PDBsum entry 2j82

Go to PDB code: 
protein metals links
Hydrolase PDB id
Protein chain
221 a.a. *
_MG ×2
_CA ×2
Waters ×136
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structural analysis of the pp2c family phosphatase tppha from thermosynechococcus elongatus
Structure: Protein serine-threonine phosphatase. Chain: a. Synonym: tppha. Engineered: yes
Source: Synechococcus elongatus. Organism_taxid: 32046. Expressed in: escherichia coli. Expression_system_taxid: 469008.
1.28Å     R-factor:   0.165     R-free:   0.204
Authors: C.Schlicker,N.Kloft,K.Forchhammer,S.Becker
Key ref:
C.Schlicker et al. (2008). Structural analysis of the PP2C phosphatase tPphA from Thermosynechococcus elongatus: a flexible flap subdomain controls access to the catalytic site. J Mol Biol, 376, 570-581. PubMed id: 18164312 DOI: 10.1016/j.jmb.2007.11.097
18-Oct-06     Release date:   06-Nov-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8DGS1  (Q8DGS1_THEEB) -  Protein serin-threonin phosphatase
240 a.a.
221 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     3 terms  


DOI no: 10.1016/j.jmb.2007.11.097 J Mol Biol 376:570-581 (2008)
PubMed id: 18164312  
Structural analysis of the PP2C phosphatase tPphA from Thermosynechococcus elongatus: a flexible flap subdomain controls access to the catalytic site.
C.Schlicker, O.Fokina, N.Kloft, T.Grüne, S.Becker, G.M.Sheldrick, K.Forchhammer.
The homologue of the phosphoprotein PII phosphatase PphA from Thermosynechococcus elongatus, termed tPphA, was identified and its structure was resolved in two different space groups, C222(1) and P4(1)2(1)2, at a resolution of 1.28 and 3.05 A, respectively. tPphA belongs to a large and widely distributed subfamily of Mg(2+)/Mn(2+)-dependent phosphatases of the PPM superfamily characterized by the lack of catalytic and regulatory domains. The core structure of tPphA shows a high degree of similarity to the two PPM structures identified so far. In contrast to human PP2C, but similar to Mycobacterium tuberculosis phosphatase PstP, the catalytic centre exhibits a third metal ion in addition to the dinuclear metal centre universally conserved in all PPM members. The fact that the third metal is only liganded by amino acids, which are universally conserved in all PPM members, implies that the third metal could be general for all members of this family. As a specific feature of tPphA, a flexible subdomain, previously recognized as a flap domain, could be revealed. Comparison of different structural isomers of tPphA as well as site-specific mutagenesis implied that the flap domain is involved in substrate binding and catalytic activity. The structural arrangement of the flap domain was accompanied by a large side-chain movement of an Arg residue (Arg169) at the basis of the flap. Mutation of this residue strongly impaired protein stability as well as catalytic activity, emphasizing the importance of this amino acid for the regional polysterism of the flap subdomain and confirming the assumption that flap domain flexibility is involved in catalysis.
  Selected figure(s)  
Figure 3.
Fig. 3. Structure of tPphA in different space groups and the active site. (a) tPphA structure in C222[1]. The metal ions are shown as spheres: Mg^2+, pink; Ca^2+ and mixture of Mg^2+ and Ca^2+, dark pink. All structural figures were generated with PyMOL []. (b) tPphA structure in P4[1]2[1]2 monomer A. (c) tPphA structure in P4[1]2[1]2 monomer B. (d) Active site of tPphA in C222[1]. M1: Mg^2+, M2: mixture of Mg^2 and Ca^2+, M3: Ca^2+. Hydrogen bonds are shown with dashed lines.
Figure 4.
Fig. 4. Comparison of the different tPphA monomers. (a) Superposition of the three monomers of tPphA from different space groups. Blue: tPphA in C222[1], cyan: tPphA monomer A in P4[1]2[1]2, grey: tPphA monomer B in P4[1]2[1]2. (b) Different position of Arg169 in the three tPphA monomers. Hydrogen bonds are shown with dashed lines. (c) Superposition of the active site in the three tPphA monomers. Metal ions are shown in black. Blue, tPphA in C222[1]; cyan, tPphA monomer A in P4[1]2[1]2; grey, tPphA monomer B in P4[1]2[1]2.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 376, 570-581) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21190057 J.S.Fraser, and C.J.Jackson (2011).
Mining electron density for functionally relevant protein polysterism in crystal structures.
  Cell Mol Life Sci, 68, 1829-1841.  
21282331 Y.Ohashi, W.Shi, N.Takatani, M.Aichi, S.Maeda, S.Watanabe, H.Yoshikawa, and T.Omata (2011).
Regulation of nitrate assimilation in cyanobacteria.
  J Exp Bot, 62, 1411-1424.  
21734656 Y.Tan, and Z.Q.Luo (2011).
Legionella pneumophila SidD is a deAMPylase that modifies Rab1.
  Nature, 475, 506-509.  
20836557 E.Sierecki, W.Sinko, J.A.McCammon, and A.C.Newton (2010).
Discovery of small molecule inhibitors of the PH domain leucine-rich repeat protein phosphatase (PHLPP) by chemical and virtual screening.
  J Med Chem, 53, 6899-6911.  
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.  
19893533 P.Yin, H.Fan, Q.Hao, X.Yuan, D.Wu, Y.Pang, C.Yan, W.Li, J.Wang, and N.Yan (2009).
Structural insights into the mechanism of abscisic acid signaling by PYL proteins.
  Nat Struct Mol Biol, 16, 1230-1236.
PDB codes: 3kdh 3kdi 3kdj
19262998 T.Sugiura, and Y.Noguchi (2009).
Substrate-dependent metal preference of PPM1H, a cancer-associated protein phosphatase 2C: comparison with other family members.
  Biometals, 22, 469-477.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.