2oqa
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:2oqa.jpg|left|200px]] | + | [[Image:2oqa.jpg|left|200px]] |
| - | + | ||
| - | '''X-ray Sequence and Crystal Structure of Luffaculin 1, a Novel Type 1 Ribosome-inactivating Protein''' | + | {{Structure |
| + | |PDB= 2oqa |SIZE=350|CAPTION= <scene name='initialview01'>2oqa</scene>, resolution 1.40Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene> and <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''X-ray Sequence and Crystal Structure of Luffaculin 1, a Novel Type 1 Ribosome-inactivating Protein''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 2OQA is a [ | + | 2OQA is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Luffa_acutangula Luffa acutangula]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OQA OCA]. |
==Reference== | ==Reference== | ||
| - | 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:[http:// | + | 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:[http://www.ncbi.nlm.nih.gov/pubmed/17470286 17470286] |
[[Category: Luffa acutangula]] | [[Category: Luffa acutangula]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| Line 20: | Line 29: | ||
[[Category: mixed alpha helix and beta sheet]] | [[Category: mixed alpha helix and beta sheet]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:03:06 2008'' |
Revision as of 16:03, 20 March 2008
| |||||||
| , resolution 1.40Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , and | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
X-ray Sequence and Crystal Structure of Luffaculin 1, a Novel Type 1 Ribosome-inactivating Protein
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.
About this Structure
2OQA is a Protein complex structure of sequences from Luffa acutangula. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Thu Mar 20 18:03:06 2008
