2oqa: Difference between revisions

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X-ray Sequence and Crystal Structure of Luffaculin 1, a Novel Type 1 Ribosome-inactivating Protein

OverviewOverview

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 1 is a new type 1 ribosome-inactivating protein (RIP) isolated from the seeds of Luffa acutangula. Besides rRNA N-glycosidase activity, luffaculin 1 also demonstrates activities including inhibiting tumor cells' proliferation and inducing tumor cells' differentiation. RESULTS: The crystal structure of luffaculin 1 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 1 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 1 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 1 is a new type 1 RIP.

About this StructureAbout this Structure

2OQA is a Protein complex structure of sequences from Luffa acutangula with , and as ligands. Full crystallographic information is available from OCA.

ReferenceReference

X-ray sequence and crystal structure of luffaculin 1, a novel type 1 ribosome-inactivating protein., Hou X, Chen M, Chen L, Meehan EJ, Xie J, Huang M, BMC Struct Biol. 2007 Apr 30;7:29. PMID:17470286

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 ==Overview==
-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 1 is a new type 1 ribosome-inactivating protein, (RIP) isolated from the seeds of Luffa acutangula. Besides rRNA, N-glycosidase activity, luffaculin 1 also demonstrates activities, including inhibiting tumor cells' proliferation and inducing tumor cells', differentiation. RESULTS: The crystal structure of luffaculin 1 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 1 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 1 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 1 is, a new type 1 RIP.
+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 1 is a new type 1 ribosome-inactivating protein (RIP) isolated from the seeds of Luffa acutangula. Besides rRNA N-glycosidase activity, luffaculin 1 also demonstrates activities including inhibiting tumor cells' proliferation and inducing tumor cells' differentiation. RESULTS: The crystal structure of luffaculin 1 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 1 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 1 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 1 is a new type 1 RIP.
 ==About this Structure==
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 [[Category: mixed alpha helix and beta sheet]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:07:09 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:21:25 2008''