Histidinol phosphate phosphatase from Mycobacterium tuberculosis

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Identification and structural characterization of a histidinol phosphate phosphatase from Mycobacterium tuberculosis

Jha, B.Kumar, D.Sharma, A.Dwivedy, A.Singh, R.Biswal, B.K.

(2018) J Biol Chem 293: 10102-10118

  • DOI: https://doi.org/10.1074/jbc.RA118.002299
  • Primary Citation of Related Structures:  
    5YHT, 5ZON

  • PubMed Abstract: 

    The absence of a histidine biosynthesis pathway in humans, coupled with histidine essentiality for survival of the important human pathogen Mycobacterium tuberculosis ( Mtb ), underscores the importance of the bacterial enzymes of this pathway as major antituberculosis drug targets. However, the identity of the mycobacterial enzyme that functions as the histidinol phosphate phosphatase (HolPase) of this pathway remains to be established. Here, we demonstrate that the enzyme encoded by the Rv3137 gene, belonging to the inositol monophosphatase (IMPase) family, functions as the Mtb HolPase and specifically dephosphorylates histidinol phosphate. The crystal structure of Rv3137 in apo form enabled us to dissect its distinct structural features. Furthermore, the holo-complex structure revealed that a unique cocatalytic multizinc-assisted mode of substrate binding and catalysis is the hallmark of Mtb HolPase. Interestingly, the enzyme-substrate complex structure unveiled that although monomers possess individual catalytic sites they share a common product-exit channel at the dimer interface. Furthermore, target-based screening against HolPase identified several small-molecule inhibitors of this enzyme. Taken together, our study unravels the missing enzyme link in the Mtb histidine biosynthesis pathway, augments our current mechanistic understanding of histidine production in Mtb , and has helped identify potential inhibitors of this bacterial pathway.

  • Organizational Affiliation

    From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
267Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: hisNimpCRv3137
Find proteins for P95189 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P95189 
Go to UniProtKB:  P95189
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP95189
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth B]
K [auth B]
L [auth B]
O [auth C]
G [auth A],
H [auth B],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
U [auth D],
V [auth D]
O4 P
Query on GOL

Download Ideal Coordinates CCD File 
Q [auth C],
R [auth C]
C3 H8 O3
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
I [auth B]
J [auth B]
M [auth C]
E [auth A],
F [auth A],
I [auth B],
J [auth B],
M [auth C],
N [auth C],
S [auth D],
T [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.03α = 92.16
b = 71.062β = 96.16
c = 91.586γ = 101.94
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-09-19
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description