PDBsum entry 1u7p

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
164 a.a. *
WO4 ×2
_MG ×4
Waters ×416
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: X-ray crystal structure of the hypothetical phosphotyrosine phosphatase mdp-1 of the haloacid dehalogenase superfamily
Structure: Magnesium-dependent phosphatase-1. Chain: a, b, c, d. Synonym: mdp-1. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: af230273. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.90Å     R-factor:   0.190     R-free:   0.236
Authors: E.Peisach,J.D.Selengut,D.Dunaway-Mariano,K.N.Allen
Key ref:
E.Peisach et al. (2004). X-ray crystal structure of the hypothetical phosphotyrosine phosphatase MDP-1 of the haloacid dehalogenase superfamily. Biochemistry, 43, 12770-12779. PubMed id: 15461449 DOI: 10.1021/bi0490688
04-Aug-04     Release date:   19-Oct-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9D967  (MGDP1_MOUSE) -  Magnesium-dependent phosphatase 1
164 a.a.
164 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     peptidyl-tyrosine dephosphorylation   3 terms 
  Biochemical function     hydrolase activity     5 terms  


DOI no: 10.1021/bi0490688 Biochemistry 43:12770-12779 (2004)
PubMed id: 15461449  
X-ray crystal structure of the hypothetical phosphotyrosine phosphatase MDP-1 of the haloacid dehalogenase superfamily.
E.Peisach, J.D.Selengut, D.Dunaway-Mariano, K.N.Allen.
The haloacid dehalogenase (HAD) superfamily is comprised of structurally homologous enzymes that share several conserved sequence motifs (loops I-IV) in their active site. The majority of HAD members are phosphohydrolases and may be divided into three subclasses depending on domain organization. In classes I and II, a mobile "cap" domain reorients upon substrate binding, closing the active site to bulk solvent. Members of the third class lack this additional domain. Herein, we report the 1.9 A X-ray crystal structures of a member of the third subclass, magnesium-dependent phosphatase-1 (MDP-1) both in its unliganded form and with the product analogue, tungstate, bound to the active site. The secondary structure of MDP-1 is similar to that of the "core" domain of other type I and type II HAD members with the addition of a small, 28-amino acid insert that does not close down to exclude bulk solvent in the presence of ligand. In addition, the monomeric oligomeric state of MDP-1 does not allow the participation of a second subunit in the formation and solvent protection of the active site. The binding sites for the phosphate portion of the substrate and Mg(II) cofactor are also similar to those of other HAD members, with all previously observed contacts conserved. Unlike other subclass III HAD members, MDP-1 appears to be equally able to dephosphorylate phosphotyrosine and closed-ring phosphosugars. Modeling of possible substrates in the active site of MDP-1 reveals very few potential interactions with the substrate leaving group. The mapping of conserved residues in sequences of MDP-1 from different eukaryotic organisms reveals that they colocalize to a large region on the surface of the protein outside the active site. This observation combined with the modeling studies suggests that the target of MDP-1 is most likely a phosphotyrosine in an unknown protein rather than a small sugar-based substrate.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20050614 H.H.Nguyen, L.Wang, H.Huang, E.Peisach, D.Dunaway-Mariano, and K.N.Allen (2010).
Structural determinants of substrate recognition in the HAD superfamily member D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB) .
  Biochemistry, 49, 1082-1092.
PDB codes: 3l8e 3l8f 3l8g 3l8h
19889535 K.N.Allen, and D.Dunaway-Mariano (2009).
Markers of fitness in a successful enzyme superfamily.
  Curr Opin Struct Biol, 19, 658-665.  
19363079 T.J.Reilly, D.L.Chance, M.J.Calcutt, J.J.Tanner, R.L.Felts, S.C.Waller, M.T.Henzl, T.P.Mawhinney, I.K.Ganjam, and W.H.Fales (2009).
Characterization of a unique class C acid phosphatase from Clostridium perfringens.
  Appl Environ Microbiol, 75, 3745-3754.  
18986982 Z.Lu, L.Wang, D.Dunaway-Mariano, and K.N.Allen (2009).
Structure-function analysis of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphatase defines specificity elements in type C0 haloalkanoate dehalogenase family members.
  J Biol Chem, 284, 1224-1233.
PDB codes: 3e81 3e84 3e8m
17654544 E.Peisach, L.Wang, A.M.Burroughs, L.Aravind, D.Dunaway-Mariano, and K.N.Allen (2008).
The X-ray crystallographic structure and activity analysis of a Pseudomonas-specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function.
  Proteins, 70, 197-207.
PDB code: 2oda
18931414 H.Yamamoto, K.Takio, M.Sugahara, and N.Kunishima (2008).
Structure of a haloacid dehalogenase superfamily phosphatase PH1421 from Pyrococcus horikoshii OT3: oligomeric state and thermoadaptation mechanism.
  Acta Crystallogr D Biol Crystallogr, 64, 1068-1077.
PDB code: 1wr8
18058037 S.C.Almo, J.B.Bonanno, J.M.Sauder, S.Emtage, T.P.Dilorenzo, V.Malashkevich, S.R.Wasserman, S.Swaminathan, S.Eswaramoorthy, R.Agarwal, D.Kumaran, M.Madegowda, S.Ragumani, Y.Patskovsky, J.Alvarado, U.A.Ramagopal, J.Faber-Barata, M.R.Chance, A.Sali, A.Fiser, Z.Y.Zhang, D.S.Lawrence, and S.K.Burley (2007).
Structural genomics of protein phosphatases.
  J Struct Funct Genomics, 8, 121-140.
PDB codes: 1rxd 2fh7 2g59 2hcm 2hhl 2hxp 2hy3 2i0o 2i1y 2i44 2iq1 2irm 2isn 2nv5 2oyc 2p27 2p4u 2p69 2p8e 2pbn 2q5e 2qjc 2r0b
17390589 T.Schuhmann, D.Vollmar, and S.Grond (2007).
Biosynthetic origin of the methoxyl extender unit in bafilomycin and concanamycin using stereospecifically labeled precursors.
  J Antibiot (Tokyo), 60, 52-60.  
16966333 E.S.Rangarajan, A.Proteau, J.Wagner, M.N.Hung, A.Matte, and M.Cygler (2006).
Structural snapshots of Escherichia coli histidinol phosphate phosphatase along the reaction pathway.
  J Biol Chem, 281, 37930-37941.
PDB codes: 2fpr 2fps 2fpu 2fpw 2fpx
16670083 J.Fortpied, P.Maliekal, D.Vertommen, and E.Van Schaftingen (2006).
Magnesium-dependent phosphatase-1 is a protein-fructosamine-6-phosphatase potentially involved in glycation repair.
  J Biol Chem, 281, 18378-18385.  
16540464 N.R.Silvaggi, C.Zhang, Z.Lu, J.Dai, D.Dunaway-Mariano, and K.N.Allen (2006).
The X-ray crystal structures of human alpha-phosphomannomutase 1 reveal the structural basis of congenital disorder of glycosylation type 1a.
  J Biol Chem, 281, 14918-14926.
PDB codes: 2fuc 2fue
16183635 F.J.Sandoval, and S.Roje (2005).
An FMN hydrolase is fused to a riboflavin kinase homolog in plants.
  J Biol Chem, 280, 38337-38345.  
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.