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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C472S MUTANT OF HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5 (STEP, STRIATUM ENRICHED PHOSPHATASE) IN COMPLEX WITH PHOSPHOTYROSINE
 
Authors :  J. E. Debreczeni, A. J. Barr, J. Eswaran, C. Smee, N. Burgess, O. Gileadi P. Savitsky, M. Sundstrom, C. Arrowsmith, A. Edwards, J. Weigelt, S. K F. Von Delft
Date :  10 Apr 06  (Deposition) - 16 May 06  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Phosphatase, Step, Ptpn5, Hydrolase, Phosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. J. Barr, E. Ugochukwu, W. H. Lee, O. N. F. 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 - HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPLIC SGC
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorT7
    FragmentPHOSPHATASE DOMAIN, RESIDUES 258-539
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN-TYROSINE PHOSPHATASE STRIATUM-ENRICHED, STEP, NEURAL- SPECIFIC PROTEIN-TYROSINE PHOSPHATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PTR1Ligand/IonO-PHOSPHOTYROSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:304 , ILE A:307 , SER A:472 , SER A:473 , ALA A:474 , GLY A:475 , ILE A:476 , GLY A:477 , ARG A:478 , HOH A:2213BINDING SITE FOR RESIDUE PTR A1537
2AC2SOFTWAREPHE A:280 , PHE A:281 , ILE A:283 , MET A:285 , ARG A:508 , HOH A:2194BINDING SITE FOR RESIDUE EDO A1538

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:319 -Pro A:320

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTN5_HUMAN300-555  1A:276-531
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTN5_HUMAN469-546  1A:445-522
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTN5_HUMAN494-504  1A:470-480

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003585401bENSE00001333579chr11:18813389-18813072318PTN5_HUMAN-00--
1.2aENST000003585402aENSE00001399458chr11:18793618-18793486133PTN5_HUMAN1-770--
1.3ENST000003585403ENSE00001702786chr11:18787430-1878735477PTN5_HUMAN7-33270--
1.4bENST000003585404bENSE00001129124chr11:18765746-18765553194PTN5_HUMAN33-97650--
1.5bENST000003585405bENSE00000706715chr11:18764976-18764869108PTN5_HUMAN98-133360--
1.6ENST000003585406ENSE00000706722chr11:18764622-1876453984PTN5_HUMAN134-161280--
1.7ENST000003585407ENSE00000706726chr11:18764050-18763809242PTN5_HUMAN162-242810--
1.8bENST000003585408bENSE00000706728chr11:18762339-18762150190PTN5_HUMAN242-305641A:-7-28131
1.9ENST000003585409ENSE00000706730chr11:18759511-1875942785PTN5_HUMAN306-334291A:282-31029
1.10ENST0000035854010ENSE00000706732chr11:18755182-1875510380PTN5_HUMAN334-360271A:310-33627
1.11ENST0000035854011ENSE00000706737chr11:18754919-18754782138PTN5_HUMAN361-406461A:337-37539
1.12ENST0000035854012ENSE00001150710chr11:18754249-18754139111PTN5_HUMAN407-443371A:385-41935
1.13bENST0000035854013bENSE00001150704chr11:18751365-18751205161PTN5_HUMAN444-497541A:420-473 (gaps)54
1.14ENST0000035854014ENSE00001150696chr11:18751113-18751000114PTN5_HUMAN497-535391A:473-51139
1.15cENST0000035854015cENSE00001819428chr11:18750574-187494751100PTN5_HUMAN535-565311A:511-53626

(-) 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:275
 aligned with PTN5_HUMAN | P54829 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:286
                                   284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554      
           PTN5_HUMAN   275 REYLLSASRVLQAEELHEKALDPFLLQAEFFEIPMNFVDPKEYDIPGLVRKNRYKTILPNPHSRVCLTSPDPDDPLSSYINANYIRGYGGEEKVYIATQGPIVSTVADFWRMVWQEHTPIIVMITNIEEMNEKCTEYWPEEQVAYDGVEITVQKVIHTEDYRLRLISLKSGTEERGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQQEGPHCAPIIVHCSAGIGRTGCFIATSICCQQLRQEGVVDILKTTCQLRQDRGGMIQTCEQYQFVHHVMSLYEKQLS 560
               SCOP domains d2cjza_ A: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2cjzA00 A:-7-536 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhh.hhhhhhhhhh.......hhhhh...hhhhhh.......hhhh..................eeee.hhhhh...eeeee..hhhhhhhhhhhhhhhh..eeeee.---------.......eeee..eeeeeeeeee...eeeeeeeee.--.eeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------TYR_PHOSPHATASE_PTP  PDB: A:276-531 UniProt: 300-555                                                                                                                                                                                                            ----- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:445-522 UniProt: 469-546                            -------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA-------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.8b  PDB: A:-7-281       ----------------------------Exon 1.10  PDB: A:310-336  Exon 1.11  PDB: A:337-375 UniProt: 361-406    Exon 1.12  PDB: A:385-419            Exon 1.13b  PDB: A:420-473 (gaps) UniProt: 444-497    -------------------------------------Exon 1.15c  PDB: A:511-536 Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.9  PDB: A:282-310     ------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.14  PDB: A:473-511              ------------------------- Transcript 1 (2)
                 2cjz A  -7 NLYFQSMSRVLQAEELHEKALDPFLLQAEFFEIPMNFVDPKEYDIPGLVRKNRYKTILPNPHSRVCLTSPDPDDPLSSYINANYIRGYGGEEKVYIATQGPIVSTVADFWRMVWQEHTPIIVMIT---------TEYWPEEQVAYDGVEITVQKVIHTEDYRLRLISLKS--EERGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQQEGPHCAPIIVHSSAGIGRTGCFIATSICCQQLRQEGVVDILKTTCQLRQDRGGMIQTCEQYQFVHHVMSLYEKQLS 536
                                  |260       270       280       290       300       310       320       330       340       350       360       370    |    -    |  390       400       410       420  |    430       440       450       460       470       480       490       500       510       520       530      
                                 -1|                                                                                                                  375       385                                420  |                                                                                                                 
                                 258                                                                                                                                                                  423                                                                                                                 

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (35, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTN5_HUMAN | P54829)
molecular function
    GO:0035254    glutamate receptor binding    Interacting selectively and non-covalently with a glutamate receptor.
    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:0051019    mitogen-activated protein kinase binding    Interacting selectively and non-covalently with a mitogen-activated protein kinase.
    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:0001784    phosphotyrosine residue binding    Interacting selectively and non-covalently with a phosphorylated tyrosine residue within a protein.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    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:0035640    exploration behavior    The specific behavior of an organism in response to a novel environment or stimulus.
    GO:0043407    negative regulation of MAP kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:1900273    positive regulation of long-term synaptic potentiation    Any process that activates or increases the frequency, rate or extent of long-term synaptic potentiation.
    GO:1901216    positive regulation of neuron death    Any process that activates or increases the frequency, rate or extent of neuron death.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0033160    positive regulation of protein import into nucleus, translocation    Any process that activates or increases the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    GO:0002092    positive regulation of receptor internalization    Any process that activates or increases the frequency, rate or extent of receptor internalization.
    GO:2001025    positive regulation of response to drug    Any process that activates or increases the frequency, rate or extent of response to drug.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:1903492    response to acetylsalicylate    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an aspirin (acetylsalicylate) stimulus. Aspirin is a non-steroidal anti-inflammatory drug with moA cyclooxygenase inhibitor activity.
    GO:0001975    response to amphetamine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amphetamine stimulus. Amphetamines consist of a group of compounds related to alpha-methylphenethylamine.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0035902    response to immobilization stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of being rendered immobile.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    GO:1990635    proximal dendrite    That part of the dendrite closest to the cell body of the neuron.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTN5_HUMAN | P548292bij 2bv5

(-) Related Entries Specified in the PDB File

2bij CRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5 (STEP, STRIATUM ENRICHED ENRICHED PHOSPHATASE)
2bv5 CRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5 AT 1.8A RESOLUTION