5IJW

Glutamate Racemase (MurI) from Mycobacterium smegmatis with bound D-glutamate, 1.8 Angstrom resolution, X-ray diffraction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Exploring the structure of glutamate racemase from Mycobacterium tuberculosis as a template for anti-mycobacterial drug discovery.

Poen, S.Nakatani, Y.Opel-Reading, H.K.Lasse, M.Dobson, R.C.Krause, K.L.

(2016) Biochem J 473: 1267-1280

  • DOI: 10.1042/BCJ20160186
  • Primary Citation of Related Structures:  
    5HJ7, 5IJW

  • PubMed Abstract: 
  • Glutamate racemase (MurI) is responsible for providing D-glutamate for peptidoglycan biosynthesis in bacteria and has been a favoured target in pharmaceutical drug design efforts. It has recently been proven to be essential in Mycobacterium tuberculosis, the causative organism of tuberculosis, a disease for which new medications are urgently needed ...

    Glutamate racemase (MurI) is responsible for providing D-glutamate for peptidoglycan biosynthesis in bacteria and has been a favoured target in pharmaceutical drug design efforts. It has recently been proven to be essential in Mycobacterium tuberculosis, the causative organism of tuberculosis, a disease for which new medications are urgently needed. In the present study, we have determined the protein crystal structures of MurI from both M. tuberculosis and Mycobacterium smegmatis in complex with D-glutamate to 2.3 Å and 1.8 Å resolution respectively. These structures are conserved, but reveal differences in their active site architecture compared with that of other MurI structures. Furthermore, compounds designed to target other glutamate racemases have been screened but do not inhibit mycobacterial MurI, suggesting that a new drug design effort will be needed to develop inhibitors. A new type of MurI dimer arrangement has been observed in both structures, and this arrangement becomes the third biological dimer geometry for MurI found to date. The mycobacterial MurI dimer is tightly associated, with a KD in the nanomolar range. The enzyme binds D- and L-glutamate specifically, but is inactive in solution unless the dimer interface is mutated. We created triple mutants of this interface in the M. smegmatis glutamate racemase (D26R/R105A/G194R or E) that have appreciable activity (kcat=0.056-0.160 min(-1) and KM=0.26-0.51 mM) and can be utilized to screen proposed antimicrobial candidates for inhibition.


    Organizational Affiliation

    Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand kurt.krause@otago.ac.nz.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate racemaseA, B279Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: murIMSMEG_4903MSMEI_4776
EC: 5.1.1.3
UniProt
Find proteins for A0R1X0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R1X0 
Go to UniProtKB:  A0R1X0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R1X0
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.1α = 90
b = 90.1β = 90
c = 101.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystalCleardata collection
CrystalClearphasing
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of OtagoNew ZealandDoctoral Scholarship

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Database references, Derived calculations, Refinement description, Structure summary