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PDBsum entry 1dfa

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protein links
Hydrolase PDB id
1dfa
Jmol
Contents
Protein chain
405 a.a. *
Waters ×576
* Residue conservation analysis
PDB id:
1dfa
Name: Hydrolase
Title: Crystal structure of pi-scei in c2 space group
Structure: Pi-scei endonuclease. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.210     R-free:   0.280
Authors: D.Hu,M.Crist,X.Duan,F.A.Quiocho,F.S.Gimble
Key ref:
D.Hu et al. (2000). Probing the structure of the PI-SceI-DNA complex by affinity cleavage and affinity photocross-linking. J Biol Chem, 275, 2705-2712. PubMed id: 10644733 DOI: 10.1074/jbc.275.4.2705
Date:
18-Nov-99     Release date:   08-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P17255  (VATA_YEAST) -  V-type proton ATPase catalytic subunit A
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1071 a.a.
405 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.3.14  - H(+)-transporting two-sector ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + H+(In) = ADP + phosphate + H+(Out)
ATP
+ H(2)O
+ H(+)(In)
= ADP
+ 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  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.275.4.2705 J Biol Chem 275:2705-2712 (2000)
PubMed id: 10644733  
 
 
Probing the structure of the PI-SceI-DNA complex by affinity cleavage and affinity photocross-linking.
D.Hu, M.Crist, X.Duan, F.A.Quiocho, F.S.Gimble.
 
  ABSTRACT  
 
The PI-SceI protein is an intein-encoded homing endonuclease that initiates the mobility of its gene by making a double strand break at a single site in the yeast genome. The PI-SceI protein splicing and endonucleolytic active sites are separately located in each of two domains in the PI-SceI structure. To determine the spatial relationship between bases in the PI-SceI recognition sequence and selected PI-SceI amino acids, the PI-SceI-DNA complex was probed by photocross-linking and affinity cleavage methods. Unique solvent-accessible cysteine residues were introduced into the two PI-SceI domains at positions 91, 97, 170, 230, 376, and 378, and the mutant proteins were modified with either 4-azidophenacyl bromide or iron (S)-1-(p-bromoacetamidobenzyl)-ethylenediaminetetraacetate (FeBABE). The phenyl azide-coupled proteins cross-linked to the PI-SceI target sequence, and the FeBABE-modified proteins cleaved the DNA proximal to the derivatized amino acid. The results suggest that an extended beta-hairpin loop in the endonuclease domain that contains residues 376 and 378 contacts the major groove near the PI-SceI cleavage site. Conversely, residues 91, 97, and 170 in the protein splicing domain are in close proximity to a distant region of the substrate. To interpret our results, we used a new PI-SceI structure that is ordered in regions of the protein that bind DNA. The data strongly support a model of the PI-SceI-DNA complex derived from this structure.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Location of cysteine-substituted residues in PI-SceI. The structure of PI-SceI showing the position of the side chains of Arg-91, Lys-97, His-170, Ser-230, Lys-376, and Lys-378 that have been individually mutated to cysteine and conjugated to FeBABE and/or phenyl azide moieties.
Figure 6.
Fig. 6. Affinity photocross-linking of the top and bottom strands of the 219-bp fragment containing a single PI-SceI recognition site by phenyl azide-conjugated PI-SceI proteins. The DNA strand that is end-labeled with 32P is indicated at the top of each set of lanes. The locations of photocross-linking products generated by azidophenacyl-PI-SceI ( 5Cys) are indicated by open arrows, and those produced by azidophenacyl-PI-SceI[97], azidophenacyl-PI-SceI[170], and azidophenacyl-PI-SceI[376] are indicated by solid arrows. The location of the PI-SceI cleavage site and the extent of the PI-SceI recognition sequence are indicated as in Fig. 5.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 2705-2712) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21525927 K.Yamada, T.D.Frouws, B.Angst, D.J.Fitzgerald, C.DeLuca, K.Schimmele, D.F.Sargent, and T.J.Richmond (2011).
Structure and mechanism of the chromatin remodelling factor ISW1a.
  Nature, 472, 448-453.
PDB codes: 2y9y 2y9z
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
16100733 S.Bräse, C.Gil, K.Knepper, and V.Zimmermann (2005).
Organic azides: an exploding diversity of a unique class of compounds.
  Angew Chem Int Ed Engl, 44, 5188-5240.  
15020462 A.Bakhrat, M.S.Jurica, B.L.Stoddard, and D.Raveh (2004).
Homology modeling and mutational analysis of Ho endonuclease of yeast.
  Genetics, 166, 721-728.  
14764082 R.David, M.P.Richter, and A.G.Beck-Sickinger (2004).
Expressed protein ligation. Method and applications.
  Eur J Biochem, 271, 663-677.  
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.  
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.  
12219083 C.M.Moure, F.S.Gimble, and F.A.Quiocho (2002).
Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence.
  Nat Struct Biol, 9, 764-770.
PDB codes: 1lws 1lwt
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
12142479 J.P.Gogarten, A.G.Senejani, O.Zhaxybayeva, L.Olendzenski, and E.Hilario (2002).
Inteins: structure, function, and evolution.
  Annu Rev Microbiol, 56, 263-287.  
11841209 K.L.Posey, and F.S.Gimble (2002).
Insertion of a reversible redox switch into a rare-cutting DNA endonuclease.
  Biochemistry, 41, 2184-2190.  
12112231 S.Nogami, T.Fukuda, Y.Nagai, S.Yabe, M.Sugiura, R.Mizutani, Y.Satow, Y.Anraku, and Y.Ohya (2002).
Homing at an extragenic locus mediated by VDE (PI-SceI) in Saccharomyces cerevisiae.
  Yeast, 19, 773-782.  
11557808 B.S.Chevalier, and B.L.Stoddard (2001).
Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility.
  Nucleic Acids Res, 29, 3757-3774.  
11600710 F.S.Gimble (2001).
Degeneration of a homing endonuclease and its target sequence in a wild yeast strain.
  Nucleic Acids Res, 29, 4215-4223.  
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.