PDBsum entry 1ahb

Glycosidase

PDB id: 1ahb

Contents

Protein chain

246 a.a. *

Ligands

FMP

Waters ×80

* Residue conservation analysis

PDB id:

1ahb

Name:

Glycosidase

Title:

The n-glycosidase mechanism of ribosome-inactivating proteins implied by crystal structures of alpha-momorcharin

Structure:

Alpha-momorcharin. Chain: a. Engineered: yes

Source:

Momordica charantia. Balsam pear. Organism_taxid: 3673

Resolution:

2.20Å R-factor: 0.175

Authors:

J.Ren,Y.Wang,Y.Dong,D.I.Stuart

Key ref:

J.Ren et al. (1994). The N-glycosidase mechanism of ribosome-inactivating proteins implied by crystal structures of alpha-momorcharin. Structure, 2, 7. PubMed id: 8075985 DOI: 10.1016/S0969-2126(00)00004-6

Date:

07-Jan-94 Release date: 22-Jun-94

Protein chain

P16094  (RIP1_MOMCH) -  Ribosome-inactivating protein momordin I from Momordica charantia

Seq: 286 a.a.

Struc: 246 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.2.22 - rRNA N-glycosylase.
• Reaction: Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.

DOI no: 10.1016/S0969-2126(00)00004-6

Structure 2:7 (1994)

PubMed id: 8075985

The N-glycosidase mechanism of ribosome-inactivating proteins implied by crystal structures of alpha-momorcharin.

J.Ren, Y.Wang, Y.Dong, D.I.Stuart.

ABSTRACT

BACKGROUND: alpha-Momorcharin (alpha MMC) is a type I ribosome-inactivating protein. It inhibits protein synthesis by hydrolytically removing a specific adenine residue from a highly conserved, single-stranded loop of rRNA. RESULTS: Here we describe the determination and refinement of the crystal structures of alpha MMC in the native state and in complexes with the product, adenine, and a substrate analogue, formycin 5'-monophosphate (FMP) at high resolution. Both adenine and the base of FMP are tightly bound; the ribose of bound FMP adopts a strained, high-energy conformation, which may mimic the structure of the transition state. CONCLUSIONS: These structures indicate that residues Tyr70, Glu160 and Arg163 of alpha MMC are the most critical for catalysis. We propose that the strained conformation of the ribose in the target adenosine weakens the glycoside bond. Partial protonation mediated by Arg163 then facilitates N-glycoside bond cleavage, leading to the formation of an oxycarbonium ion intermediate which is stabilized by the negatively-charged Glu160. Tyr70 adopts subtly different conformations in the three structures implying that it may be important in substrate recognition and perhaps catalysis.

Selected figure(s)

Figure 3.
Figure 3. Schematic ribbon representation of the αMMC molecule as viewed towards the active site cleft. The bound FMP molecule is shown in a stick representation. The secondary structural elements are: α[1], 11– 23; α[2], 86–91; α[3], 111–118; α[4], 129–139; α[5], 144–163; α[6], 165–173; α[7], 183–191; α[8], 192–202; α[9], 231–234; β[1], 3–5; β[2], 27–31; β[3], 34–37; β[4], 47–53; β[5], 59–65; β[6], 70–76; β[7], 79–82; β[8], 101–104; β[9], 208–215; β[10], 223–227. Figure 3. Schematic ribbon representation of the αMMC molecule as viewed towards the active site cleft. The bound FMP molecule is shown in a stick representation. The secondary structural elements are: α[1], 11– 23; α[2], 86–91; α[3], 111–118; α[4], 129–139; α[5], 144–163; α[6], 165–173; α[7], 183–191; α[8], 192–202; α[9], 231–234; β[1], 3–5; β[2], 27–31; β[3], 34–37; β[4], 47–53; β[5], 59–65; β[6], 70–76; β[7], 79–82; β[8], 101–104; β[9], 208–215; β[10], 223–227.

Figure 5.
Figure 5. A schematic diagram showing the mechanism of N-glycoside bond hydrolysis catalyzed by αMMC. Hydrogen bonding at N3 and N1 by Arg163 and Ile71, respectively, facilitates the cleavage of the glycoside bond (N9–C1′ ) and leads to the formation of a transition state with oxycarbonium ion development on the ribose. The oxycarbonium ion is then stabilized by the negative charge of Glu160. The adenine ring rotates by about 15° to the position found in the adenine-bound structures to give enough space for the OH^−of the nucleophile to bond to C1′. Meanwhile, movement and conformational change of the ribose may occur because of the release of the straining force after the N9–C1′ bond is broken. A water molecule, OH0 or OH2, attacks the oxycarbonium ion at C1′ and the proton is transferred to N9. Figure 5. A schematic diagram showing the mechanism of N-glycoside bond hydrolysis catalyzed by αMMC. Hydrogen bonding at N3 and N1 by Arg163 and Ile71, respectively, facilitates the cleavage of the glycoside bond (N9–C1′ ) and leads to the formation of a transition state with oxycarbonium ion development on the ribose. The oxycarbonium ion is then stabilized by the negative charge of Glu160. The adenine ring rotates by about 15° to the position found in the adenine-bound structures to give enough space for the OH^−of the nucleophile to bond to C1′. Meanwhile, movement and conformational change of the ribose may occur because of the release of the straining force after the N9–C1′ bond is broken. A water molecule, OH0 or OH2, attacks the oxycarbonium ion at C1′ and the proton is transferred to N9.

The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 7-0) copyright 1994.

Figures were selected by an automated process.