PDBsum entry 2v06

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protein metals links
Hydrolase PDB id
Protein chain
234 a.a. *
_MG ×3
Waters ×387
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the ppm ser-thr phosphatase mspp from mycobacterium smegmatis at ph 5.5
Structure: Ser-thr phosphatase mspp. Chain: a. Engineered: yes
Source: Mycobacterium smegmatis. Organism_taxid: 1772. Strain: mc2155. Expressed in: escherichia coli. Expression_system_taxid: 469008.
1.05Å     R-factor:   0.132     R-free:   0.187
Authors: A.Wehenkel,M.Bellinzoni,F.Schaeffer,A.Villarino,P.M.Alzari
Key ref:
M.Bellinzoni et al. (2007). Insights into the catalytic mechanism of PPM Ser/Thr phosphatases from the atomic resolution structures of a mycobacterial enzyme. Structure, 15, 863-872. PubMed id: 17637345 DOI: 10.1016/j.str.2007.06.002
08-May-07     Release date:   16-Oct-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
A0QTQ6  (A0QTQ6_MYCS2) -  Protein serine/threonine phosphatase
233 a.a.
234 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Protein-serine/threonine phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: [a protein]-serine/threonine phosphate + H2O = [a protein]- serine/threonine + phosphate
[a protein]-serine/threonine phosphate
+ H(2)O
= [a protein]- serine/threonine
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     4 terms  


    Key reference    
DOI no: 10.1016/j.str.2007.06.002 Structure 15:863-872 (2007)
PubMed id: 17637345  
Insights into the catalytic mechanism of PPM Ser/Thr phosphatases from the atomic resolution structures of a mycobacterial enzyme.
M.Bellinzoni, A.Wehenkel, W.Shepard, P.M.Alzari.
Serine/threonine-specific phosphatases (PPs) represent, after protein tyrosine phosphatases, the second major class of enzymes that catalyze the dephosphorylation of proteins. They are classed in two large families, known as PPP and PPM, on the basis of sequence similarities, metal ion dependence, and inhibitor sensitivity. Despite their wide species distribution and broad physiological roles, the catalytic mechanism of PPM phosphatases has been primarily inferred from studies of a single enzyme, human PP2Calpha. Here, we report the biochemical characterization and the atomic resolution structures of a soluble PPM phosphatase from the saprophyte Mycobacterium smegmatis in complex with different ligands. The structures provide putative snapshots along the catalytic cycle, which support an associative reaction mechanism that differs in some important aspects from the currently accepted model and reinforces the hypothesis of convergent evolution in PPs.
  Selected figure(s)  
Figure 1.
Figure 1. Overall Structure of MspP
(A) Superposition of MspP (in blue) and MtPstP (PDB code: 1TXO, in green). The rmsd is 1.76 Å for 212 core residues. The inset shows a close view of the catalytic centers, with the three Mn^2+ ions and some coordinating residues labeled.
(B) Superposition of MspP (in blue) and PP2Cα (PDB code: 1A6Q, in red), with a rmsd of 2.37 Å for 189 core residues. Note the different structure and orientation of the flap segment (shown by arrows).
(C) General view of the molecular surface of MspP in complex with phosphate. The flap segment is shown in yellow.
Figure 3.
Figure 3. The Catalytic Mechanism of MspP
(A) Stereoview of the active site showing the trinuclear metal center and selected amino acid residues (His153 is shown in two conformations as observed in the structures of the enzyme-cacodylate and enzyme-phosphate complexes, respectively). The three positions of phosphate, as deduced from the corresponding crystal structures (see text), are shown in different colors: competent substrate (blue), reaction product (orange), and incoming substrate or outgoing product (green).
(B) Schematic view illustrating the proposed catalytic mechanism. Interatomic distances shown in red correspond to the MspP-phosphate complex at 0.83 Å resolution, those in blue to the MspP-cacodylate complex at 1.4 Å resolution. The octahedral coordination of metals M1 and M2 is completed by the carboxylate group of Asp 35 (not shown for clarity), with distances M1 − O[δ2] = 2.10 Å and M2 − O[δ1] = 2.00 Å. Water molecules (not shown) complete the octahedral coordination at site M3. The putative proton donor (XH^+) may correspond to either a water molecule or a substrate group.
  The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 863-872) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19039517 H.Dahche, A.Abdullah, M.Ben Potters, and P.J.Kennelly (2009).
A PPM-family protein phosphatase from the thermoacidophile Thermoplasma volcanium hydrolyzes protein-bound phosphotyrosine.
  Extremophiles, 13, 371-377.  
19432806 M.S.Brody, V.Stewart, and C.W.Price (2009).
Bypass suppression analysis maps the signalling pathway within a multidomain protein: the RsbP energy stress phosphatase 2C from Bacillus subtilis.
  Mol Microbiol, 72, 1221-1234.  
19879837 Y.Shi (2009).
Serine/threonine phosphatases: mechanism through structure.
  Cell, 139, 468-484.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.