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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PROTEIN TYROSINE PHOSPHATASE N4 (PTPN4)
 
Authors :  E. Ugochukwu, A. Barr, P. Savitsky, N. Burgess, S. Das, A. Turnbull, F. V M. Sundstrom, A. Edwards, C. Arrowsmith, J. Weigelt, S. Knapp, Struct Genomics Consortium (Sgc)
Date :  30 Aug 06  (Deposition) - 17 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Ptpn4, Ptp, Tyrosine Phosphatase, Meg-1, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Barr, E. Ugochukwu, W. H. Lee, O. N. King, P. Filippakopoulos, I. Alfano, P. Savitsky, N. A. Burgess-Brown, S. Muller, S. Knapp
Large-Scale Structural Analysis Of The Classical Human Protein Tyrosine Phosphatome.
Cell(Cambridge, Mass. ) V. 136 352 2009
PubMed-ID: 19167335  |  Reference-DOI: 10.1016/J.CELL.2008.11.038

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4
    Chains: A
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21 (DE3)R3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PTPN4
    Gene: PTPN4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN-TYROSINE PHOSPHATASE MEG1, PTPASE-MEG1, MEG

 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
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:853BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREARG A:664 , LYS A:665BINDING SITE FOR RESIDUE SO4 A 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I75)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I75)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I75)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTN4_HUMAN655-911  1A:655-911
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTN4_HUMAN828-902  1A:828-902
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTN4_HUMAN850-860  1A:850-860

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002637081aENSE00001202414chr2:120517207-120517960754PTN4_HUMAN-00--
1.4bENST000002637084bENSE00002161456chr2:120567413-120567567155PTN4_HUMAN1-46460--
1.5bENST000002637085bENSE00001071386chr2:120620112-120620219108PTN4_HUMAN47-82360--
1.6ENST000002637086ENSE00001071393chr2:120634899-12063494143PTN4_HUMAN83-97150--
1.7bENST000002637087bENSE00001071383chr2:120635040-12063511879PTN4_HUMAN97-123270--
1.9bENST000002637089bENSE00001071380chr2:120639362-12063940645PTN4_HUMAN123-138160--
1.10aENST0000026370810aENSE00001071395chr2:120639673-12063972553PTN4_HUMAN138-156190--
1.11bENST0000026370811bENSE00001071376chr2:120640079-120640199121PTN4_HUMAN156-196410--
1.12ENST0000026370812ENSE00001071384chr2:120643371-12064345888PTN4_HUMAN196-225300--
1.13ENST0000026370813ENSE00001730738chr2:120658294-12065838289PTN4_HUMAN226-255300--
1.14aENST0000026370814aENSE00001694309chr2:120672755-12067281864PTN4_HUMAN255-276220--
1.15ENST0000026370815ENSE00001803769chr2:120677645-120677817173PTN4_HUMAN277-334580--
1.16ENST0000026370816ENSE00001640493chr2:120684174-12068424269PTN4_HUMAN334-357240--
1.17bENST0000026370817bENSE00001645678chr2:120690000-120690125126PTN4_HUMAN357-399430--
1.18aENST0000026370818aENSE00001696851chr2:120692376-120692534159PTN4_HUMAN399-452540--
1.19ENST0000026370819ENSE00001749019chr2:120702657-120702816160PTN4_HUMAN452-505540--
1.20ENST0000026370820ENSE00001771605chr2:120703917-12070400084PTN4_HUMAN506-533280--
1.21aENST0000026370821aENSE00001594878chr2:120704094-12070415057PTN4_HUMAN534-552190--
1.22ENST0000026370822ENSE00001621051chr2:120709549-120709705157PTN4_HUMAN553-605530--
1.23ENST0000026370823ENSE00001731922chr2:120712733-120712899167PTN4_HUMAN605-660561A:638-66023
1.24ENST0000026370824ENSE00001660931chr2:120714420-12071451091PTN4_HUMAN661-691311A:661-69131
1.25ENST0000026370825ENSE00001797325chr2:120714592-12071465362PTN4_HUMAN691-711211A:691-711 (gaps)21
1.26bENST0000026370826bENSE00001751186chr2:120718383-120718529147PTN4_HUMAN712-760491A:712-760 (gaps)49
1.27ENST0000026370827ENSE00001765275chr2:120720192-120720320129PTN4_HUMAN761-803431A:761-80343
1.28ENST0000026370828ENSE00001760145chr2:120723073-120723221149PTN4_HUMAN804-853501A:804-85350
1.29bENST0000026370829bENSE00001771727chr2:120725413-120725548136PTN4_HUMAN853-898461A:853-89846
1.30cENST0000026370830cENSE00001703057chr2:120734560-1207413946835PTN4_HUMAN899-926281A:899-91315

(-) 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:273
 aligned with PTN4_HUMAN | P29074 from UniProtKB/Swiss-Prot  Length:926

    Alignment length:276
                                   647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907      
           PTN4_HUMAN   638 SLRESMIQLAEGLITGTVLTQFDQLYRKKPGMTMSCAKLPQNISKNRYRDISPYDATRVILKGNEDYINANYINMEIPSSSIINQYIACQGPLPHTCTDFWQMTWEQGSSMVVMLTTQVERGRVKCHQYWPEPTGSSSYGCYQVTCHSEEGNTAYIFRKMTLFNQEKNESRPLTQIQYIAWPDHGVPDDSSDFLDFVCHVRNKRAGKEEPVVVHCSAGIGRTGVLITMETAMCLIECNQPVYPLDIVRTMRDQRAMMIQTPSQYRFVCEAILKVYE 913
               SCOP domains d2i75a_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh................hhhhh.......hhh.eee....-.eeeeeeeeee...--.eeeeeee...hhhhhhhhhhhhhhh...eeee....ee..ee...........eeee..eeeee........eeeeeeeeee....eeeeeeeeee...........hhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------TYR_PHOSPHATASE_PTP  PDB: A:655-911 UniProt: 655-911                                                                                                                                                                                                             -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:828-902 UniProt: 828-902                         ----------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.23 [INCOMPLETE] Exon 1.24  PDB: A:661-691      --------------------Exon 1.26b  PDB: A:712-760 (gaps)                Exon 1.27  PDB: A:761-803 UniProt: 761-803 Exon 1.28  PDB: A:804-853 UniProt: 804-853        ---------------------------------------------Exon 1.30c      Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.25            ---------------------------------------------------------------------------------------------------------------------------------------------Exon 1.29b  PDB: A:853-898 UniProt: 853-898   --------------- Transcript 1 (2)
                 2i75 A 638 SLRESMIQLAEGLITGTVLTQFDQLYRKKPGMTMSCAKLPQNISKNRYRDISPYDATRVILKGN-DYINANYINMEIPS--IINQYIACQGPLPHTCTDFWQMTWEQGSSMVVMLTTQVERGRVKCHQYWPEPTGSSSYGCYQVTCHSEEGNTAYIFRKMTLFNQEKNESRPLTQIQYIAWPDHGVPDDSSDFLDFVCHVRNKRAGKEEPVVVHCSAGIGRTGVLITMETAMCLIECNQPVYPLDIVRTMRDQRAMMIQTPSQYRFVCEAILKVYE 913
                                   647       657       667       677       687       697   | | 707        |- |     727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907      
                                                                                         701 |          716  |                                                                                                                                                                                                  
                                                                                           703             719
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I75)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I75)

(-) Gene Ontology  (15, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTN4_HUMAN | P29074)
molecular function
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    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:0004726    non-membrane spanning protein tyrosine phosphatase activity    Catalysis of the reaction: non-membrane spanning protein tyrosine phosphate + H2O = non-membrane spanning protein tyrosine + phosphate.
    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.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    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: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: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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  2i75
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 Related Entries

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

UniProtKB/Swiss-Prot
        PTN4_HUMAN | P29074: 2cs5 2vph 3nfk 3nfl 5eyz 5ez0

(-) Related Entries Specified in the PDB File

2b49 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 3