PDBsum entry 1jva

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Hydrolase PDB id
Protein chains
427 a.a. *
Waters ×205
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the vma1-derived endonuclease bearing the n and c extein propeptides
Structure: Vma1-derived homing endonuclease x10sss. Chain: a, b. Fragment: residues 274-747. Synonym: x10sss vde. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: vma1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
2.10Å     R-factor:   0.198     R-free:   0.240
Authors: R.Mizutani,Y.Satow
Key ref:
R.Mizutani et al. (2002). Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides. J Mol Biol, 316, 919-929. PubMed id: 11884132 DOI: 10.1006/jmbi.2001.5357
29-Aug-01     Release date:   29-Aug-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P17255  (VATA_YEAST) -  V-type proton ATPase catalytic subunit A
1071 a.a.
427 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - H(+)-transporting two-sector ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + H+(In) = ADP + phosphate + H+(Out)
+ H(2)O
+ H(+)(In)
+ phosphate
+ H(+)(Out)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein splicing   2 terms 
  Biochemical function     DNA binding     2 terms  


DOI no: 10.1006/jmbi.2001.5357 J Mol Biol 316:919-929 (2002)
PubMed id: 11884132  
Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides.
R.Mizutani, S.Nogami, M.Kawasaki, Y.Ohya, Y.Anraku, Y.Satow.
Protein splicing excises an internal intein segment from a protein precursor precisely, and concomitantly ligates flanking N and C-extein polypeptides at the respective sides of the precursor. Here, a series of precursor recombinants bearing 11 N-extein and ten C-extein residues is prepared for the intein of the Saccharomyces cerevisiae VMA1-derived homing endonuclease referred to as VDE and as PI-SceI. The recombinant with replacements of C284S, H362N, N737S, and C738S is chosen as a spliceable precursor model and is then subjected to a 2.1A resolution crystallographic analysis. The crystal structure shows that the introduced extein polypeptides are located in the vicinity of the splicing site, and that each of their peptide bonds is in the trans conformation. The S284 O(gamma) atom located at a distance of 3.1A from the G283 C atom in the N-terminal junction suggests that a nucleophilic attack of the C284 S(gamma) atom on the G283 C atom forms a tetrahedral intermediate containing a five-membered thiazolidine ring. The tetrahedral intermediate is supposedly resolved into a thioester acyl group upon the cleavage of the linkage between the G283 C and C284 N atoms, and this thioester acyl formation completes the initial steps of Nright arrowS acyl shift at the junction between the N-extein and intein. The S738 O(gamma) atom in the C-terminal junction is placed in close proximity to the S284 O(gamma) atom at a distance of 3.6A, and is well suited for another nucleophilic attack on the resultant thioester acyl group that is then subjected to the transesterification in the next step. The reaction steps proposed for the acyl shift are driven entirely by protonation and deprotonation, in which proton ingress and egress is balanced within the splicing site.
  Selected figure(s)  
Figure 1.
Figure 1. A diagram for the mechanism of the protein-splicing reaction. N and C-extein polypeptides in the N and C-terminal sides of the VDE intein are indicated by the boxes and their N and C labels, respectively. In the N ! S acyl shift step, a thioester intermediate is formed at C284. This step is further examined here as shown in Figure 6. A branched intermediate is formed by the transesterification that follows a nucleophilic attack on the thioester moiety by the side-chain of the conserved C738. In the next step, the intervening region from C284 to N737 is excised by the peptide bond cleavage upon succinimide formation at the conserved N737. The transient ligation product then under- goes the final S ! N acyl rearrangement from a thioester to an amide bond.
Figure 4.
Figure 4. Structure of the X10SSS VDE protein. (a) X10SSS VDE molecules in the asymmetric unit. Molecules A and B are viewed along the non-crystallographic 2-fold axis. The C and N-extein residues are illustrated as stick models. Molecule B is highlighted by colors; red, the N-extein residues; light green, the splicing region of the domain II; green, the DNA-recognition region of domain II; blue, the domain I; yellow, the C-extein residues. This Figure was produced with the program MOLSCRIPT. 27 (b) Stereo view of the electron-density map superposed on the residues located at the splicing site of molecule B. For the calculation of this difference-Fourier map, residues 279-284 and 737- 741 were omitted from the model, and then the resultant model was further refined. The map is contoured at the 3 s level using TURBO-FRODO. 26
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 316, 919-929) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21539790 P.T.Shemella, N.I.Topilina, I.Soga, B.Pereira, G.Belfort, M.Belfort, and S.K.Nayak (2011).
Electronic structure of neighboring extein residue modulates intein C-terminal cleavage activity.
  Biophys J, 100, 2217-2225.  
19940146 K.Tori, B.Dassa, M.A.Johnson, M.W.Southworth, L.E.Brace, Y.Ishino, S.Pietrokovski, and F.B.Perler (2010).
Splicing of the mycobacteriophage Bethlehem DnaB intein: identification of a new mechanistic class of inteins that contain an obligate block F nucleophile.
  J Biol Chem, 285, 2515-2526.  
20521254 L.E.Brace, M.W.Southworth, K.Tori, M.L.Cushing, and F.Perler (2010).
The Deinococcus radiodurans Snf2 intein caught in the act: detection of the Class 3 intein signature Block F branched intermediate.
  Protein Sci, 19, 1525-1533.  
20495572 S.Frutos, M.Goger, B.Giovani, D.Cowburn, and T.W.Muir (2010).
Branched intermediate formation stimulates peptide bond cleavage in protein splicing.
  Nat Chem Biol, 6, 527-533.  
19630416 Z.Du, P.T.Shemella, Y.Liu, S.A.McCallum, B.Pereira, S.K.Nayak, G.Belfort, M.Belfort, and C.Wang (2009).
Highly conserved histidine plays a dual catalytic role in protein splicing: a pKa shift mechanism.
  J Am Chem Soc, 131, 11581-11589.  
18625708 C.Ludwig, D.Schwarzer, and H.D.Mootz (2008).
Interaction studies and alanine scanning analysis of a semi-synthetic split intein reveal thiazoline ring formation from an intermediate of the protein splicing reaction.
  J Biol Chem, 283, 25264-25272.  
17586768 M.A.Johnson, M.W.Southworth, T.Herrmann, L.Brace, F.B.Perler, and K.Wüthrich (2007).
NMR structure of a KlbA intein precursor from Methanococcus jannaschii.
  Protein Sci, 16, 1316-1328.
PDB codes: 2jmz 2jnq
17085503 P.Shemella, B.Pereira, Y.Zhang, P.Van Roey, G.Belfort, S.Garde, and S.K.Nayak (2007).
Mechanism for intein C-terminal cleavage: a proposal from quantum mechanical calculations.
  Biophys J, 92, 847-853.  
16540435 F.B.Perler (2006).
Protein splicing mechanisms and applications.
  IUBMB Life, 58, 63.  
15862101 T.C.Evans, M.Q.Xu, and S.Pradhan (2005).
Protein splicing elements and plants: from transgene containment to protein purification.
  Annu Rev Plant Biol, 56, 375-392.  
15087498 A.Romanelli, A.Shekhtman, D.Cowburn, and T.W.Muir (2004).
Semisynthesis of a segmental isotopically labeled protein splicing precursor: NMR evidence for an unusual peptide bond at the N-extein-intein junction.
  Proc Natl Acad Sci U S A, 101, 6397-6402.  
14764082 R.David, M.P.Richter, and A.G.Beck-Sickinger (2004).
Expressed protein ligation. Method and applications.
  Eur J Biochem, 271, 663-677.  
14633979 F.Schmitzberger, M.L.Kilkenny, C.M.Lobley, M.E.Webb, M.Vinkovic, D.Matak-Vinkovic, M.Witty, D.Y.Chirgadze, A.G.Smith, C.Abell, and T.L.Blundell (2003).
Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase.
  EMBO J, 22, 6193-6204.
PDB codes: 1ppy 1pqe 1pqf 1pqh 1pt0 1pt1 1pyq 1pyu
12839620 T.Fukuda, S.Nogami, and Y.Ohya (2003).
VDE-initiated intein homing in Saccharomyces cerevisiae proceeds in a meiotic recombination-like manner.
  Genes Cells, 8, 587-602.  
12878593 Y.Ding, M.Q.Xu, I.Ghosh, X.Chen, S.Ferrandon, G.Lesage, and Z.Rao (2003).
Crystal structure of a mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing.
  J Biol Chem, 278, 39133-39142.
PDB code: 1mi8
12235380 E.Werner, W.Wende, A.Pingoud, and U.Heinemann (2002).
High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI.
  Nucleic Acids Res, 30, 3962-3971.
PDB code: 1gpp
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.