PDBsum entry: 1oql

Hydrolase/sugar binding protein

PDB id: 1oql

Contents

Protein chains

248 a.a. *

263 a.a. *

Ligands

NAG ×2

GAL ×2

NAG-NAG ×2

Waters ×47

* Residue conservation analysis

PDB id:

1oql

Name:

Hydrolase/sugar binding protein

Title:

Mistletoe lectin i from viscum album complexed with galactos

Structure:

Mistletoe lectin i. Chain: a. Synonym: mli a-chain, n-glycosidase. Mistletoe lectin i. Chain: b. Synonym: mli b-chain, galactose-specific lectin

Source:

Viscum album. European mistletoe. Organism_taxid: 3972. Organism_taxid: 3972

Biol. unit:

Dimer (from PDB file)

Resolution:

3.00Å R-factor: 0.199 R-free: 0.240

Authors:

H.Niwa,A.G.Tonevitsky,I.I.Agapov,S.Saward,U.Pfuller,R.A.Palm

Key ref:

H.Niwa et al. (2003). Crystal structure at 3 A of mistletoe lectin I, a dimeric type-II ribosome-inactivating protein, complexed with galactose. Eur J Biochem, 270, 2739-2749. PubMed id: 12823544 DOI: 10.1046/j.1432-1033.2003.03646.x

Date:

10-Mar-03 Release date: 01-Jul-03

Protein chain

P81446  (ML1_VISAL) -  Beta-galactoside-specific lectin 1

Seq: 564 a.a.

Struc: 248 a.a.*

Protein chain

P81446  (ML1_VISAL) -  Beta-galactoside-specific lectin 1

Seq: 564 a.a.

Struc: 263 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

Enzyme reactions

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

 Gene Ontology (GO) functional annotation 

• Biological process: negative regulation of translation (1 term)
• Biochemical function: rRNA N-glycosylase activity (1 term)

DOI no: 10.1046/j.1432-1033.2003.03646.x

Eur J Biochem 270:2739-2749 (2003)

PubMed id: 12823544

Crystal structure at 3 A of mistletoe lectin I, a dimeric type-II ribosome-inactivating protein, complexed with galactose.

H.Niwa, A.G.Tonevitsky, I.I.Agapov, S.Saward, U.Pfüller, R.A.Palmer.

ABSTRACT

The X-ray structure of mistletoe lectin I (MLI), a type-II ribosome-inactivating protein (RIP), cocrystallized with galactose is described. The model was refined at 3.0 A resolution to an R-factor of 19.9% using 21 899 reflections, with Rfree 24.0%. MLI forms a homodimer (A-B)2 in the crystal, as it does in solution at high concentration. The dimer is formed through contacts between the N-terminal domains of two B-chains involving weak polar and non-polar interactions. Consequently, the overall arrangement of sugar-binding sites in MLI differs from those in monomeric type-II RIPs: two N-terminal sugar-binding sites are 15 A apart on one side of the dimer, and two C-terminal sugar-binding sites are 87 A apart on the other side. Galactose binding is achieved by common hydrogen bonds for the two binding sites via hydroxy groups 3-OH and 4-OH and hydrophobic contact by an aromatic ring. In addition, at the N-terminal site 2-OH forms hydrogen bonds with Asp27 and Lys41, and at the C-terminal site 3-OH and 6-OH undergo water-mediated interactions and C5 has a hydrophobic contact. MLI is a galactose-specific lectin and shows little affinity for N-acetylgalactosamine. The reason for this is discussed. Structural differences among the RIPs investigated in this study (their quaternary structures, location of sugar-binding sites, and fine sugar specificities of their B-chains, which could have diverged through evolution from a two-domain protein) may affect the binding sites, and consequently the cellular transport processes and biological responses of these toxins.

Selected figure(s)

Figure 1.
Fig. 1. Ribbon representation of the structure of MLI. The A-chain is located above and the B-chain is below. The disulfide bond between the two chains is shown in yellow. The glycosylating sugars included in the final structure are shown in brown. Galactose molecules are depicted in ball-and-stick. Tyr76 and Tyr115 in the active site of the A-chain, and Asp23 in the N-terminal sugar-binding site of the B-chain are shown in red.

Figure 5.
Fig. 5. Schematic drawings of the sugar-binding sites of MLB and RTB. (A) MLB N-terminal site. (B) MLB C-terminal site. (C) RTB N-terminal site. (D) RTB C-terminal site. Key residues, hydrogen bonds that are formed with bound sugar, and secondary-structure elements are shown.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2003, 270, 2739-2749) copyright 2003.

Figures were selected by an automated process.