4WUO

Structure of the E270A Mutant Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Glutamate 270 plays an essential role in K(+)-activation and domain closure of Thermus thermophilus isopropylmalate dehydrogenase.

Graczer, E.Pallo, A.Olah, J.Szimler, T.Konarev, P.V.Svergun, D.I.Merli, A.Zavodszky, P.Weiss, M.S.Vas, M.

(2015) Febs Lett. 589: 240-245

  • DOI: 10.1016/j.febslet.2014.12.005

  • PubMed Abstract: 
  • The mutant E270A of Thermus thermophilus 3-isopropylmalate dehydrogenase exhibits largely reduced (∼1%) catalytic activity and negligible activation by K(+) compared to the wild-type enzyme. A 3-4 kcal/mol increase in the activation energy of the cat ...

    The mutant E270A of Thermus thermophilus 3-isopropylmalate dehydrogenase exhibits largely reduced (∼1%) catalytic activity and negligible activation by K(+) compared to the wild-type enzyme. A 3-4 kcal/mol increase in the activation energy of the catalysed reaction upon this mutation could also be predicted by QM/MM calculations. In the X-ray structure of the E270A mutant a water molecule was observed to take the place of K(+). SAXS and FRET experiments revealed the essential role of E270 in stabilisation of the active domain-closed conformation of the enzyme. In addition, E270 seems to position K(+) into close proximity of the nicotinamide ring of NAD(+) and the electron-withdrawing effect of K(+) may help to polarise the aromatic ring in order to aid the hydride-transfer.


    Organizational Affiliation

    Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., H-1117 Budapest, Hungary.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-isopropylmalate dehydrogenase
A, B
359Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 1 
Gene Names: leuB
EC: 1.1.1.85
Find proteins for Q5SIY4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIY4
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

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Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
IPM
Query on IPM

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Download CCD File 
A
3-ISOPROPYLMALIC ACID
C7 H12 O5
RNQHMTFBUSSBJQ-CRCLSJGQSA-N
 Ligand Interaction
EOH
Query on EOH

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Download CCD File 
A, B
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.170 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 50.180α = 90.00
b = 143.250β = 90.00
c = 174.890γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
MAR345dtbdata collection
Cootmodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
HungaryNK 108642

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2015-01-21
    Type: Database references