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PDBsum entry 1xww

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Hydrolase PDB id
1xww
Jmol
Contents
Protein chain
157 a.a. *
Ligands
SO4
GOL
Waters ×139
* Residue conservation analysis
PDB id:
1xww
Name: Hydrolase
Title: Crystal structure of human b-form low molecular weight phosp phosphatase at 1.6 angstrom resolution
Structure: Low molecular weight phosphotyrosine protein phos chain: a. Synonym: lmw-ptp, low molecular weight cytosolic acid phosp red cell acid phosphatase 1, ptpase, adipocyte acid phospha engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: acp1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.63Å     R-factor:   0.164     R-free:   0.216
Authors: C.V.Stauffacher,A.P.R.Zabell
Key ref:
A.P.Zabell et al. (2006). Crystal structure of the human B-form low molecular weight phosphotyrosyl phosphatase at 1.6-A resolution. J Biol Chem, 281, 6520-6527. PubMed id: 16253994 DOI: 10.1074/jbc.M506285200
Date:
02-Nov-04     Release date:   01-Nov-05    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24666  (PPAC_HUMAN) -  Low molecular weight phosphotyrosine protein phosphatase
Seq:
Struc:
158 a.a.
157 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 20 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: E.C.3.1.3.2  - Acid phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A phosphate monoester + H2O = an alcohol + phosphate
phosphate monoester
+ H(2)O
= alcohol
+ phosphate
   Enzyme class 3: 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
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     peptidyl-tyrosine dephosphorylation   2 terms 
  Biochemical function     protein binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M506285200 J Biol Chem 281:6520-6527 (2006)
PubMed id: 16253994  
 
 
Crystal structure of the human B-form low molecular weight phosphotyrosyl phosphatase at 1.6-A resolution.
A.P.Zabell, A.D.Schroff, B.E.Bain, R.L.Van Etten, O.Wiest, C.V.Stauffacher.
 
  ABSTRACT  
 
The crystal structure of HPTP-B, a human isoenzyme of the low molecular weight phosphotyrosyl phosphatase (LMW PTPase) is reported here at a resolution of 1.6 A. This high resolution structure of the second human LMW PTPase isoenzyme provides the opportunity to examine the structural basis of different substrate and inhibitor/activator responses. The crystal packing of HPTP-B positions a normally surface-exposed arginine in a position equivalent to the tyrosyl substrate. A comparison of all deposited crystallographic coordinates of these PTPases reveals three atomic positions within the active site cavity occupied by hydrogen bond donor or acceptor atoms on bound molecules, suggesting useful design elements for synthetic inhibitors. A selection of inhibitor and activator molecules as well as small molecule and peptide substrates were tested against each human isoenzyme. These results along with the crystal packing seen in HPTP-B suggest relevant sequence elements in the currently unknown target sequence.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Ribbon model of HPTP-B colored by secondary structure. The active site P-loop is highlighted with a thick cyan ribbon, and the variable region between the isoenzymes is colored blue. All molecular figures were produced using PyMol (46) and Bobscript (47).
Figure 2.
FIGURE 2. Detail views of selected regions of the HPTP-B crystal structure. Electron density is from the final 2F[o] - F[c] map contoured at 1.5 . Hydrogen bonds, defined with an interatomic distance less than 3.5 Å, are shown as dotted lines. Symmetry related molecules, when present, are colored with green bonds and labeled in italic. A, hydrogen bond network between P-loop residues 13–18 and a bound sulfate at the base of the active site. B, intercalation of Arg^101 from a symmetry-related monomer, showing the hydrogen bonding network involving the catalytic residues Cys^12, Arg^18, Asp^129, and the bound sulfate group. C, cation- stacking between Tyr^131 and Tyr^132 with the symmetry-related Arg^101 and Lys^102. Stacking is shown with the gray disks, and the sulfate is included as a reference to the previous panel. D, conserved hydrogen-bonding positions among the various crystal structures for LMW PTPases. HPTP-B is drawn as a ball-and-stick model. The HPTP-A, bovine, and yeast crystal structures are shown as sticks along with the bound MES (blue), crystallographically related tyrosine (green), and adenine (magenta) from each respective structure. The three conserved positions for bound substrate moieties are circled in red and connected by a yellow bar to either a hydrogen bond donor or acceptor atom on the enzyme; in HPTP-B these positions are filled with N -1 and N -2 of a crystallographic copy of Arg^101 and a water molecule.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 6520-6527) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19678837 J.Blobel, P.Bernadó, H.Xu, C.Jin, and M.Pons (2009).
Weak oligomerization of low-molecular-weight protein tyrosine phosphatase is conserved from mammals to bacteria.
  FEBS J, 276, 4346-4357.  
19288492 R.Maccari, R.Ottanà, R.Ciurleo, P.Paoli, G.Manao, G.Camici, C.Laggner, and T.Langer (2009).
Structure-based optimization of benzoic acids as inhibitors of protein tyrosine phosphatase 1B and low molecular weight protein tyrosine phosphatase.
  ChemMedChem, 4, 957-962.  
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.