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PDBsum entry 1rpm

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protein Protein-protein interface(s) links
Receptor PDB id
1rpm
Jmol
Contents
Protein chain
278 a.a. *
Waters ×350
* Residue conservation analysis
PDB id:
1rpm
Name: Receptor
Title: Human receptor protein tyrosine phosphatase mu, domain 1
Structure: Receptor protein tyrosine phosphatase mu. Chain: a, b. Fragment: cytosolic membrane proximal catalytic domain. Synonym: d1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.195     R-free:   0.260
Authors: K.M.V.Hoffmann,N.K.Tonks,D.Barford
Key ref:
K.M.Hoffmann et al. (1997). The crystal structure of domain 1 of receptor protein-tyrosine phosphatase mu. J Biol Chem, 272, 27505-27508. PubMed id: 9346878 DOI: 10.1074/jbc.272.44.27505
Date:
11-Sep-97     Release date:   01-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P28827  (PTPRM_HUMAN) -  Receptor-type tyrosine-protein phosphatase mu
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1452 a.a.
278 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.3.48  - 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   2 terms 
  Biochemical function     phosphatase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.272.44.27505 J Biol Chem 272:27505-27508 (1997)
PubMed id: 9346878  
 
 
The crystal structure of domain 1 of receptor protein-tyrosine phosphatase mu.
K.M.Hoffmann, N.K.Tonks, D.Barford.
 
  ABSTRACT  
 
Receptor-like protein-tyrosine phosphatases (RPTPs) play important roles in regulating intracellular processes. We have been investigating the regulation and function of RPTPmu, a receptor-like PTP related to the Ig superfamily of cell adhesion molecules. Recently, the crystal structure of a dimer of the membrane proximal domain of RPTPalpha (RPTPalpha D1) was described (Bilwes, A. M., den Hertog, J., Hunter, T., and Noel J. P. (1996) Nature 382, 555-559). Within this crystal structure, the catalytic site of each subunit of the dimer is sterically blocked by the insertion of the N-terminal helix-turn-helix segment of the dyad-related monomer. It was proposed that dimerization would lead to inhibition of catalytic activity and may provide a paradigm for the regulation of the RPTP family. We have determined the crystal structure, to 2.3 A resolution, of RPTPmu D1, which shares 46% sequence identity with that of RPTPalpha D1. Although the tertiary structures of RPTPalpha D1 and RPTPmu D1 are very similar, with a root mean square deviation between equivalent Calpha atoms of 1.1 A, the quaternary structures of these two proteins are different. Neither the catalytic site nor the N-terminal helix-turn-helix segment of RPTPmu D1 participates in protein-protein interactions. The catalytic site of RPTPmu D1 is unhindered and adopts an open conformation similar to that of the cytosolic PTP, PTP1B (Barford, D., Flint, A. J., and Tonks, N. K. (1994) Science 263, 1397-1404). We propose that dimerization-induced modulation of RPTP activity may not be a general feature of this family of enzymes.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Ribbon diagram of the receptor PTPµ D1 dimer. The molecular dyad axis is indicated by an arrow. The catalytic site^ cysteine (Cys1095), the helix-turn-helix segment ( 1 , 2 ), and the N-terminal -strand ( x) that forms a -sheet with y within RPTPs D1 are^ indicated within one subunit (left). The 8 and 10 strands participate^ in the dimer interface of RPTPµ D1. C atoms of the equivalent catalytic site residues that form the dimer interface of RPTP D1 are shown as spheres and labeled. Figure was drawn using MOLSCRIPT (22).
Figure 3.
Fig. 3. Sequence alignment of representative RPTP D1s in the regions that form the dimer interfaces of RPTP and RPTPµ. Top left, x-helix-turn-helix segment; top right, residues of the^ Tyr(P) recognition loop of the catalytic site. Bottom, residues from 8 through to the WPD loop of the catalytic site. Residues of RPTPµ D1 and RPTP D1 that form interactions at their respective^ dimer interfaces are indicated with vertical arrows (top) and^ stars (bottom), respectively. The residues that form the dimer interface of RPTPµ D1 are poorly conserved throughout the family, whereas residues of the RPTP D1 interface are poorly conserved^ within the helix-turn-helix segment, but well conserved within the catalytic site. Invariant residues are in white type on a^ black background, and highly conserved residues are boxed.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1997, 272, 27505-27508) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20197094 S.A.Oblander, and S.M.Brady-Kalnay (2010).
Distinct PTPmu-associated signaling molecules differentially regulate neurite outgrowth on E-, N-, and R-cadherin.
  Mol Cell Neurosci, 44, 78-93.  
19573017 A.E.Hower, P.J.Beltran, and J.L.Bixby (2009).
Dimerization of tyrosine phosphatase PTPRO decreases its activity and ability to inactivate TrkC.
  J Neurochem, 110, 1635-1647.  
19816407 S.H.Lim, S.K.Kwon, M.K.Lee, J.Moon, D.G.Jeong, E.Park, S.J.Kim, B.C.Park, S.C.Lee, S.E.Ryu, D.Y.Yu, B.H.Chung, E.Kim, P.K.Myung, and J.R.Lee (2009).
Synapse formation regulated by protein tyrosine phosphatase receptor T through interaction with cell adhesion molecules and Fyn.
  EMBO J, 28, 3564-3578.  
18298793 L.Tabernero, A.R.Aricescu, E.Y.Jones, and S.E.Szedlacsek (2008).
Protein tyrosine phosphatases: structure-function relationships.
  FEBS J, 275, 867-882.  
17400699 H.C.Matozo, M.A.Santos, M.de Oliveira Neto, L.Bleicher, L.M.Lima, R.Iuliano, A.Fusco, and I.Polikarpov (2007).
Low-resolution structure and fluorescence anisotropy analysis of protein tyrosine phosphatase eta catalytic domain.
  Biophys J, 92, 4424-4432.  
17276081 S.A.Oblander, S.E.Ensslen-Craig, F.M.Longo, and S.M.Brady-Kalnay (2007).
E-cadherin promotes retinal ganglion cell neurite outgrowth in a protein tyrosine phosphatase-mu-dependent manner.
  Mol Cell Neurosci, 34, 481-492.  
17546659 T.S.Girish, and B.Gopal (2007).
The crystal structure of the catalytic domain of the chick retinal neurite inhibitor-receptor protein tyrosine phosphatase CRYP-2/cPTPRO.
  Proteins, 68, 1011-1015.
PDB code: 2pi7
17139078 A.G.Evdokimov, M.Pokross, R.Walter, M.Mekel, B.Cox, C.Li, R.Bechard, F.Genbauffe, R.Andrews, C.Diven, B.Howard, V.Rastogi, J.Gray, M.Maier, and K.G.Peters (2006).
Engineering the catalytic domain of human protein tyrosine phosphatase beta for structure-based drug discovery.
  Acta Crystallogr D Biol Crystallogr, 62, 1435-1445.
PDB codes: 2hc1 2hc2 2i3r 2i3u 2i4e 2i4g 2i4h 2i5x
16456543 A.R.Aricescu, W.C.Hon, C.Siebold, W.Lu, P.A.van der Merwe, and E.Y.Jones (2006).
Molecular analysis of receptor protein tyrosine phosphatase mu-mediated cell adhesion.
  EMBO J, 25, 701-712.
PDB code: 2c9a
16672235 J.Eswaran, J.E.Debreczeni, E.Longman, A.J.Barr, and S.Knapp (2006).
The crystal structure of human receptor protein tyrosine phosphatase kappa phosphatase domain 1.
  Protein Sci, 15, 1500-1505.
PDB codes: 2a3k 2c7s
16597593 T.Takahashi, K.Takahashi, R.L.Mernaugh, N.Tsuboi, H.Liu, and T.O.Daniel (2006).
A monoclonal antibody against CD148, a receptor-like tyrosine phosphatase, inhibits endothelial-cell growth and angiogenesis.
  Blood, 108, 1234-1242.  
15743966 C.Madhurantakam, E.Rajakumara, P.A.Mazumdar, B.Saha, D.Mitra, H.G.Wiker, R.Sankaranarayanan, and A.K.Das (2005).
Crystal structure of low-molecular-weight protein tyrosine phosphatase from Mycobacterium tuberculosis at 1.9-A resolution.
  J Bacteriol, 187, 2175-2181.
PDB codes: 1u2p 1u2q
15684325 H.J.Nam, F.Poy, H.Saito, and C.A.Frederick (2005).
Structural basis for the function and regulation of the receptor protein tyrosine phosphatase CD45.
  J Exp Med, 201, 441-452.
PDB codes: 1ygr 1ygu
  16511047 T.S.Girish, and B.Gopal (2005).
Crystallization and preliminary X-ray diffraction studies on the catalytic domain of the chick retinal neurite-inhibitory factor CRYP-2.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 381-383.  
15521065 W.H.Lee, A.Raas-Rotschild, M.A.Miteva, G.Bolasco, A.Rein, D.Gillis, D.Vidaud, M.Vidaud, B.O.Villoutreix, and B.Parfait (2005).
Noonan syndrome type I with PTPN11 3 bp deletion: structure-function implications.
  Proteins, 58, 7.  
15333922 A.K.Pedersen, G.H.Peters G, K.B.Møller, L.F.Iversen, and J.S.Kastrup (2004).
Water-molecule network and active-site flexibility of apo protein tyrosine phosphatase 1B.
  Acta Crystallogr D Biol Crystallogr, 60, 1527-1534.
PDB code: 1sug
12861030 H.Toledano-Katchalski, Z.Tiran, T.Sines, G.Shani, S.Granot-Attas, J.den Hertog, and A.Elson (2003).
Dimerization in vivo and inhibition of the nonreceptor form of protein tyrosine phosphatase epsilon.
  Mol Cell Biol, 23, 5460-5471.  
11847098 C.Blanchetot, L.G.Tertoolen, and J.den Hertog (2002).
Regulation of receptor protein-tyrosine phosphatase alpha by oxidative stress.
  EMBO J, 21, 493-503.  
  11423001 J.A.Besco, A.Frostholm, M.C.Popesco, A.H.Burghes, and A.Rotter (2001).
Genomic organization and alternative splicing of the human and mouse RPTPrho genes.
  BMC Genomics, 2, 1.  
11585896 J.N.Andersen, O.H.Mortensen, G.H.Peters, P.G.Drake, L.F.Iversen, O.H.Olsen, P.G.Jansen, H.S.Andersen, N.K.Tonks, and N.P.Møller (2001).
Structural and evolutionary relationships among protein tyrosine phosphatase domains.
  Mol Cell Biol, 21, 7117-7136.  
11401727 L.G.Tertoolen, C.Blanchetot, G.Jiang, J.Overvoorde, T.W.Gadella, T.Hunter, and J.den Hertog (2001).
Dimerization of receptor protein-tyrosine phosphatase alpha in living cells.
  BMC Cell Biol, 2, 8.  
11248552 N.K.Tonks, and B.G.Neel (2001).
Combinatorial control of the specificity of protein tyrosine phosphatases.
  Curr Opin Cell Biol, 13, 182-195.  
10934323 B.K.Mueller, M.M.Ledig, and S.Wahl (2000).
The receptor tyrosine phosphatase CRYPalpha affects growth cone morphology.
  J Neurobiol, 44, 204-218.  
10913175 G.Jiang, J.den Hertog, and T.Hunter (2000).
Receptor-like protein tyrosine phosphatase alpha homodimerizes on the cell surface.
  Mol Cell Biol, 20, 5917-5929.  
10982240 H.Avraham, S.Avraham, and Y.Taniguchi (2000).
Receptor protein tyrosine phosphatases in hematopoietic cells.
  J Hematother Stem Cell Res, 9, 425-432.  
10735562 N.R.Glover, and A.S.Tracey (2000).
The phosphatase domains of LAR, CD45, and PTP1B: structural correlations with peptide-based inhibitors.
  Biochem Cell Biol, 78, 39-50.  
10684639 S.Wang, L.Tabernero, M.Zhang, E.Harms, R.L.Van Etten, and C.V.Stauffacher (2000).
Crystal structures of a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae and its complex with the substrate p-nitrophenyl phosphate.
  Biochemistry, 39, 1903-1914.
PDB codes: 1d1p 1d1q
10338209 H.J.Nam, F.Poy, N.X.Krueger, H.Saito, and C.A.Frederick (1999).
Crystal structure of the tandem phosphatase domains of RPTP LAR.
  Cell, 97, 449-457.
PDB code: 1lar
9699458 A.Stoker, and R.Dutta (1998).
Protein tyrosine phosphatases and neural development.
  Bioessays, 20, 463-472.  
9708728 A.Weiss, and J.Schlessinger (1998).
Switching signals on or off by receptor dimerization.
  Cell, 94, 277-280.  
9646865 D.Barford, A.K.Das, and M.P.Egloff (1998).
The structure and mechanism of protein phosphatases: insights into catalysis and regulation.
  Annu Rev Biophys Biomol Struct, 27, 133-164.  
9551546 D.Barford, and B.G.Neel (1998).
Revealing mechanisms for SH2 domain mediated regulation of the protein tyrosine phosphatase SHP-2.
  Structure, 6, 249-254.  
9561841 D.Van Vactor (1998).
Protein tyrosine phosphatases in the developing nervous system.
  Curr Opin Cell Biol, 10, 174-181.  
9529614 D.Van Vactor, A.M.O'Reilly, and B.G.Neel (1998).
Genetic analysis of protein tyrosine phosphatases.
  Curr Opin Genet Dev, 8, 112-126.  
9818190 J.M.Denu, and J.E.Dixon (1998).
Protein tyrosine phosphatases: mechanisms of catalysis and regulation.
  Curr Opin Chem Biol, 2, 633-641.  
9491886 P.Hof, S.Pluskey, S.Dhe-Paganon, M.J.Eck, and S.E.Shoelson (1998).
Crystal structure of the tyrosine phosphatase SHP-2.
  Cell, 92, 441-450.
PDB code: 2shp
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.