RNA] containing guanosine + H2O = an [RNA fragment]-3'-guanosine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]

DOI no: 10.1074/jbc.M206461200

J Biol Chem 277:36770-36774 (2002)

PubMed id: 12122018

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

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

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.

Selected figure(s)

Figure 1.
Fig. 1. Classical acid/base mechanism for RNase-catalyzed phosphoryl transfer reactions. AH and B represent the catalytic acid and base respectively; bent arrows represent the movement of electrons.

Figure 3.
Fig. 3. Correlation between the Mulliken charge on the nucleophilic oxygen atom and the experimentally observed second order rate constant (36) for the attack of phenolate, p-cyanophenolate, p-chlorophenolate and p-ethoxycarboxyphenolate on methyl 2,4-dinitrophenyl phosphate (n = 4, R2 = 0.9844).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 36770-36774) copyright 2002.

Figures were selected by an automated process.