PDBsum entry 1xri

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Structural genomics, unknown function PDB id
Protein chains
151 a.a. *
SO4 ×4
Waters ×60
* Residue conservation analysis
PDB id:
Name: Structural genomics, unknown function
Title: X-ray structure of a putative phosphoprotein phosphatase fro arabidopsis thaliana gene at1g05000
Structure: At1g05000. Chain: a, b. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: at1g05000. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: pqe derivative
Biol. unit: Hexamer (from PQS)
3.30Å     R-factor:   0.204     R-free:   0.249
Authors: G.E.Wesenberg,D.W.Smith,G.N.Phillips Jr.,E.Bitto,C.A.Bingman S.T.M.Allard,Center For Eukaryotic Structural Genomics (Ces
Key ref:
D.J.Aceti et al. (2008). Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000. Proteins, 73, 241-253. PubMed id: 18433060 DOI: 10.1002/prot.22041
14-Oct-04     Release date:   26-Oct-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9ZVN4  (Y1500_ARATH) -  Probable tyrosine-protein phosphatase At1g05000
215 a.a.
151 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Protein-tyrosine-phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein tyrosine phosphate + H2O = protein tyrosine + phosphate
Protein tyrosine phosphate
+ H(2)O
= protein tyrosine
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     dephosphorylation   1 term 
  Biochemical function     phosphatase activity     2 terms  


DOI no: 10.1002/prot.22041 Proteins 73:241-253 (2008)
PubMed id: 18433060  
Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000.
D.J.Aceti, E.Bitto, A.F.Yakunin, M.Proudfoot, C.A.Bingman, R.O.Frederick, H.K.Sreenath, F.C.Vojtik, R.L.Wrobel, B.G.Fox, J.L.Markley, G.N.Phillips.
The crystal structure of the protein product of the gene locus At1g05000, a hypothetical protein from A. thaliana, was determined by the multiple-wavelength anomalous diffraction method and was refined to an R factor of 20.4% (R(free) = 24.9%) at 3.3 A. The protein adopts the alpha/beta fold found in cysteine phosphatases, a superfamily of phosphatases that possess a catalytic cysteine and form a covalent thiol-phosphate intermediate during the catalytic cycle. In At1g05000, the analogous cysteine (Cys(150)) is located at the bottom of a positively-charged pocket formed by residues that include the conserved arginine (Arg(156)) of the signature active site motif, HCxxGxxRT. Of 74 model phosphatase substrates tested, purified recombinant At1g05000 showed highest activity toward polyphosphate (poly-P(12-13)) and deoxyribo- and ribonucleoside triphosphates, and less activity toward phosphoenolpyruvate, phosphotyrosine, phosphotyrosine-containing peptides, and phosphatidyl inositols. Divalent metal cations were not required for activity and had little effect on the reaction.
  Selected figure(s)  
Figure 1.
Figure 1. Structure of At1g05000. (A) Ribbon diagram of At1g05000 is shown in a rainbow color scheme from the amino terminus (blue) to the carboxy terminus (red). Secondary structure elements are annotated as 1- 6 for helices; 1- 5 for the -strands of the central 5-stranded sheet; g1-g3 for auxiliary 3[10] helices. (B) Electrostatic surface potential of At1g05000 contoured from -10 kT (red) to 10 kT (blue). Sulfates (sticks) are clearly buried in the deep active site cavity. The active site/substrate binding portion of the surface forms the positively charged patch on the surface of the protein. (C) a C -trace of the At1g05000 hexamer viewed along its 3-fold rotational axis. (D) A stereo figure of a C -trace of a At1g05000 hexamer with two layers of trimers shown in different color families (blue and red shades). The 3-fold rotation axis and three 2-fold axes, which relate two molecules in the asymmetric units, intersect with 85.55°. The active sites of individual molecules with bound sulfates (spheres) are accessible from the top and the bottom of the hexamer.
Figure 4.
Figure 4. Phosphatase activity of At1g05000 with various substrates, metals, and pH conditions. (A) Phosphatase activity with various model substrates. p-Tyr is phosphotyrosine, PEP is phosphoenolpyruvate, and Poly-P is polyphosphate (poly-P[12-13]). (B) Metal dependence was measured with poly-P as substrate (0.14 mM) and metal concentrations were 5 mM Mg^2+, 1.0 mM Mn^2+, and 0.5 mM for other metals. (C) Phosphatase activity against poly-P with variation in pH (D) Phosphatase activity with phosphorylated peptides. The reaction contained 50 mM HEPES-K (pH 7.0), 5 mM Mg^2+, 0.5 mM peptide, and 0.6 g of At1g05000. Other experimental conditions were as described under Materials and Methods.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 73, 241-253) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21409566 C.Romá-Mateo, A.Sacristán-Reviriego, N.J.Beresford, J.A.Caparrós-Martín, F.A.Culiáñez-Macià, H.Martín, M.Molina, L.Tabernero, and R.Pulido (2011).
Phylogenetic and genetic linkage between novel atypical dual-specificity phosphatases from non-metazoan organisms.
  Mol Genet Genomics, 285, 341-354.  
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