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(-) Description

Title :  STRUCTURE OF THE CATALYTIC DOMAIN OF PROTEIN TYROSINE PHOSPHATASE SIGMA IN THE SULFENIC ACID FORM
 
Authors :  T. J. Jeon, P. N. Chien, H. J. Chun, S. E. Ryu
Date :  24 May 13  (Deposition) - 17 Jul 13  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Proteoglycan, Redox Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. J. Jeon, P. N. Chien, H. J. Chun, S. E. Ryu
Structure Of The Catalytic Domain Of Protein Tyrosine Phosphatase Sigma In The Sulfenic Acid Form
Mol. Cells V. 36 55 2013
PubMed-ID: 23820885  |  Reference-DOI: 10.1007/S10059-013-0033-X

(-) Compounds

Molecule 1 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET28A(+)
    Expression System Vector TypePLASMID
    FragmentCYTOPLASMIC PHOSPHATASE DOMAINS, RESIDUES 1367-1948
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymR-PTP-S, RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE SIGMA,

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CSO1Mod. Amino AcidS-HYDROXYCYSTEINE

(-) Sites  (0, 0)

(no "Site" information available for 4BPC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BPC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BPC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047277C1457RPTPRS_HUMANPolymorphism4807697AR1457R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTPRS_HUMAN1393-1648
1680-1939
  2A:1393-1648
A:1680-1939
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTPRS_HUMAN1568-1639
1857-1930
  2A:1568-1639
A:1857-1930
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTPRS_HUMAN1587-1597
1878-1888
  2A:1587-1597
A:1878-1888

(-) Exons   (0, 0)

(no "Exon" information available for 4BPC)

(-) 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:567
 aligned with PTPRS_HUMAN | Q13332 from UniProtKB/Swiss-Prot  Length:1948

    Alignment length:575
                                  1377      1387      1397      1407      1417      1427      1437      1447      1457      1467      1477      1487      1497      1507      1517      1527      1537      1547      1557      1567      1577      1587      1597      1607      1617      1627      1637      1647      1657      1667      1677      1687      1697      1707      1717      1727      1737      1747      1757      1767      1777      1787      1797      1807      1817      1827      1837      1847      1857      1867      1877      1887      1897      1907      1917      1927      1937     
         PTPRS_HUMAN   1368 LSHPPIPIADMAEHTERLKANDSLKLSQEYESIDPGQQFTWEHSNLEVNKPKNRYANVIAYDHSRVILQPIEGIMGSDYINANYVDGYRCQNAYIATQGPLPETFGDFWRMVWEQRSATIVMMTRLEEKSRIKCDQYWPNRGTETYGFIQVTLLDTIELATFCVRTFSLHKNGSSEKREVRQFQFTAWPDHGVPEYPTPFLAFLRRVKTCNPPDAGPIVVHCSAGVGRTGCFIVIDAMLERIKPEKTVDVYGHVTLMRSQRNYMVQTEDQYSFIHEALLEAVGCGNTEVPARSLYAYIQKLAQVEPGEHVTGMELEFKRLANSKAHTSRFISANLPCNKFKNRLVNIMPYESTRVCLQPIRGVEGSDYINASFIDGYRQQKAYIATQGPLAETTEDFWRMLWENNSTIVVMLTKLREMGREKCHQYWPAERSARYQYFVVDPMAEYNMPQYILREFKVTDARDGQSRTVRQFQFTDWPEQGVPKSGEGFIDFIGQVHKTKEQFGQDGPISVHCSAGVGRTGVFITLSIVLERMRYEGVVDIFQTVKMLRTQRPAMVQTEDEYQFCYQAALEYLGS 1942
               SCOP domains d4bpca1 A:1368-1688 automated matches                                                                                                                                                                                                                                                                                            --------d4bpca2 A:1697-1942 automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..hhhhhhhhhhhhhhhhhhhhhhh........hhhhhh..hhhhh.......hhh.eee...........eeeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh..eeee....ee..ee.........eeeee..eeeeeeeeee...eeeeeeeeee......eeeeeeee...........hhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhhhheehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....ee..hhhhhhhhhhh.......hhhhhhhhh..--------hhhhhhhhhhhhh............................eeee........eeee...hhhhhhhhhhhhhhh...eeee....ee..ee...........eee..eeeeeeeeee...eeeeeeeeee.....eeeeeeeee...........hhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------TYR_PHOSPHATASE_PTP  PDB: A:1393-1648 UniProt: 1393-1648                                                                                                                                                                                                        -------------------------------TYR_PHOSPHATASE_PTP  PDB: A:1680-1939 UniProt: 1680-1939                                                                                                                                                                                                            --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:1568-1639 UniProt: 1568-1639                  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:1857-1930 UniProt: 1857-1930                    ------------ PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------ PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4bpc A 1368 LSHPPIPIADMAEHTERLKANDSLKLSQEYESIDPGQQFTWEHSNLEVNKPKNRYANVIAYDHSRVILQPIEGIMGSDYINANYVDGYRRQNAYIATQGPLPETFGDFWRMVWEQRSATIVMMTRLEEKSRIKCDQYWPNRGTETYGFIQVTLLDTIELATFAVRTFSLHKNGSSEKREVRQFQFTAWPDHGVPEYPTPFLAFLRRVKTANPPDAGPIVVHcSAGVGRTGAFIVIDAMLERIKPEKTVDVYGHVTLMRSQRNYMVQTEDQYSFIHEALLEAVGAGNTEVPARSLYAYIQKLAQVEPGEHVTGMELEFKRLA--------FISANLPANKFKNRLVNIMPYESTRVALQPIRGVEGSDYINASFIDGYRQQKAYIATQGPLAETTEDFWRMLWENNSTIVVMLTKLREMGREKCHQYWPAERSARYQYFVVDPMAEYNMPQYILREFKVTDARDGQSRTVRQFQFTDWPEQGVPKSGEGFIDFIGQVHKTKEQFGQDGPISVHCSAGVGRTGVFITLSIVLERMRYEGVVDIFQTVKMLRTQRPAMVQTEDEYQFAYQAALEYLGS 1942
                                  1377      1387      1397      1407      1417      1427      1437      1447      1457      1467      1477      1487      1497      1507      1517      1527      1537      1547      1557      1567      1577      1587 |    1597      1607      1617      1627      1637      1647      1657      1667      1677      1687|     1697      1707      1717      1727      1737      1747      1757      1767      1777      1787      1797      1807      1817      1827      1837      1847      1857      1867      1877      1887      1897      1907      1917      1927      1937     
                                                                                                                                                                                                                                                      1589-CSO                                                                                           1688     1697                                                                                                                                                                                                                                                     

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BPC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BPC)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTPRS_HUMAN | Q13332)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0005001    transmembrane receptor protein tyrosine phosphatase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0021549    cerebellum development    The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
    GO:0021987    cerebral cortex development    The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0022038    corpus callosum development    The process whose specific outcome is the progression of the corpus callosum over time, from its formation to the mature structure. The corpus callosum is a thick bundle of nerve fibers comprising a commissural plate connecting the two cerebral hemispheres. It consists of contralateral axon projections that provide communication between the right and left cerebral hemispheres.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0090557    establishment of endothelial intestinal barrier    The establishment of a barrier between endothelial cell layers of the intestine to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition.
    GO:0021766    hippocampus development    The progression of the hippocampus over time from its initial formation until its mature state.
    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.
    GO:0021510    spinal cord development    The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues.
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.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTPRS_HUMAN | Q133322fh7 2yd2 2yd3 2yd9 4pbx

(-) Related Entries Specified in the PDB File

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