1AM2

GYRA INTEIN FROM MYCOBACTERIUM XENOPI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of GyrA intein from Mycobacterium xenopi reveals structural basis of protein splicing.

Klabunde, T.Sharma, S.Telenti, A.Jacobs Jr., W.R.Sacchettini, J.C.

(1998) Nat.Struct.Mol.Biol. 5: 31-36


  • PubMed Abstract: 
  • Several genes from prokaryotes and lower eukaryotes have been found to contain an in-frame open reading frame, which encodes for an internal protein (intein). Post-translationally, the internal polypeptide auto-splices and ligates the external sequen ...

    Several genes from prokaryotes and lower eukaryotes have been found to contain an in-frame open reading frame, which encodes for an internal protein (intein). Post-translationally, the internal polypeptide auto-splices and ligates the external sequences to yield a functional external protein (extein) and an intein. Most, but not all inteins, contain, apart from a splicing domain, a separate endonucleolytic domain that enables them to maintain their presence by a homing mechanism. We report here the crystal structure of an intein found in the gyrase A subunit from Mycobacterium xenopi at 2.2 A resolution. The structure contains an unusual beta-fold with the catalytic splice junctions at the ends of two adjacent antiparallel beta-strands. The arrangement of the active site residues Ser 1, Thr 72, His 75, His 197, and Asn 198 is consistent with a four-step mechanism for the cleavage-ligation reaction. Using site-directed mutagenesis, the N-terminal cysteine, proposed as the nucleophile in the first step of the splicing reaction, was changed to a Ser 1 and Ala 0, thus capturing the intein in a pre-spliced state.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station 77843-2128, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MXE GYRA INTEIN
A
199Mycobacterium xenopiMutation(s): 0 
Gene Names: gyrA
EC: 5.99.1.3
Find proteins for P72065 (Mycobacterium xenopi)
Go to UniProtKB:  P72065
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.187 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.700α = 90.00
b = 55.700β = 90.00
c = 133.110γ = 120.00
Software Package:
Software NamePurpose
PHASESphasing
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-24
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance