4IHI

Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis bound with NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.277 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Characterization of the proline-utilization pathway in Mycobacterium tuberculosis through structural and functional studies.

Lagautriere, T.Bashiri, G.Paterson, N.G.Berney, M.Cook, G.M.Baker, E.N.

(2014) Acta Crystallogr D Biol Crystallogr 70: 968-980

  • DOI: https://doi.org/10.1107/S1399004713034391
  • Primary Citation of Related Structures:  
    4IDM, 4IDS, 4IHI, 4JDC

  • PubMed Abstract: 

    The proline-utilization pathway in Mycobacterium tuberculosis (Mtb) has recently been identified as an important factor in Mtb persistence in vivo, suggesting that this pathway could be a valuable therapeutic target against tuberculosis (TB). In Mtb, two distinct enzymes perform the conversion of proline into glutamate: the first step is the oxidation of proline into Δ(1)-pyrroline-5-carboxylic acid (P5C) by the flavoenzyme proline dehydrogenase (PruB), and the second reaction involves converting the tautomeric form of P5C (glutamate-γ-semialdehyde) into glutamate using the NAD(+)-dependent Δ(1)-pyrroline-5-carboxylic dehydrogenase (PruA). Here, the three-dimensional structures of Mtb-PruA, determined by X-ray crystallography, in the apo state and in complex with NAD(+) are described at 2.5 and 2.1 Å resolution, respectively. The structure reveals a conserved NAD(+)-binding mode, common to other related enzymes. Species-specific conformational differences in the active site, however, linked to changes in the dimer interface, suggest possibilities for selective inhibition of Mtb-PruA despite its reasonably high sequence identity to other PruA enzymes. Using recombinant PruA and PruB, the proline-utilization pathway in Mtb has also been reconstituted in vitro. Functional validation using a novel NMR approach has demonstrated that the PruA and PruB enzymes are together sufficient to convert proline to glutamate, the first such demonstration for monofunctional proline-utilization enzymes.


  • Organizational Affiliation

    Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Delta-1-pyrroline-5-carboxylate dehydrogenase563Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: MT1224pruArocARv1187
EC: 1.5.1.12 (PDB Primary Data), 1.2.1.88 (UniProt)
UniProt
Find proteins for O50443 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O50443 
Go to UniProtKB:  O50443
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50443
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
B [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.277 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.937α = 90
b = 163.937β = 90
c = 194.025γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 1.2: 2014-11-12
    Changes: Structure summary
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations