1PC8

Crystal Structure of a novel form of mistletoe lectin from Himalayan Viscum album L. at 3.8A resolution

Summary for 1PC8

• Entry DOI: 10.2210/pdb1pc8/pdb
• Related: 1MQC
• Descriptor: Himalayan mistletoe ribosome-inactivating protein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (6 entities in total)
• Functional Keywords: novel form, mistletoe lectin, hydrolase
• Biological source: Viscum album (European mistletoe); More
• Total number of polymer chains: 2
• Total formula weight: 55857.11

Authors

Mishra, V.,Ethayathulla, A.S.,Paramasivam, M.,Singh, G.,Yadav, S.,Kaur, P.,Sharma, R.S.,Babu, C.R.,Singh, T.P. (deposition date: 2003-05-16, release date: 2004-06-22, Last modification date: 2024-10-30)

Primary citation

Mishra, V.,Ethayathulla, A.S.,Sharma, R.S.,Yadav, S.,Krauspenhaar, R.,Betzel, C.,Babu, C.R.,Singh, T.P.
Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern Himalayas.
Acta Crystallogr.,Sect.D, 60:2295-2304, 2004

PubMed 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.

PubMed: 15583377
DOI: 10.1107/S0907444904023534

Experimental method

X-RAY DIFFRACTION (3.8 Å)