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PDBsum entry 1gpp
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protein links
Endonuclease PDB id
1gpp

 

 

 

 

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Contents
Protein chain
217 a.a. *
Waters ×303
* Residue conservation analysis
PDB id:
1gpp
Name: Endonuclease
Title: Crystal structure of the s.Cerevisiae homing endonuclease pi-scei domain i
Structure: Endonuclease pi-scei. Chain: a. Fragment: protein splicing domain, residues 284-466,693-736, see remark 999. Synonym: homing endonuclease pi-scei, vma1-derived endonuclease. Engineered: yes. Mutation: yes. Other_details: gly183 links ile182 and ala410, where in the full length protein is domain ii
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.35Å     R-factor:   0.153     R-free:   0.189
Authors: E.Werner,W.Wende,A.Pingoud,U.Heinemann
Key ref: E.Werner et al. (2002). High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI. Nucleic Acids Res, 30, 3962-3971. PubMed id: 12235380 DOI: 10.1093/nar/gkf523
Date:
07-Nov-01     Release date:   19-Sep-02    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P17255  (VATA_YEAST) -  V-type proton ATPase catalytic subunit A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1071 a.a.
217 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 48 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: E.C.3.1.-.-
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 3: E.C.7.1.2.2  - H(+)-transporting two-sector ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + 4 H+(in) = ADP + phosphate + 5 H+(out)
ATP
 + H2O
 + 4 × H(+)(in)
 = ADP
 + phosphate
 + 5 × H(+)(out)
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1093/nar/gkf523 Nucleic Acids Res 30:3962-3971 (2002)
PubMed id: 12235380  
 
 
High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI.
E.Werner, W.Wende, A.Pingoud, U.Heinemann.
 
  ABSTRACT  
 
The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is involved in binding and recognition of the specific DNA substrate. Domain II of PI-SceI, the endonuclease domain, which is structurally homologous to other homing endonucleases from the LAGLIDADG family, harbors the endonucleolytic center of PI-SceI, which in vivo initiates the homing process by introducing a double-strand cut in the approximately 35 bp recognition sequence. At 1.35 A resolution, the crystal structure of PI-SceI domain I provides a detailed view of the part of the protein that is responsible for tight and specific DNA binding. A geometry-based docking of the 75 degrees bent recognition sequence to the full-length protein implies a conformational change or hinge movement of a subdomain of domain I, the tongs part, that is predicted to reach into the major groove near base pairs +16 to +18.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17452357 J.Prieto, P.Redondo, D.Padró, S.Arnould, J.C.Epinat, F.Pâques, F.J.Blanco, and G.Montoya (2007).
The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage.
  Nucleic Acids Res, 35, 3262-3271.
PDB code: 2o7m
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
  18084082 P.Redondo, J.Prieto, E.Ramos, F.J.Blanco, and G.Montoya (2007).
Crystallization and preliminary X-ray diffraction analysis on the homing endonuclease I-Dmo-I in complex with its target DNA.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1017-1020.  
17254599 P.Van Roey, B.Pereira, Z.Li, K.Hiraga, M.Belfort, and V.Derbyshire (2007).
Crystallographic and mutational studies of Mycobacterium tuberculosis recA mini-inteins suggest a pivotal role for a highly conserved aspartate residue.
  J Mol Biol, 367, 162-173.
PDB codes: 2imz 2in0 2in8 2in9
16830226 J.Yang, T.V.Henry-Smith, and M.Qi (2006).
Functional analysis of the split Synechocystis DnaE intein in plant tissues by biolistic particle bombardment.
  Transgenic Res, 15, 583-593.  
16544141 S.Elleuche, N.Nolting, and S.Pöggeler (2006).
Protein splicing of PRP8 mini-inteins from species of the genus Penicillium.
  Appl Microbiol Biotechnol, 72, 959-967.  
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.  
14745027 G.Butler, C.Kenny, A.Fagan, C.Kurischko, C.Gaillardin, and K.H.Wolfe (2004).
Evolution of the MAT locus and its Ho endonuclease in yeast species.
  Proc Natl Acad Sci U S A, 101, 1632-1637.  
12771221 J.C.Epinat, S.Arnould, P.Chames, P.Rochaix, D.Desfontaines, C.Puzin, A.Patin, A.Zanghellini, F.Pâques, and E.Lacroix (2003).
A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells.
  Nucleic Acids Res, 31, 2952-2962.  
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 code is shown on the right.

 

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