Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21364.07 
• Atom Count: 1374 
• Residue Count: 199 
• Unique protein chains: 1

1AM2

GYRA INTEIN FROM MYCOBACTERIUM XENOPI

• DOI: 10.2210/pdb1AM2/pdb

• Classification: INTEIN
• Organism(s): Mycobacterium xenopi
• Expression System: Escherichia coli


• Deposited: 1997-06-20 Released: 1998-06-24 
• Deposition Author(s): Klabunde, T., Sharma, S., Sacchettini, J.C.

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Experimental Data Snapshot

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

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: 9437427 


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
MXE GYRA INTEIN	A	199	Mycobacterium xenopi	Mutation(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 = 55.700	α = 90.00
b = 55.700	β = 90.00
c = 133.110	γ = 120.00

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	refinement
X-PLOR	model building
X-PLOR	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-06-20 
• Released Date: 1998-06-24 
• Deposition Author(s): Klabunde, T., Sharma, S., Sacchettini, J.C.

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