X-ray sequence and crystal structure of luffaculin I, a novel type I ribosome-inactivating protein

	X-ray sequence and crystal structure of luffaculin I, a novel type I ribosome-inactivating protein
	X. M. Hou ; M. H. Chen ; L. Q. Chen ; E. J. Meehan ; J. M. Xie ; M. D. Huang
刊名	Bmc Structural Biology
	2007-04
卷号	7
关键词	3-dimensional structure molecular replacement swiss-model active-site angstrom saporin ricin seeds nmr
ISSN号	1471-2237
中文摘要	Background: Protein sequence can be obtained through Edman degradation, mass spectrometry, or cDNA sequencing. High resolution X-ray crystallography can also be used to derive protein sequence information, but faces the difficulty in distinguishing the Asp/Asn, Glu/Gln, and Val/Thr pairs. Luffaculin I is a new type I ribosome-inactivating protein (RIP) isolated from the seeds of Luffa acutangula. Besides rRNA N-glycosidase activity, luffaculini I also demonstrates activities including inhibiting tumor cells' proliferation and inducing tumor cells' differentiation. Results: The crystal structure of luffaculin I was determined at 1.4 A resolution. Its amino-acid sequence was derived from this high resolution structure using the following criteria: 1) high resolution electron density; 2) comparison of electron density between two molecules that exist in the same crystal; 3) evaluation of the chemical environment of residues to break down the sequence assignment ambiguity in residue pairs Glu/Gln, Asp/Asn, and Val/Thr; 4) comparison with sequences of the homologous proteins. Using the criteria 1 and 2, 66% of the residues can be assigned. By incorporating with criterion 3, 86% of the residues were assigned, suggesting the effectiveness of chemical environment evaluation in breaking down residue ambiguity. In total, 94% of the luffaculin I sequence was assigned with high confidence using this improved X-ray sequencing strategy. Two N-acetylglucosamine moieties, linked respectively to the residues Asn77 and Asn84, can be identified in the structure. Residues Tyr70, Tyr110, Glu159 and Arg162 define the active site of luffaculin I as an RNA N-glycosidase. Conclusion: X-ray sequencing method can be effective to derive sequence information of proteins. The evaluation of the chemical environment of residues is a useful method to break down the assignment ambiguity in Glu/Gln, Asp/Asn, and Val/Thr pairs. The sequence and the crystal structure confirm that luffaculin I is a new type I RIP.
语种	英语
公开日期	2013-04-01
内容类型	期刊论文
源URL	[http://ir.fjirsm.ac.cn/handle/350002/6285]
专题	福建物质结构研究所_中科院福建物质结构研究所_期刊论文
推荐引用方式 GB/T 7714	X. M. Hou,M. H. Chen,L. Q. Chen,et al. X-ray sequence and crystal structure of luffaculin I, a novel type I ribosome-inactivating protein[J]. Bmc Structural Biology,2007,7.
APA	X. M. Hou,M. H. Chen,L. Q. Chen,E. J. Meehan,J. M. Xie,&M. D. Huang.(2007).X-ray sequence and crystal structure of luffaculin I, a novel type I ribosome-inactivating protein.Bmc Structural Biology,7.
MLA	X. M. Hou,et al."X-ray sequence and crystal structure of luffaculin I, a novel type I ribosome-inactivating protein".Bmc Structural Biology 7(2007).