1UM2

Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment

Summary for 1UM2

• Entry DOI: 10.2210/pdb1um2/pdb
• Related: 1JVA
• Descriptor: ENDONUCLEASE PI-SCEI, 21-mer from Vacuolar ATP synthase catalytic subunit A (3 entities in total)
• Functional Keywords: protein splicing, vma1-derived endonuclease, vde, intein, extein, thiazolidine, hydrolase
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 4
• Total formula weight: 106390.38

Authors

Mizutani, R.,Anraku, Y.,Satow, Y. (deposition date: 2003-09-22, release date: 2004-09-22, Last modification date: 2023-10-25)

Primary citation

Mizutani, R.,Anraku, Y.,Satow, Y.
Protein splicing of yeast VMA1-derived endonuclease via thiazolidine intermediates.
J.Synchrotron Radiat., 11:109-112, 2004

PubMed Abstract: Protein splicing precisely excises out an internal intein segment from a protein precursor, and concomitantly ligates the N- and C-terminal extein polypeptides flanking the intein. A recombinant X10SNS bearing N- and C-extein polypeptides has been prepared for the intein endonuclease derived from the Saccharomyces cerevisiae VMA1 gene. X10SNS has replacements of C284S, H362N and C738S, and forms the intein and extein segments in the crystal lattice. The crystal structure of X10SNS revealed a linkage between the N- and C-extein segments, and showed that the C284 amino group of the resultant intein segment is in interaction with the G283 O atom of the N-extein segment. A mechanism for the final S --> N acyl shift step proposes that a tetrahedral intermediate involves a five-membered thiazolidine ring at G283-C738 junction. An oxyanion of the thiazolidine intermediate is to be stabilized by the C284 N atom.

PubMed: 14646148
DOI: 10.1107/s0909049503023495

Experimental method

X-RAY DIFFRACTION (2.9 Å)