3ZZN

5-Mutant (R79W, R151A, E279A, E299A,E313A) Lactate-Dehydrogenase from Thermus thermophillus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Sampling the conformational energy landscape of a hyperthermophilic protein by engineering key substitutions.

Colletier, J.P.Aleksandrov, A.Coquelle, N.Mraihi, S.Mendoza-Barbera, E.Field, M.Madern, D.

(2012) Mol. Biol. Evol. 29: 1683-1694

  • DOI: 10.1093/molbev/mss015
  • Primary Citation of Related Structures:  
  • Also Cited By: 4CL3, 4BGV, 4BGU, 4BGT

  • PubMed Abstract: 
  • Proteins exist as a dynamic ensemble of interconverting substates, which defines their conformational energy landscapes. Recent work has indicated that mutations that shift the balance between conformational substates (CSs) are one of the main mechan ...

    Proteins exist as a dynamic ensemble of interconverting substates, which defines their conformational energy landscapes. Recent work has indicated that mutations that shift the balance between conformational substates (CSs) are one of the main mechanisms by which proteins evolve new functions. In the present study, we probe this assertion by examining phenotypic protein adaptation to extreme conditions, using the allosteric tetrameric lactate dehydrogenase (LDH) from the hyperthermophilic bacterium Thermus thermophilus (Tt) as a model enzyme. In the presence of fructose 1, 6 bis-phosphate (FBP), allosteric LDHs catalyze the conversion of pyruvate to lactate with concomitant oxidation of nicotinamide adenine dinucleotide, reduced form (NADH). The catalysis involves a structural transition between a low-affinity inactive "T-state" and a high-affinity active "R-state" with bound FBP. During this structural transition, two important residues undergo changes in their side chain conformations. These are R171 and H188, which are involved in substrate and FBP binding, respectively. We designed two mutants of Tt-LDH with one ("1-Mut") and five ("5-Mut") mutations distant from the active site and characterized their catalytic, dynamical, and structural properties. In 1-Mut Tt-LDH, without FBP, the K(m)(Pyr) is reduced compared with that of the wild type, which is consistent with a complete shifting of the CS equilibrium of H188 to that observed in the R-state. By contrast, the CS populations of R171, k(cat) and protein stability are little changed. In 5-Mut Tt-LDH, without FBP, K(m)(Pyr) approaches the values it has with FBP and becomes almost temperature independent, k(cat) increases substantially, and the CS populations of R171 shift toward those of the R-state. These changes are accompanied by a decrease in protein stability at higher temperature, which is consistent with an increased flexibility at lower temperature. Together, these results show that the thermal properties of an enzyme can be strongly modified by only a few or even a single mutation, which serve to alter the equilibrium and, hence, the relative populations of functionally important native-state CSs, without changing the nature of the CSs themselves. They also provide insights into the types of mutational pathways by which protein adaptation to temperature is achieved.


    Organizational Affiliation

    Dynamop Group, Institut de Biologie Structurale J.-P. Ebel, CEA CNRS UJF, UMR 5075, Grenoble cedex 01, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LACTATE DEHYDROGENASE
A, B, C, D
310Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 5 
Gene Names: ldh
EC: 1.1.1.27
Find proteins for Q5SJA1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJA1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 157.123α = 90.00
b = 59.597β = 93.37
c = 153.076γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-03-07
    Type: Other
  • Version 1.2: 2012-05-30
    Type: Other
  • Version 1.3: 2018-02-28
    Type: Advisory, Database references, Source and taxonomy
  • Version 1.4: 2019-04-03
    Type: Data collection, Experimental preparation
  • Version 1.5: 2019-05-29
    Type: Data collection, Experimental preparation