3H5J

LeuD_1-168 small subunit of isopropylmalate isomerase (Rv2987c) from mycobacterium tuberculosis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structural studies on the enzyme complex isopropylmalate isomerase (LeuCD) from Mycobacterium tuberculosis

Manikandan, K., Geerlof, A., Zozulya, A.V., Svergun, D.I., Weiss, M.S.

(2011) Proteins 79: 35-49

  • DOI: 10.1002/prot.22856
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The absence of the leucine biosynthesis pathway in humans makes the enzymes of this pathway in pathogenic bacteria such as Mycobacterium tuberculosis potential candidates for developing novel antibacterial drugs. One of these enzymes is isopropylmala ...

    The absence of the leucine biosynthesis pathway in humans makes the enzymes of this pathway in pathogenic bacteria such as Mycobacterium tuberculosis potential candidates for developing novel antibacterial drugs. One of these enzymes is isopropylmalate isomerase (IPMI). IPMI exists as a complex of two subunits: the large (LeuC) and the small (LeuD) subunit. The functional LeuCD complex catalyzes the stereospecific conversion reaction of α-isopropylmalate to β-isopropylmalate. Three C-terminally truncated variants of LeuD have been analyzed by X-ray crystallography to resolutions of 2.0 Å (LeuD_1-156), 1.2 Å (LeuD_1-168), and 2.5 Å (LeuD_1-186), respectively. The two most flexible parts of the structure are the regions of residues 30-37, the substrate discriminating loop, and of residues 70-74, the substrate binding loop. The three determined structures were also compared with the structures of other bacterial LeuDs. This comparison suggests the presence of two LeuD subfamilies. A model for the structure of the inactive enzyme complex has been obtained from solution X-ray scattering experiments. The crystal structure of LeuD was shown to be compatible with the solution X-ray scattering data from the small subunit. In contrast, the solution scattering results suggest that the large subunit LeuC and the LeuCD complex have overall shapes, which are radically different from the ones observed in the crystals of the functional homolog mitochondrial aconitase.

    Related Citations: 
    • Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the small subunit of isopropylmalate isomerase (Rv2987c) from Mycobacterium tuberculosis
      Manikandan, K.,Geerlof, A.,Schuldt, L.,Mueller-Dieckmann, C.,Weiss, M.S.
      (2009) Acta Crystallogr.,Sect.F 65: 136

    Organizational Affiliation: 

    EMBL Hamburg Outstation, c/o DESY, Notkestr. 85, D-22603 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-isopropylmalate dehydratase small subunit
A, B
171Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: leuD
EC: 4.2.1.33
Find proteins for P9WK95 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WK95
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.070α = 90.00
b = 75.710β = 103.22
c = 48.840γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
SHELXL-97refinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance