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(-) Description

Title :  CRYSTAL STRUCTURE OF MURINE CHRONOPHIN (PYRIDOXAL PHOSPHATE PHOSPHATASE) IN COMPLEX WITH BERYLLIUM TRIFLUORIDE
 
Authors :  G. Knobloch, A. Gohla, H. Schindelin
Date :  08 Jul 13  (Deposition) - 25 Dec 13  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Pdxp, Had Phosphatase, Had-Like Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Kestler, G. Knobloch, I. Tessmer, E. Jeanclos, H. Schindelin, A. Gohla
Chronophin Dimerization Is Required For Proper Positioning Of Its Substrate Specificity Loop.
J. Biol. Chem. V. 289 3094 2014
PubMed-ID: 24338687  |  Reference-DOI: 10.1074/JBC.M113.536482

(-) Compounds

Molecule 1 - PYRIDOXAL PHOSPHATE PHOSPHATASE
    ChainsA, B
    EC Number3.1.3.74, 3.1.3.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM-11
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymPLP PHOSPHATASE, CHRONOPHIN, PLPP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1BEF2Ligand/IonBERYLLIUM TRIFLUORIDE ION
2GOL3Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:25 , CYS A:26 , ASP A:27 , SER A:58 , ASN A:59 , LYS A:209 , MG A:301 , HOH A:2006 , HOH A:2007BINDING SITE FOR RESIDUE BEF A 302
2AC2SOFTWAREASP B:25 , CYS B:26 , ASP B:27 , SER B:58 , ASN B:59 , LYS B:209 , MG B:301 , HOH B:2003 , HOH B:2004 , HOH B:2065BINDING SITE FOR RESIDUE BEF B 302
3AC3SOFTWAREASN B:59 , ASN B:60 , SER B:61 , ARG B:62 , TYR B:146 , HIS B:178 , HOH B:2008 , HOH B:2015 , HOH B:2016 , HOH B:2060BINDING SITE FOR RESIDUE GOL B1000
4AC4SOFTWAREASN A:60 , SER A:61 , ARG A:62 , TYR A:146 , HIS A:178 , HOH A:2024BINDING SITE FOR RESIDUE GOL A1000
5AC5SOFTWAREASP A:27 , TRP A:31 , ASN A:60 , ARG A:63 , ARG A:71 , HOH A:2013BINDING SITE FOR RESIDUE GOL A1001
6AC6SOFTWAREASP A:25 , ASP A:27 , ASP A:234 , BEF A:302 , HOH A:2006 , HOH A:2007BINDING SITE FOR RESIDUE MG A 301
7AC7SOFTWAREASP B:25 , ASP B:27 , ASP B:234 , BEF B:302 , HOH B:2003 , HOH B:2004BINDING SITE FOR RESIDUE MG B 301

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:91 -A:217
2B:91 -B:217

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:209 -Pro A:210
2Lys B:209 -Pro B:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BX2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BX2)

(-) Exons   (0, 0)

(no "Exon" information available for 4BX2)

(-) 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:292
 aligned with PLPP_MOUSE | P60487 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:292
                             1                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  
           PLPP_MOUSE     - -MARCERLRGAALRDVLGQAQGVLFDCDGVLWNGERIVPGAPELLQRLARAGKNTLFVSNNSRRARPELALRFARLGFAGLRAEQLFSSALCAARLLRQRLSGPPDASGAVFVLGGEGLRAELRAAGLRLAGDPGEDPRVRAVLVGYDEQFSFSRLTEACAHLRDPDCLLVATDRDPWHPLSDGSRTPGTGSLAAAVETASGRQALVVGKPSPYMFQCITEDFSVDPARTLMVGDRLETDILFGHRCGMTTVLTLTGVSSLEEAQAYLTAGQRDLVPHYYVESIADLMEGLE 291
               SCOP domains d4bx2a_ A: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhhhhhhhhhh.eeeee.....ee..ee..hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhh....hhh.eeehhhhhhhhhhhhh........eeeee.hhhhhhhhhhh..ee.........eeeeee......hhhhhhhhhhhhh....eeee.....eee.....eeehhhhhhhhhhhhhh...ee.....hhhhhhhhhhh..hhh.eeeee....hhhhhhhhhh.eeeee.....hhhhhhhhhhh.hhhhh..eee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bx2 A   0 GMARCERLRGAALRDVLGQAQGVLFDCDGVLWNGERIVPGAPELLQRLARAGKNTLFVSNNSRRARPELALRFARLGFAGLRAEQLFSSALCAARLLRQRLPGPPDASGAVFVLGGEGLRAELRAAGLRLAGDPGEDPRVRAVLVGYDEQFSFSRLTEACAHLRDPDCLLVATDRDPWHPLSDGSRTPGTGSLAAAVETASGRQALVVGKPSPYMFQCITEDFSVDPARTLMVGDRLETDILFGHRCGMTTVLTLTGVSSLEEAQAYLTAGQRDLVPHYYVESIADLMEGLE 291
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  

Chain B from PDB  Type:PROTEIN  Length:290
 aligned with PLPP_MOUSE | P60487 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:290
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
           PLPP_MOUSE     1 MARCERLRGAALRDVLGQAQGVLFDCDGVLWNGERIVPGAPELLQRLARAGKNTLFVSNNSRRARPELALRFARLGFAGLRAEQLFSSALCAARLLRQRLSGPPDASGAVFVLGGEGLRAELRAAGLRLAGDPGEDPRVRAVLVGYDEQFSFSRLTEACAHLRDPDCLLVATDRDPWHPLSDGSRTPGTGSLAAAVETASGRQALVVGKPSPYMFQCITEDFSVDPARTLMVGDRLETDILFGHRCGMTTVLTLTGVSSLEEAQAYLTAGQRDLVPHYYVESIADLMEGL 290
               SCOP domains d4bx2b_ B: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhhhhhhhhh.eeee......ee..ee..hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhh....hhh.eeehhhhhhhhhhhhh........eeeee.hhhhhhhhhhh..ee.........eeeeee......hhhhhhhhhhhhhh...eeee.....eee.....eeehhhhhhhhhhhhhh...ee.....hhhhhhhhh....hhh.eeeee....hhhhhhhhhh.eeeee.....hhhhhhhhhhh.hhhhh..eee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bx2 B   1 MARCERLRGAALRDVLGQAQGVLFDCDGVLWNGERIVPGAPELLQRLARAGKNTLFVSNNSRRARPELALRFARLGFAGLRAEQLFSSALCAARLLRQRLPGPPDASGAVFVLGGEGLRAELRAAGLRLAGDPGEDPRVRAVLVGYDEQFSFSRLTEACAHLRDPDCLLVATDRDPWHPLSDGSRTPGTGSLAAAVETASGRQALVVGKPSPYMFQCITEDFSVDPARTLMVGDRLETDILFGHRCGMTTVLTLTGVSSLEEAQAYLTAGQRDLVPHYYVESIADLMEGL 290
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290

   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 4BX2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BX2)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PLPP_MOUSE | P60487)
molecular function
    GO:0031072    heat shock protein binding    Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0004647    phosphoserine phosphatase activity    Catalysis of the reaction: L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0033883    pyridoxal phosphatase activity    Catalysis of the reaction: pyridoxal 5'-phosphate + H2O = pyridoxal + phosphate.
biological process
    GO:0031247    actin rod assembly    The assembly of actin rods, a cellular structure consisting of parallel, hexagonally arranged actin tubules.
    GO:0071318    cellular response to ATP    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ATP (adenosine 5'-triphosphate) stimulus.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0030836    positive regulation of actin filament depolymerization    Any process that activates or increases the frequency, rate or extent of actin depolymerization.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0032361    pyridoxal phosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
    GO:0032465    regulation of cytokinesis    Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.
    GO:0007088    regulation of mitotic nuclear division    Any process that modulates the frequency, rate or extent of mitosis.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0032154    cleavage furrow    The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
    GO:0070938    contractile ring    A cytoskeletal structure composed of filamentous protein that forms beneath the membrane of many cells or organelles, in the plane of cell or organelle division. Ring contraction is associated with centripetal growth of the membrane that divides the cytoplasm of the two daughter cells or organelles.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0031258    lamellipodium membrane    The portion of the plasma membrane surrounding a lamellipodium.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    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:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PLPP_MOUSE | P604874bkm 4bx0 4bx3 5aes

(-) Related Entries Specified in the PDB File

4bx0 CRYSTAL STRUCTURE OF A MONOMERIC VARIANT OF MURINE CHRONOPHIN (PYRIDOXAL PHOSPHATE PHOSPHATASE)
4bx3 CRYSTAL STRUCTURE OF MURINE CHRONOPHIN (PYRIDOXAL PHOSPHATE PHOSPHATASE)