4OZ6

Structure of the Branched Intermediate in Protein Splicing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.786 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the branched intermediate in protein splicing.

Liu, Z.Frutos, S.Bick, M.J.Vila-Perello, M.Debelouchina, G.T.Darst, S.A.Muir, T.W.

(2014) Proc.Natl.Acad.Sci.USA 111: 8422-8427

  • DOI: 10.1073/pnas.1402942111

  • PubMed Abstract: 
  • Inteins are autoprocessing domains that cut themselves out of host proteins in a traceless manner. This process, known as protein splicing, involves multiple chemical steps that must be coordinated to ensure fidelity in the process. The committed ste ...

    Inteins are autoprocessing domains that cut themselves out of host proteins in a traceless manner. This process, known as protein splicing, involves multiple chemical steps that must be coordinated to ensure fidelity in the process. The committed step in splicing involves attack of a conserved Asn side-chain amide on the adjacent backbone amide, leading to an intein-succinimide product and scission of that peptide bond. This cleavage reaction is stimulated by formation of a branched intermediate in the splicing process. The mechanism by which the Asn side-chain becomes activated as a nucleophile is not understood. Here we solve the crystal structure of an intein trapped in the branched intermediate step in protein splicing. Guided by this structure, we use protein-engineering approaches to show that intein-succinimide formation is critically dependent on a backbone-to-side-chain hydrogen-bond. We propose that this interaction serves to both position the side-chain amide for attack and to activate its nitrogen as a nucleophile. Collectively, these data provide an unprecedented view of an intein poised to carry out the rate-limiting step in protein splicing, shedding light on how a nominally nonnucleophilic group, a primary amide, can become activated in a protein active site.


    Organizational Affiliation

    Frick Laboratory, Department of Chemistry, Princeton University, Princeton, NJ 08544; and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mxe gyrA intein
A
202Mycobacterium xenopiMutation(s): 4 
Gene Names: gyrA
EC: 5.99.1.3
Find proteins for P72065 (Mycobacterium xenopi)
Go to UniProtKB:  P72065
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALA-MET-ARG-TYR
B
4Mycobacterium xenopiMutation(s): 0 
Gene Names: gyrA
EC: 5.99.1.3
Find proteins for P72065 (Mycobacterium xenopi)
Go to UniProtKB:  P72065
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TIH
Query on TIH
A
L-PEPTIDE LINKINGC7 H9 N O2 SALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.786 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.230 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.746α = 90.00
b = 58.746β = 90.00
c = 111.762γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM086868
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41 GM103403
Department of Energy (United States)United StatesDE-AC02-06CH11357

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-07-16
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary