PDBsum entry: 1pc8

Hydrolase

PDB id: 1pc8

Contents

Protein chains

240 a.a. *

255 a.a. *

Ligands

NAG

NDG-NAG

NAG-NAG-BMA

NAG-NAG

Waters ×13

* Residue conservation analysis

PDB id:

1pc8

Name:

Hydrolase

Title:

Crystal structure of a novel form of mistletoe lectin from h viscum album l. At 3.8a resolution

Structure:

Himalayan mistletoe ribosome-inactivating protein chain: a. Synonym: mistletoe lectin. Himalayan mistletoe ribosome-inactivating protein chain: b. Synonym: mistletoe lectin. Ec: 3.2.2.22

Source:

Viscum album. European mistletoe. Organism_taxid: 3972. Strain: himalayan v.Album. Strain: himalayan v.Album

Biol. unit:

Dimer (from PQS)

Resolution:

3.80Å R-factor: 0.231 R-free: 0.271

Authors:

V.Mishra,A.S.Ethayathulla,M.Paramasivam,G.Singh,S.Yadav,P.Ka R.S.Sharma,C.R.Babu,T.P.Singh

Key ref:

V.Mishra et al. (2004). Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern Himalayas. Acta Crystallogr D Biol Crystallogr, 60, 2295-2304. PubMed id: 15583377 DOI: 10.1107/S0907444904023534

Date:

16-May-03 Release date: 22-Jun-04

Protein chain

Q6ITZ3  (ML4_VISAL) -  Beta-galactoside-specific lectin 4

Seq: 520 a.a.

Struc: 240 a.a.

Protein chain

Q6ITZ3  (ML4_VISAL) -  Beta-galactoside-specific lectin 4

Seq: 520 a.a.

Struc: 255 a.a.

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/S0907444904023534

Acta Crystallogr D Biol Crystallogr 60:2295-2304 (2004)

PubMed id: 15583377

Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern Himalayas.

V.Mishra, A.S.Ethayathulla, R.S.Sharma, S.Yadav, R.Krauspenhaar, C.Betzel, C.R.Babu, T.P.Singh.

ABSTRACT

This is the first report of the structural studies of a novel ribosome-inactivating protein (RIP) obtained from the Himalayan mistletoe (Viscum album) (HmRip). HmRip is a type II heterodimeric protein consisting of a toxic enzyme (A-chain) with an active site for ribosome inactivation and a lectin subunit (B-chain) with well defined sugar-binding sites. The crystal structure of HmRip has been determined at 3.8 A resolution and refined to a crystallographic R factor of 0.228 (R(free) = 0.271). A comparison of this structure with other type II RIPs reveals the presence of distinct structural features in the active site of the A-chain and in the 2gamma sugar-binding site of the B-chain. The conformation of the side chain of Tyr110, which is a conserved active-site residue in the A subunit, is strikingly different from those observed in other mistletoe RIPs, indicating its unique substrate-binding preference. The deletion of two important residues from the kink region after Ala231 in the 2gamma subdomain of the B-chain results in a significantly different conformation of the sugar-binding pocket. A ribosome-recognition site has also been identified in HmRip. The site is a shallow cavity, with the conserved residues Arg51, Asp70, Thr72 and Asn73 involved in the binding. The conformations of the antigenic epitopes of residues 1-20, 85-103 and 206-223 differ from those observed in other type II RIPs, resulting in the distinct antigenicity and pharmacological properties of HmRip.

Selected figure(s)

Figure 5.
Figure 5 Overall fold of the B-chain (yellow) showing the location of the 2 [gamma] sugar-binding site (red) in the B2 domain and the 1 [alpha] sugar-binding site (blue) in the B1 domain. The sugar-binding residues are also shown as a ball-and-stick model. The figure was drawn with MOLSCRIPT (Merritt & Murphy, 1994 [Merritt, E. A. & Murphy, M. E. P. (1994). Acta Cryst. D50, 869-873.]-[bluearr.gif] ) and RASTER3D (Kraulis, 1991 [Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]-[bluearr.gif] ).

Figure 8.
Figure 8 The ribosome-recognition site has its roof represented by the highly antigenic peptide (red). The ribosome-binding residues are shown as a ball-and-stick model. (b) GRASP (Nicholls et al., 1991 [Nicholls, A., Sharp, K. & Honig, B. (1991). Proteins, 11, 281-296.]-[bluearr.gif] ) figure showing a shallow cavity representing the ribosome-recognition site and a well defined cleft corresponding to the N-glycosidase activity site, connected by a shallow channel. The ribosome-binding residues are shown in cyan and key active-site residues are shown in yellow. (c) Superposition of the C^ [alpha] traces of HmRip (yellow), ML-I (pink) and ricin (blue), showing the highly variable nature of the antigenic peptide that results in different architectures of the ribosome-recognition sites.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 2295-2304) copyright 2004.

Figures were selected by an automated process.