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(-) Description

Title :  MAGNESIUM DEPENDENT PHOSPHATASE 1 (MDP-1)
 
Authors :  E. Peisach, J. D. Selengut, D. Dunaway-Mariano, K. N. Allen
Date :  04 Aug 04  (Deposition) - 26 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Had Superfamily, Phosphoryl Transfer, Phosphotyrosine Phosphatase, Aspartate Nucleophile, Enzyme Evolution, Structural Enzymology, Class Iii, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Peisach, J. D. Selengut, D. Dunaway-Mariano, K. N. Allen
X-Ray Crystal Structure Of The Hypothetical Phosphotyrosine Phosphatase Mdp-1 Of The Haloacid Dehalogenase Superfamily
Biochemistry V. 43 12770 2004
PubMed-ID: 15461449  |  Reference-DOI: 10.1021/BI0490688
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MAGNESIUM-DEPENDENT PHOSPHATASE-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AF230273
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MDP-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:24 , ARG A:38 , GLN A:43 , HOH A:249BINDING SITE FOR RESIDUE ACT A 165
2AC2SOFTWAREGLU A:50 , GLY A:98 , SER A:99BINDING SITE FOR RESIDUE ACT A 166

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U7O)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:27 -Pro A:28

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U7O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U7O)

(-) Exons   (0, 0)

(no "Exon" information available for 1U7O)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:163
 aligned with MGDP1_MOUSE | Q9D967 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   
          MGDP1_MOUSE     1 MTRLPKLAVFDLDYTLWPFWVDTHVDPPFHKSSDGTVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASRTSEIQGANQLLELFDLGKYFIQREIYPGSKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGMSLQTLTQGLETFAKAQAG 163
               SCOP domains d1u7oa_ A: Magnesium-dependent phosphatase-1, Mdp1                                                                                                                  SCOP domains
               CATH domains 1u7oA00 A:1-163  [code=3.40.50.1000, no name defined]                                                                                                               CATH domains
               Pfam domains --Acid_PPase-1u7oA01 A:3-160                                                                                                                                    --- Pfam domains
         Sec.struct. author ......eeee..................eee.....eee....ee....hhhhhhhhhhhh...eeeee...hhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u7o A   1 MTRLPKLAVFDLDYTLWPFWVDTHVDPPFHKSSDGTVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASRTSEIQGANQLLELFDLGKYFIQREIYPGSKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGMSLQTLTQGLETFAKAQAG 163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MGDP1_MOUSE | Q9D967)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0030389    fructosamine metabolic process    The chemical reactions and pathways involving fructosamine, a fructose molecule containing an amino group in place of a hydroxyl group.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 Related Entries

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        MGDP1_MOUSE | Q9D967: 1u7p

(-) Related Entries Specified in the PDB File

1u7p STRUCTURE OF MDP-1 WITH TUNGSTATE BOUND