PDBsum entry: 1puu

Sugar binding protein

PDB id: 1puu

Contents

Protein chains

249 a.a. *

263 a.a. *

Ligands

NAG ×2

SO4 ×3

DIO

GOL ×16

FUL-NAG-NAG

NAG-NAG

LAT ×2

Metals

_CL ×3

Waters ×328

* Residue conservation analysis

PDB id:

1puu

Name:

Sugar binding protein

Title:

Mistletoe lectin i in complex with lactose

Structure:

Lectin i a chain. Chain: a. Lectin i b chain. Chain: b

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.207 R-free: 0.232

Authors:

R.Krauspenhaar,W.Voelter,S.Stoeva,A.Mikhailov,N.Konareva,C.B

Key ref:

R.Mikeska et al. (2005). Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties. Acta Crystallograph Sect F Struct Biol Cryst Commun, 61, 17-25. PubMed id: 16508080 DOI: 10.1107/S1744309104031501

Date:

25-Jun-03 Release date: 25-Jun-04

Protein chain

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

Seq: 564 a.a.

Struc: 249 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 41 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: 10.1107/S1744309104031501

Acta Crystallograph Sect F Struct Biol Cryst Commun 61:17-25 (2005)

PubMed id: 16508080

Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties.

R.Mikeska, R.Wacker, R.Arni, T.P.Singh, A.Mikhailov, A.Gabdoulkhakov, W.Voelter, C.Betzel.

ABSTRACT

The structures of mistletoe lectin I (ML-I) from Viscum album complexed with lactose and galactose have been determined at 2.3 A resolution and refined to R factors of 20.9% (Rfree = 23.6%) and 20.9 (Rfree = 24.6%), respectively. ML-I is a heterodimer and belongs to the class of ribosome-inactivating proteins of type II, which consist of two chains. The A-chain has rRNA N-glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B-chain is a lectin and preferentially binds to galactose-terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains alpha1 and gamma2 of the ML-I B-chain separated by approximately 62 A from each other. The favoured binding of galactose in subdomain alpha1 is achieved via hydrogen bonds connecting the 4-hydroxyl and 3-hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar-lectin complex. In the galactose-binding site II of subdomain gamma2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen-bonding partners for galactose. In the case of the galactose-binding site I, the 2-hydroxyl group also stabilizes the sugar-protein complex, an interaction thus far rarely detected in galactose-specific lectins. Finally, a potential third low-affinity galactose-binding site in subunit beta1 was identified in the present ML-I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound.

Selected figure(s)

Figure 6.
Figure 6 (a) Stereo representation of the superposition of the galactose-binding site I of ML-I in red and ebulin in blue as a ball-and-stick model. The galactose molecule is coloured red-orange in ML-I and blue in ebulin. Accordingly, hydrogen bonds are shown as red dashed lines for the ML-I and in blue for the ebulin complex. Water molecules in the ML-I complex are marked as red circles. (b) Superposition of the galactose-binding site II of ML-I in red and of ebulin in blue; stereoview in ball-and-stick mode. The galactose molecule is coloured red-orange in ML-I and in blue in ebulin. Accordingly, the hydrogen bonds are shown as red dashed lines for the ML-I and in blue for the ebulin complex. Water molecules in the ML-I complex are indicated as red circles.

Figure 7.
Figure 7 (a) Stereo representation of the superposition of the galactose-binding site I of ML-I in red and of ricin in blue as a ball-and-stick model. The bound lactose molecule is coloured red-orange in ML-I and blue in ricin. Hydrogen bonds are shown as red dashed lines for ML-I and in blue for ricin. Water molecules are marked as red circles in the ML-I complex and in blue in the ricin complex. (b) Superposition of galactose-binding site II of ML-I and ricin. The colour code is similar to (a).

The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallograph Sect F Struct Biol Cryst Commun (2005, 61, 17-25) copyright 2005.

Figures were selected by an automated process.