5Y8J

Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + (R)-3-hydroxyisobutyrate (R-HIBA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure, interactions and action ofMycobacterium tuberculosis3-hydroxyisobutyric acid dehydrogenase.

Srikalaivani, R.Singh, A.Vijayan, M.Surolia, A.

(2018) Biochem J 475: 2457-2471

  • DOI: 10.1042/BCJ20180271
  • Primary Citation of Related Structures:  
    5Y8M, 5Y8L, 5Y8O, 5Y8N, 5Y8P, 5Y8G, 5Y8I, 5Y8H, 5Y8K, 5Y8J

  • PubMed Abstract: 
  • Biochemical and crystallographic studies on Mycobacterium tuberculosis 3-hydroxyisobutyric acid dehydrogenase ( Mt HIBADH), a member of the 3-hydroxyacid dehydrogenase superfamily, have been carried out. Gel filtration and blue native PAGE of Mt HIBADH show that the enzyme is a dimer ...

    Biochemical and crystallographic studies on Mycobacterium tuberculosis 3-hydroxyisobutyric acid dehydrogenase ( Mt HIBADH), a member of the 3-hydroxyacid dehydrogenase superfamily, have been carried out. Gel filtration and blue native PAGE of Mt HIBADH show that the enzyme is a dimer. The enzyme preferentially uses NAD + as the cofactor and is specific to S -hydroxyisobutyric acid (HIBA). It can also use R -HIBA, l-serine and 3-hydroxypropanoic acid (3-HP) as substrates, but with much less efficiency. The pH optimum for activity is ∼11. Structures of the native enzyme, the holoenzyme, binary complexes with NAD + , S -HIBA, R -HIBA, l-serine and 3-HP and ternary complexes involving the substrates and NAD + have been determined. None of the already known structures of HIBADH contain a substrate molecule at the binding site. The structures reported here provide for the first time, among other things, a clear indication of the location and interactions of the substrates at the active site. They also define the entrance of the substrates to the active site region. The structures provide information on the role of specific residues at the active site and the entrance. The results obtained from crystal structures are consistent with solution studies including mutational analysis. They lead to the proposal of a plausible mechanism of the action of the enzyme.


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India surolia@iisc.ac.in mv@iisc.ac.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable 3-hydroxyisobutyrate dehydrogenaseA, B295Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: mmsBRv0751cMTV041.25c
EC: 1.1.1.31
UniProt
Find proteins for P9WNY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNY5 
Go to UniProtKB:  P9WNY5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.53α = 90
b = 128.53β = 90
c = 70.2γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references