1RWI

Extracellular domain of Mycobacterium tuberculosis PknD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Sensor Domain of the Mycobacterium tuberculosis Receptor Ser/Thr Protein Kinase, PknD, forms a Highly Symmetric beta Propeller.

Good, M.C.Greenstein, A.E.Young, T.A.Ng, H.L.Alber, T.

(2004) J Mol Biol 339: 459-469

  • DOI: 10.1016/j.jmb.2004.03.063
  • Primary Citation of Related Structures:  
    1RWL, 1RWI

  • PubMed Abstract: 
  • Diverse pathogenic bacteria produce transmembrane receptor Ser/Thr protein kinases (STPKs), but little is known about the signals mediated by these "eukaryotic-like" proteins. To explore the basis for signaling in the bacterial STPK receptor family, ...

    Diverse pathogenic bacteria produce transmembrane receptor Ser/Thr protein kinases (STPKs), but little is known about the signals mediated by these "eukaryotic-like" proteins. To explore the basis for signaling in the bacterial STPK receptor family, we determined the structure of the sensor domain of Mycobacterium tuberculosis PknD. In two crystal forms, the PknD sensor domain forms a rigid, six-bladed beta-propeller with a flexible tether to the transmembrane domain. The PknD sensor domain is the most symmetric beta-propeller structure described. All residues that vary most among the blade subdomains cluster in the large "cup" motif, analogous to the ligand-binding surface in many beta-propeller proteins. These results suggest that PknD binds a multivalent ligand that signals by changing the quaternary structure of the intracellular kinase domain.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pknDAB270Mycobacterium tuberculosisMutation(s): 0 
Gene Names: pknDRv0931cMT0958MTCY08C9.08
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
Find proteins for P9WI79 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WI79 
Go to UniProtKB:  P9WI79
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.94α = 90
b = 94.58β = 98.1
c = 71.77γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
DMmodel building
REFMACrefinement
CCP4data scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance