6UNC | pdb_00006unc

The crystal structure of Phosphopantetheinyl Hydrolase (PptH) from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.222 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural insights into phosphopantetheinyl hydrolase PptH from Mycobacterium tuberculosis.

Mosior, J.Bourland, R.Soma, S.Nathan, C.Sacchettini, J.

(2020) Protein Sci 29: 744-757

  • DOI: https://doi.org/10.1002/pro.3813
  • Primary Citation Related Structures: 
    6UNC

  • PubMed Abstract: 

    The amidinourea 8918 was recently reported to inhibit the type II phosphopantetheinyl transferase (PPTase) of Mycobacterium tuberculosis (Mtb), PptT, a potential drug-target that activates synthases and synthetases involved in cell wall biosynthesis and secondary metabolism. Surprisingly, high-level resistance to 8918 occurred in Mtb harboring mutations within the gene adjacent to pptT, rv2795c, highlighting the role of the encoded protein as a potentiator of the bactericidal action of the amidinourea. Those studies revealed that Rv2795c (PptH) is a phosphopantetheinyl (PpT) hydrolase, possessing activity antagonistic with respect to PptT. We have solved the crystal structure of Mtb's phosphopantetheinyl hydrolase, making it the first phosphopantetheinyl (carrier protein) hydrolase structurally characterized. The 2.5 Å structure revealed the hydrolases' four-layer (α/β/β/α) sandwich fold featuring a Mn-Fe binuclear center within the active site. A structural similarity search confirmed that PptH most closely resembles previously characterized metallophosphoesterases (MPEs), particularly within the vicinity of the active site, suggesting that it may utilize a similar catalytic mechanism. In addition, analysis of the structure has allowed for the rationalization of the previously reported PptH mutations associated with 8918-resistance. Notably, differences in the sequences and predicted structural characteristics of the PpT hydrolases PptH of Mtb and E. coli's acyl carrier protein hydrolase (AcpH) indicate that the two enzymes evolved convergently and therefore are representative of two distinct PpT hydrolase families.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, Texas.

Macromolecule Content 

  • Total Structure Weight: 145.96 kDa 
  • Atom Count: 9,287 
  • Modeled Residue Count: 1,118 
  • Deposited Residue Count: 1,252 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metallophos domain-containing protein
A, B, C, D
313Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv2795c
EC: 3.1.4.14
UniProt
Find proteins for I6YEE1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6YEE1 
Go to UniProtKB:  I6YEE1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6YEE1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE
(Subject of Investigation/LOI)

Query on FE



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MN
(Subject of Investigation/LOI)

Query on MN



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.222 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.19α = 90
b = 92.534β = 90
c = 183.626γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
HKL-2000data reduction
XDSdata scaling
HKL-2000data scaling
CRANK2phasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesP01AI095208
Welch FoundationUnited StatesA-0015

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary