2.0 Angstrom crystal structure of a DnaB intein from Synechocystis sp. PCC 6803

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.226 

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Crystal structure of mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing

Ding, Y.Xu, M.Q.Ghosh, I.Chen, X.Ferrandon, S.Lesage, G.Rao, Z.

(2003) J Biol Chem 278: 39133-39142

  • DOI: https://doi.org/10.1074/jbc.M306197200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We have determined the crystal structure of a 154-residue intein derived from the dnaB gene of Synechocystis sp. strain PCC6803 and refined it to a 2.0-A resolution. The x-ray structure suggests that this intein possesses two catalytic sites that appear to be separately responsible for splicing and cleavage of the N- and C-terminal scissile bonds. The conserved intein block F residues are the important components of a catalytic site for side chain cyclization of the last intein residue, Asn-154. The data suggest that the imidazole ring of His-143 is involved in the activation of the side chain Ndelta atom of Asn-154, leading to a nucleophilic attack on the carbonyl carbon of Asn-154. Substitution of His-143 with Ala or Gln resulted in the inhibition of C-terminal cleavage. His-153, Asp-136, and a water molecule appear to constitute an oxyanion binding site by contacting the carbonyl oxygen of Asn-154 to stabilize the transition state. The structure and mutagenesis data also support that the close contact between the hydroxyl groups of Thr-138 and Ser-155, whose side chain participates in an S --> O acyl shift, plays an important role in the nucleophile orientation. Our structural modeling suggests that this catalytic module is conserved in the C-terminal subdomains of inteins from diverse organisms.

  • Organizational Affiliation

    Laboratory of Structural Biology and the Ministry of Education Laboratory of Protein Science, School of Life Science and Engineering, Tsinghua University, Beijing 100084, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DnaB intein158Synechocystis sp. PCC 6803Mutation(s): 4 
EC: 3.6.1
Find proteins for Q55418 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore Q55418 
Go to UniProtKB:  Q55418
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ55418
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.226 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.17α = 90
b = 58.17β = 90
c = 70.28γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-19
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2021-11-10
    Changes: Database references
  • Version 1.5: 2024-05-29
    Changes: Data collection