PDBsum entry 1vde

Endonuclease

PDB id: 1vde

Contents

Protein chains

429 a.a. *

Waters ×347

* Residue conservation analysis

PDB id:

1vde

Name:

Endonuclease

Title:

Pi-scei, a homing endonuclease with protein splicing activity

Structure:

Pi-scei. Chain: a, b. 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:

2.40Å R-factor: 0.192 R-free: 0.238

Authors:

X.Duan,F.A.Quiocho

Key ref:

X.Duan et al. (1997). Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity. Cell, 89, 555-564. PubMed id: 9160747 DOI: 10.1016/S0092-8674(00)80237-8

Date:

01-Apr-97 Release date: 08-Apr-98

Protein chains

P17255  (VATA_YEAST) -  V-type proton ATPase catalytic subunit A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1071 a.a.

Struc: 429 a.a.

Enzyme reactions

• Enzyme class 2: E.C.3.1.-.-
• Enzyme class 3: E.C.7.1.2.2 - H(+)-transporting two-sector ATPase.
• Reaction: 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: 10.1016/S0092-8674(00)80237-8

Cell 89:555-564 (1997)

PubMed id: 9160747

Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity.

X.Duan, F.S.Gimble, F.A.Quiocho.

ABSTRACT

PI-Scel is a bifunctional yeast protein that propagates its mobile gene by catalyzing protein splicing and site-specific DNA double-strand cleavage. Here, we report the 2.4 A crystal structure of the PI-Scel protein. The structure is composed of two separate domains (I and II) with novel folds and different functions. Domain I, which is elongated and formed largely from seven beta sheets, harbors the N and C termini residues and two His residues that are implicated in protein splicing. Domain II, which is compact and is primarily composed of two similar alpha/beta motifs related by local two-fold symmetry, contains the putative nuclease active site with a cluster of two acidic residues and one basic residue commonly found in restriction endonucleases. This report presents prototypic structures of domains with single endonuclease and protein splicing active sites.

Selected figure(s)

Figure 1.
Figure 1. Stereo View of the Final 2.4 Å 2Fo−Fc Electron Density Map in the Region of the Putative Nuclease Active Site Containing Asp-218, Asp-326, and Lys-301The map was contoured at 1σ.

Figure 4.
Figure 4. Stereo Views of the Functional Sites in PI-SceI(A) The protein self-splicing site containing the essential N-terminal Cys-1 and C-terminal Asn-454 residues viewed from the back of domain I, as shown in Figure 2. His-79 and His-453, positioned proximal to the terminal residues, are extremely conserved between self-splicing proteins and could perform as general acids/bases in the autocatalytic splicing reaction. Three of the β strands that are identified are further linked to subsequent strands in the site shown (e.g., β3 to β6, β7 to β8, and β24 to β28).(B) The endonuclease active site containing the charged cluster of three residues (see text). The orientations of the two symmetry-related α4 and α7 dodecapeptide repeats are similar to those shown in Figure 2.

The above figures are reprinted by permission from Cell Press: Cell (1997, 89, 555-564) copyright 1997.

Figures were selected by an automated process.