4Y90

Crystal structure of Triosephosphate Isomerase from Deinococcus radiodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins.

Romero-Romero, S.Costas, M.Rodriguez-Romero, A.Alejandro Fernandez-Velasco, D.

(2015) Phys Chem Chem Phys 17: 20699-20714

  • DOI: 10.1039/c5cp01599e
  • Primary Citation of Related Structures:  
    4Y8F, 4Y90, 4Y96, 4Y9A

  • PubMed Abstract: 
  • Temperature is one of the main variables that modulate protein function and stability. Thermodynamic studies of oligomeric proteins, the dominant protein natural form, have been often hampered because irreversible aggregation and/or slow reactions are common ...

    Temperature is one of the main variables that modulate protein function and stability. Thermodynamic studies of oligomeric proteins, the dominant protein natural form, have been often hampered because irreversible aggregation and/or slow reactions are common. There are no reports on the reversible equilibrium thermal unfolding of proteins composed of (β/α)8 barrel subunits, albeit this "TIM barrel" topology is one of the most abundant and versatile in nature. We studied the eponymous TIM barrel, triosephosphate isomerase (TIM), belonging to five species of different bacterial taxa. All of them were found to be catalytically efficient dimers. The three-dimensional structure of four enzymes was solved at high/medium resolution. Irreversibility and kinetic control were observed in the thermal unfolding of two TIMs, while for the other three the thermal unfolding was found to follow a two-state equilibrium reversible process. Shifts in the global stability curves of these three proteins are related to the organismal temperature range of optimal growth and modulated by variations in maximum stability temperature and in the enthalpy change at that temperature. Reversibility appears to correlate with the low isoelectric point, the absence of a residual structure in the unfolded state, small cavity volume in the native state, low conformational stability and a low melting temperature. Furthermore, the strong coupling between dimer dissociation and monomer unfolding may reduce aggregation and favour reversibility. It is therefore very thought-provoking to find that a common topological ensemble, such as the TIM barrel, can unfold/refold in the Anfinsen way, i.e. without the help of the cellular machinery.


    Organizational Affiliation

    Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Distrito Federal, Mexico. fdaniel@unam.mx.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Triosephosphate isomeraseA, B, C, D247Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: tpiADR_1339
EC: 5.3.1.1
UniProt
Find proteins for Q9RUP5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RUP5 
Go to UniProtKB:  Q9RUP5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], J [auth B], K [auth B], Q [auth C], W [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , H [auth A] , L [auth B] , M [auth B] , N [auth B] , R [auth C] , S [auth C] , 
F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], R [auth C], S [auth C], X [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
I [auth A], O [auth B], P [auth B], V [auth C], Z [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
T [auth C], U [auth C], Y [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.62α = 90
b = 169.62β = 90
c = 202.266γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
CrystalCleardata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Consejo Nacional de Ciencia y Tecnologia de MexicoMexico166472
Consejo Nacional de Ciencia y Tecnologia de MexicoMexico99857

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Data collection
  • Version 1.2: 2015-08-12
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Author supporting evidence, Derived calculations