1TN5

Structure of bacterorhodopsin mutant K41P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Proline substitutions are not easily accommodated in a membrane protein

Yohannan, S.Yang, D.Faham, S.Boulting, G.Whitelegge, J.Bowie, J.U.

(2004) J.Mol.Biol. 341: 1-6

  • DOI: 10.1016/j.jmb.2004.06.025
  • Primary Citation of Related Structures:  1TN0

  • PubMed Abstract: 
  • Proline residues are relatively common in transmembrane helices. This suggests that proline substitutions may be readily tolerated in membrane proteins, even though they invariably produce deviations from canonical helical structure. We have experime ...

    Proline residues are relatively common in transmembrane helices. This suggests that proline substitutions may be readily tolerated in membrane proteins, even though they invariably produce deviations from canonical helical structure. We have experimentally tested this possibility by making proline substitutions at 15 positions throughout the N-terminal half of bacteriorhodopsin helix B. We find that six of the substitutions yielded no active protein and all the others were destabilizing. Three mutations were only slightly destabilizing, however, reducing stability by about 0.5 kcal/mol, and these all occurred close to the N terminus. This result is consistent with the observation that proline is more common near the ends of TM helices. To learn how proline side-chains could be structurally accommodated at different locations in the helix, we solved the structures of a moderately destabilized mutant positioned near the N terminus of the helix, K41P, and a severely destabilized mutant positioned near the middle of the helix, A51P. The K41P mutation produced only local structural alterations, while the A51P mutation resulted in small, but widely distributed structural changes in helix B. Our results indicate that proline is not easily accommodated in transmembrane helices and that the tolerance to proline substitution is dependent, in a complex way, on the position in the structure.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, DOE Center for Genomics and Proteomics, Molecular Biology Institute, 655 Boyer Hall, 611 Charles E. Young Dr. E, University of California, Los Angeles, Los Angeles, CA 90095-1570, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bacteriorhodopsin
A, B
249Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)Gene Names: bop
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Go to UniProtKB:  P02945
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download SDF File 
Download CCD File 
A, B
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.249 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.360α = 90.00
b = 109.120β = 113.41
c = 55.770γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation