1TXO

Crystal structure of the Mycobacterium tuberculosis serine/threonine phosphatase PstP/Ppp at 1.95 A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

An Alternate Conformation and a Third Metal in PstP/Ppp, the M. tuberculosis PP2C-Family Ser/Thr Protein Phosphatase.

Pullen, K.E.Ng, H.L.Sung, P.Y.Good, M.C.Smith, S.M.Alber, T.

(2004) Structure 12: 1947-1954

  • DOI: https://doi.org/10.1016/j.str.2004.09.008
  • Primary Citation of Related Structures:  
    1TXO

  • PubMed Abstract: 
  • Serine/threonine protein phosphatases are central mediators of phosphorylation-dependent signals in eukaryotes and a variety of pathogenic bacteria. Here, we report the crystal structure of the intracellular catalytic domain of Mycobacterium tuberculosis PstPpp, a membrane-anchored phosphatase in the PP2C family ...

    Serine/threonine protein phosphatases are central mediators of phosphorylation-dependent signals in eukaryotes and a variety of pathogenic bacteria. Here, we report the crystal structure of the intracellular catalytic domain of Mycobacterium tuberculosis PstPpp, a membrane-anchored phosphatase in the PP2C family. Despite sharing the fold and two-metal center of human PP2Calpha, the PstPpp catalytic domain binds a third Mn(2+) in a site created by a large shift in a previously unrecognized flap subdomain adjacent to the active site. Mutations in this site selectively increased the Michaelis constant for Mn(2+) in the reaction of a noncognate, small-molecule substrate, p-nitrophenyl phosphate. The PstP/Ppp structure reveals core functional motifs that advance the framework for understanding the mechanisms of substrate recognition, catalysis, and regulation of PP2C phosphatases.


    Organizational Affiliation

    Department of Molecular and Cell Biology, 339 Hildebrand Hall #3206, University of California, Berkeley, Berkeley, CA 94720, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative Bacterial Enzyme
A, B
237Mycobacterium tuberculosisMutation(s): 6 
EC: 3.1.3.16
UniProt
Find proteins for P9WHW5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHW5 
Go to UniProtKB:  P9WHW5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHW5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.638α = 90
b = 58.757β = 102.15
c = 73.815γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
ELVESdata reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-09-10
    Changes: Database references
  • Version 1.4: 2016-09-21
    Changes: Other
  • Version 1.5: 2017-10-11
    Changes: Refinement description