4LX3

Conserved Residues that Modulate Protein trans-Splicing of Npu DnaE Split Intein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.167 

wwPDB Validation 3D Report Full Report



Literature

Conserved Residues that Modulate Protein trans-Splicing of Npu DnaE Split Intein

Wu, Q.Gao, Z.Wei, Y.Ma, G.Zheng, Y.Dong, Y.Liu, Y.

(2014) Biochem J 

  • DOI: 10.1042/BJ20140287
  • Primary Citation of Related Structures:  
    4LX3

  • PubMed Abstract: 
  • The first crystal trans-structure of a naturally occurring split intein has been determined for the Npu (Nostoc punctiforme PCC73102) DnaE split intein. Guided by this structure, the residues NArg50 and CSer35, well conserved in DnaE split inteins, a ...

    The first crystal trans-structure of a naturally occurring split intein has been determined for the Npu (Nostoc punctiforme PCC73102) DnaE split intein. Guided by this structure, the residues NArg50 and CSer35, well conserved in DnaE split inteins, are identified to be critical in the trans-splicing of Npu DnaE split intein. An in vitro splicing assay demonstrates that NArg50 and CSer35 play synergistic roles in modulating its intein activity. The C-terminal CAsn36 exhibits two orientations of its side chain and interacts with both NArg50 and CSer35 through hydrogen bonding. These interactions likely facilitate the cyclization of asparagine in the course of protein splicing. The mutation of either residue reduces intein activity, and correlates with the low activity of the Ssp (Cyanobacterium synechocystis sp. strain PCC6803) DnaE split intein. On the other hand, NArg50 also forms a hydrogen bond with the highly conserved F-block CAsp17, thus influencing the N-S acyl shift during N-terminal cleavage. Sequence alignments show that residues NArg50 and CSer35 are rather conserved in those split inteins that lack a penultimate histidine residue. The conserved non-catalytic residues of split inteins modulate the efficiency of protein trans-splicing by hydrogen-bond interactions with the catalytic residues at the splice junction.


    Organizational Affiliation

    *CAS Key Laboratory of Soft Matter Chemistry, CAS High Magnetic Field Laboratory, Department of Chemistry, University of Science and Technology of China, 230026 Hefei, Anhui, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III, alpha subunitA108Nostoc punctiforme PCC 73102Mutation(s): 0 
Gene Names: Npun_F4872
EC: 2.7.7.7
Find proteins for B2J066 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102))
Explore B2J066 
Go to UniProtKB:  B2J066
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleic acid binding, OB-fold, tRNA/helicase-typeB36Nostoc punctiforme PCC 73102Mutation(s): 0 
Gene Names: Npun_F5684
EC: 2.7.7.7
Find proteins for B2J821 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102))
Explore B2J821 
Go to UniProtKB:  B2J821
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.167 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.029α = 90
b = 61.199β = 90
c = 103.997γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release