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(-) Description

Title :  PRL-1 (PTP4A)
 
Authors :  Z. Y. Zhang, J. P. Sun, S. Liu, W. Q. Wang, H. Yang
Date :  20 Apr 05  (Deposition) - 11 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tyrosine Phosphatase, Prl-1, Dual Specific Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. P. Sun, W. Q. Wang, H. Yang, S. Liu, F. Liang, A. A. Fedorov, S. C. Almo, Z. Y. Zhang
Structure And Biochemical Properties Of Prl-1, A Phosphatase Implicated In Cell Growth, Differentiation, And Tumor Invasion(, )
Biochemistry V. 44 12009 2005
PubMed-ID: 16142898  |  Reference-DOI: 10.1021/BI0509191
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN TYROSINE PHOSPHATASE 4A1
    ChainsA, B
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET15B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-160
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPRL-1, PTP4A1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1X24)

(-) Sites  (0, 0)

(no "Site" information available for 1X24)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:49 -A:104
2B:49 -B:104

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X24)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X24)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.TP4A1_RAT82-148
 
  2A:82-148
B:82-148

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000162371ENSRNOE00000212269chr9:29625197-29624998200TP4A1_RAT-00--
1.2ENSRNOT000000162372ENSRNOE00000114913chr9:29622349-29621728622TP4A1_RAT1-35352A:9-35
B:9-35
27
27
1.3ENSRNOT000000162373ENSRNOE00000111519chr9:29620650-2962055893TP4A1_RAT36-66312A:36-66
B:36-66
31
31
1.4ENSRNOT000000162374ENSRNOE00000111637chr9:29620296-29620166131TP4A1_RAT67-110442A:67-110
B:67-110
44
44
1.5ENSRNOT000000162375ENSRNOE00000111754chr9:29619604-2961953075TP4A1_RAT110-135262A:110-135
B:110-135
26
26
1.6ENSRNOT000000162376ENSRNOE00000115313chr9:29618971-296176371335TP4A1_RAT135-173392A:135-160
B:135-160
26
26

(-) 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:152
 aligned with TP4A1_RAT | Q78EG7 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:152
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158  
            TP4A1_RAT     9 PVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEKEGIHVLDWPFDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRRGAFNSKQLLYLEKYRPKMRLRF 160
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1x24A00 A:9-160 Protein tyrosine phosphatase superfamily                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeee......hhhhhhhhhhhh.eeeeee.......hhhhhh...eeee..........hhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:82-148 UniProt: 82-148                   ------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:9-35      Exon 1.3  PDB: A:36-66         Exon 1.4  PDB: A:67-110 UniProt: 67-110     ------------------------Exon 1.6  PDB: A:135-160   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:110-135  ------------------------- Transcript 1 (2)
                 1x24 A   9 PVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEKEGIHVLDWPFDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRRGAFNSKQLLYLEKYRPKMRLRF 160
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158  

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with TP4A1_RAT | Q78EG7 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:152
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158  
            TP4A1_RAT     9 PVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEKEGIHVLDWPFDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRRGAFNSKQLLYLEKYRPKMRLRF 160
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1x24B00 B:9-160 Protein tyrosine phosphatase superfamily                                                                                                 CATH domains
           Pfam domains (1) ----------------DSPc-1x24B01 B:25-155                                                                                                              ----- Pfam domains (1)
           Pfam domains (2) ----------------DSPc-1x24B02 B:25-155                                                                                                              ----- Pfam domains (2)
         Sec.struct. author .eeeee..eeeeee......hhhhhhhhhhhh.eeeeee.......hhhhhh...eeee..........hhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:82-148 UniProt: 82-148                   ------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:9-35      Exon 1.3  PDB: B:36-66         Exon 1.4  PDB: B:67-110 UniProt: 67-110     ------------------------Exon 1.6  PDB: B:135-160   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------Exon 1.5  PDB: B:110-135  ------------------------- Transcript 1 (2)
                 1x24 B   9 PVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEKEGIHVLDWPFDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRRGAFNSKQLLYLEKYRPKMRLRF 160
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (0, 0)

(no "SCOP Domain" information available for 1X24)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TP4A1_RAT | Q78EG7)
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: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.
    GO:0008138    protein tyrosine/serine/threonine phosphatase activity    Catalysis of the reactions: protein serine + H2O = protein serine + phosphate; protein threonine phosphate + H2O = protein threonine + phosphate; and protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TP4A1_RAT | Q78EG71zck 1zcl 3rz2

(-) Related Entries Specified in the PDB File

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