4QVH

Crystal structure of the essential Mycobacterium tuberculosis phosphopantetheinyl transferase PptT, solved as a fusion protein with maltose binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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Literature

Crystal structure of the essential Mycobacterium tuberculosis phosphopantetheinyl transferase PptT, solved as a fusion protein with maltose binding protein.

Jung, J.Bashiri, G.Johnston, J.M.Brown, A.S.Ackerley, D.F.Baker, E.N.

(2014) J Struct Biol 188: 274-278

  • DOI: 10.1016/j.jsb.2014.10.004
  • Primary Citation of Related Structures:  
    4QVH

  • PubMed Abstract: 
  • Phosphopantetheinyl transferases (PPTases) are key enzymes in the assembly-line production of complex molecules such as fatty acids, polyketides and polypeptides, where they activate acyl or peptidyl carrier proteins, transferring a 4'-phosphopantetheinyl moiety from coenzyme A (CoA) to a reactive serine residue on the carrier protein ...

    Phosphopantetheinyl transferases (PPTases) are key enzymes in the assembly-line production of complex molecules such as fatty acids, polyketides and polypeptides, where they activate acyl or peptidyl carrier proteins, transferring a 4'-phosphopantetheinyl moiety from coenzyme A (CoA) to a reactive serine residue on the carrier protein. The human pathogen Mycobacterium tuberculosis encodes two PPTases, both essential and therefore attractive drug targets. We report the structure of the type-II PPTase PptT, obtained from crystals of a fusion protein with maltose binding protein. The structure, at 1.75Å resolution (R=0.156, Rfree=0.191), reveals an α/β fold broadly similar to other type-II PPTases, but with differences in peripheral structural elements. A bound CoA is clearly defined with its pantetheinyl arm tucked into a hydrophobic pocket. Interactions involving the CoA diphosphate, bound Mg(2+) and three active site acidic side chains suggest a plausible pathway for proton transfer during catalysis.


    Organizational Affiliation

    Maurice Wilkins Centre and School of Biological Sciences, University of Auckland, Auckland, New Zealand. Electronic address: ted.baker@auckland.ac.nz.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein, 4'-phosphopantetheinyl transferase chimeraA, B598Escherichia coliMycobacterium tuberculosis H37Rv
This entity is chimeric
Mutation(s): 0 
Gene Names: malEpptT
EC: 2.7.8.7
UniProt
Find proteins for O33336 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O33336 
Go to UniProtKB:  O33336
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC, D2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA (Subject of Investigation/LOI)
Query on COA

Download Ideal Coordinates CCD File 
E [auth A], L [auth B]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
FLC
Query on FLC

Download Ideal Coordinates CCD File 
K [auth A], Q [auth B]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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G [auth A], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A], M [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
C, Dalpha-maltoseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.699α = 90
b = 126.029β = 90
c = 143.96γ = 90
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: 2014-12-17
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary