PDBsum entry: 1um2

Hydrolase

PDB id: 1um2

Contents

Protein chains

417 a.a. *

Ligands

TYR-VAL-GLY-SER-GLY-GLU-ARG ×2

Waters ×153

* Residue conservation analysis

PDB id:

1um2

Name:

Hydrolase

Title:

Crystal structure of the vma1-derived endonuclease with the ligated extein segment

Structure:

Endonuclease pi-scei. Chain: a, b. Synonym: vma1-derived endonuclease x10sns. Engineered: yes. Mutation: yes. 21-mer from vacuolar atp synthase catalytic subunit a. Chain: c, d. Synonym: 21-mer from vma1-derived endonuclease x10sns.

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)

Resolution:

2.90Å R-factor: 0.214 R-free: 0.283

Authors:

R.Mizutani,Y.Anraku,Y.Satow

Key ref:

R.Mizutani et al. (2004). Protein splicing of yeast VMA1-derived endonuclease via thiazolidine intermediates. J Synchrotron Radiat, 11, 109-112. PubMed id: 14646148 DOI: 10.1107/S0909049503023495

Date:

22-Sep-03 Release date: 22-Sep-04

Protein chains

P17255  (VATA_YEAST) -  V-type proton ATPase catalytic subunit A

Seq: 1071 a.a.

Struc: 417 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.6.3.14 - H(+)-transporting two-sector ATPase.
• Reaction: ATP + H₂O + H⁺(In) = ADP + phosphate + H⁺(Out)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: intein-mediated protein splicing (1 term)
• Biochemical function: endonuclease activity (1 term)

reference

DOI no: 10.1107/S0909049503023495

J Synchrotron Radiat 11:109-112 (2004)

PubMed id: 14646148

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

R.Mizutani, Y.Anraku, Y.Satow.

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. 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.