PDBsum entry 1rwi

Transferase

PDB id: 1rwi

Contents

Protein chains

254 a.a. *

Metals

_CD ×14

Waters ×204

* Residue conservation analysis

PDB id:

1rwi

Name:

Transferase

Title:

Extracellular domain of mycobacterium tuberculosis pknd

Structure:

Serine/threonine-protein kinase pknd. Chain: b, a. Fragment: pknd 403-665. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: pknd, rv0931c, mt0958, mtcy08c9.08. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.193 R-free: 0.220

Authors:

M.C.Good,A.E.Greenstein,T.A.Young,H.L.Ng,T.Alber,Tb Structural Genomics Consortium (Tbsgc)

Key ref:

M.C.Good et al. (2004). Sensor domain of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknD, forms a highly symmetric beta propeller. J Mol Biol, 339, 459-469. PubMed id: 15136047 DOI: 10.1016/j.jmb.2004.03.063

Date:

16-Dec-03 Release date: 27-Apr-04

Protein chains

P9WI79  (PKND_MYCTU) -  Serine/threonine-protein kinase PknD from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 664 a.a.

Struc: 254 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2004.03.063

J Mol Biol 339:459-469 (2004)

PubMed id: 15136047

Sensor domain of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknD, forms a highly symmetric beta propeller.

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

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, 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.

Selected figure(s)

Figure 1.
Figure 1. Crystal structure of the extracellular domain of PknD. (A) Stereo view of the electron density map (2F[o] -F[c]) of monoclinic crystal form. Electron density is displayed surrounding one of the invariant prolines in the "cup" and the exposed Tyr511. (B) The PknD sensor domain forms a six-bladed b propeller. Four strands constitute each of the six blades. The numbers around the periphery indicate the blade number, with the full blade nearest the N terminus labeled 1. The "latch" formed by the N and C termini is boxed. The 3-4 loop in blade 1 is disordered. The b propeller forms an approximate cylinder with a radius of 40 Å and a height of 35 Å. (C) Electron density (2F[o] -F[c]) showing rings of ordered water molecules stacked in the central channel of the PknD b propeller. The central pseudo-symmetry axis runs vertically through the center of the rings.

Figure 2.
Figure 2. Similarity the independent PknD sensor domain structures. The two monomers from the monoclinic crystal form (P2[1], light blue and dark blue) and the model from the orthorhombic form (P2[1]2[1]2[1], red) were superimposed. The C^a rmsd between the three monomers ranged from 0.35-0.52 Å. The high similarity between the three models and the disorder of the N-terminal 11 residues (dots) implies that the PknD sensor domain forms a rigid framework that is flexibly tethered to the predicted transmembrane helix.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 339, 459-469) copyright 2004.

Figures were selected by an automated process.