PDBsum entry 1v3a

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protein links
Hydrolase PDB id
Jmol PyMol
Protein chain
162 a.a. *
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of human prl-3, the phosphatase associated with cancer metastasis
Structure: Protein tyrosine phosphatase type iva. Chain: a. Synonym: phosphatase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 1 models
Authors: Y.H.Jeon,C.Cheong
Key ref:
K.A.Kim et al. (2004). Structure of human PRL-3, the phosphatase associated with cancer metastasis. FEBS Lett, 565, 181-187. PubMed id: 15135076 DOI: 10.1016/j.febslet.2004.03.062
30-Oct-03     Release date:   30-Oct-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O75365  (TP4A3_HUMAN) -  Protein tyrosine phosphatase type IVA 3
173 a.a.
162 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!
  Cellular component     membrane   6 terms 
  Biological process     peptidyl-tyrosine dephosphorylation   10 terms 
  Biochemical function     protein binding     7 terms  


DOI no: 10.1016/j.febslet.2004.03.062 FEBS Lett 565:181-187 (2004)
PubMed id: 15135076  
Structure of human PRL-3, the phosphatase associated with cancer metastasis.
K.A.Kim, J.S.Song, J.Jee, M.R.Sheen, C.Lee, T.G.Lee, S.Ro, J.M.Cho, W.Lee, T.Yamazaki, Y.H.Jeon, C.Cheong.
PRL-3, a novel class protein of prenylated tyrosine phosphatase, is important in cancer metastasis. Due to its high levels of expression in metastatic tumors, PRL-3 may constitute a useful marker for metastasis and might be a new therapeutic target. Here, we present the solution structure of the phosphatase domain of a human PRL-3 (residues 1-162) in phosphate-free state. The nuclear magnetic resonance (NMR) structure of PRL-3 is similar to that of other known phosphatases with minor differences in the secondary structure. But the conformation and flexibility of the loops comprising the active site differ significantly. When phosphate ions or sodium orthovanadate, which is a known inhibitor, are added to the apo PRL-3, the NMR signals from the residues in the active site appeared and could be assigned, indicating that the conformation of the residues has been stabilized.
  Selected figure(s)  
Figure 3.
Fig. 3. A comparison of three structures. (A) PRL-3, (B) PAC-1, and (C) PTEN. Residues Cys104 and Arg110 of PRL-3 are marked by filled circles. Asp72 in the general acid loop of PRL-3 and the corresponding residues in PAC-1 and PTEN are shown using a ball-and-stick model.
Figure 4.
Fig. 4. Overlapping ^1H–^15N HSQC spectra of PRL-3 obtained in the presence and absence of ligand ions. The peaks representing the free form of the protein are shown in black. (A) 0.7 mM PRL-3 with 2 mM sodium orthovanadate (brown), (B) 0.7 mM PRL-3 with 20 mM phosphate (purple). The red circled peaks are the backbone amide protons that appeared in the active site (phosphate loop).
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2004, 565, 181-187) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21478108 A.Pryczynicz, K.Guzińska-Ustymowicz, X.J.Chang, J.Kiśluk, and A.Kemona (2010).
PTP4A3 (PRL-3) expression correlate with lymphatic metastases in gastric cancer.
  Folia Histochem Cytobiol, 48, 632-636.  
21116777 M.K.Moon, Y.M.Han, Y.J.Lee, L.H.Lee, J.H.Yang, B.M.Kwon, and D.K.Kim (2010).
Inhibitory activities of anthraquinones from Rubia akane on phosphatase regenerating liver-3.
  Arch Pharm Res, 33, 1747-1751.  
19341304 A.L.Skinner, A.A.Vartia, T.D.Williams, and J.S.Laurence (2009).
Enzyme activity of phosphatase of regenerating liver is controlled by the redox environment and its C-terminal residues.
  Biochemistry, 48, 4262-4272.  
19722279 J.Song, J.K.Park, J.J.Lee, Y.S.Choi, K.S.Ryu, J.H.Kim, E.Kim, K.J.Lee, Y.H.Jeon, and E.E.Kim (2009).
Structure and interaction of ubiquitin-associated domain of human Fas-associated factor 1.
  Protein Sci, 18, 2265-2276.  
19322925 N.Dai, A.P.Lu, C.C.Shou, and J.Y.Li (2009).
Expression of phosphatase regenerating liver 3 is an independent prognostic indicator for gastric cancer.
  World J Gastroenterol, 15, 1499-1505.  
19214221 R.Song, F.Qian, Y.P.Li, X.Sheng, S.X.Cao, and Q.Xu (2009).
Phosphatase of regenerating liver-3 localizes to cyto-membrane and is required for B16F1 melanoma cell metastasis in vitro and in vivo.
  PLoS ONE, 4, e4450.  
18224294 D.C.Bessette, D.Qiu, and C.J.Pallen (2008).
PRL PTPs: mediators and markers of cancer progression.
  Cancer Metastasis Rev, 27, 231-252.  
18298792 R.Pulido, and R.Hooft van Huijsduijnen (2008).
Protein tyrosine phosphatases: dual-specificity phosphatases in health and disease.
  FEBS J, 275, 848-866.  
17934070 U.M.Fagerli, R.U.Holt, T.Holien, T.K.Vaatsveen, F.Zhan, K.W.Egeberg, B.Barlogie, A.Waage, H.Aarset, H.Y.Dai, J.D.Shaughnessy, A.Sundan, and M.Børset (2008).
Overexpression and involvement in migration by the metastasis-associated phosphatase PRL-3 in human myeloma cells.
  Blood, 111, 806-815.  
  19662225 J.M.Kneller, T.Ehlen, J.P.Matisic, D.Miller, D.Van Niekerk, W.L.Lam, M.Marra, R.Richards-Kortum, M.Follen, C.Macaulay, and S.J.Jones (2007).
Using LongSAGE to Detect Biomarkers of Cervical Cancer Potentially Amenable to Optical Contrast Agent Labelling.
  Biomark Insights, 2, 447-461.  
17235563 U.A.Miskad, S.Semba, H.Kato, Y.Matsukawa, Y.Kodama, E.Mizuuchi, N.Maeda, K.Yanagihara, and H.Yokozaki (2007).
High PRL-3 expression in human gastric cancer is a marker of metastasis and grades of malignancies: an in situ hybridization study.
  Virchows Arch, 450, 303-310.  
16195543 C.L.Gustafson, C.V.Stauffacher, K.Hallenga, and R.L.Van Etten (2005).
Solution structure of the low-molecular-weight protein tyrosine phosphatase from Tritrichomonas foetus reveals a flexible phosphate binding loop.
  Protein Sci, 14, 2515-2525.
PDB code: 1p8a
15812788 D.Shin, Y.S.Heo, K.J.Lee, C.M.Kim, J.M.Yoon, J.I.Lee, Y.L.Hyun, Y.H.Jeon, T.G.Lee, J.M.Cho, and S.Ro (2005).
Structural chemoproteomics and drug discovery.
  Biopolymers, 80, 258-263.  
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 code is shown on the right.