1UM2

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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This is version 1.5 of the entry. See complete history. 


Literature

Protein splicing of yeast VMA1-derived endonuclease via thiazolidine intermediates.

Mizutani, R., Anraku, Y., Satow, Y.

(2004) J Synchrotron Radiat 11: 109-112

  • DOI: 10.1107/s0909049503023495
  • Primary Citation of Related Structures:  
    1UM2

  • 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 ...

    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.

    Related Citations: 
    • Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides
      Mizutani, R., Nogami, S., Kawasaki, M., Ohya, Y., Anraku, Y., Satow, Y.
      (2002) J Mol Biol 316: 919
    Organizational Affiliation: 

    Graduate School of Pharmaceutical Sciences, University of Tokyo, Hongo, Tokyo 113-0033, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDONUCLEASE PI-SCEIA, B454Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: VMA1
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17255 
Go to UniProtKB:  P17255
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17255
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
21-mer from Vacuolar ATP synthase catalytic subunit AC, D21Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: VMA1
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17255 
Go to UniProtKB:  P17255
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17255
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.4α = 100.4
b = 70.4β = 98.7
c = 58γ = 78.9
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.5: 2021-11-10
    Changes: Database references