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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PYRIDOXAL PHOSPHATE PHOSPHATASE WITH PLP
 
Authors :  U. A. Ramagopal, J. Freeman, M. Izuka, R. Toro, J. M. Sauder, S. K. Burley S. C. Almo, New York Sgx Research Center For Structural Genomi (Nysgxrc)
Date :  16 Mar 07  (Deposition) - 03 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Phosphatase, Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. C. Almo, J. B. Bonanno, J. M. Sauder, S. Emtage, T. P. Dilorenzo, V. Malashkevich, S. R. Wasserman, S. Swaminathan, S. Eswaramoorthy, R. Agarwal, D. Kumaran, M. Madegowda, S. Ragumani, Y. Patskovsky, J. Alvarado, U. A. Ramagopal, J. Faber-Barata, M. R. Chance, A. Sali, A. Fiser, Z. Y. Zhang, D. S. Lawrence, S. K. Burley
Structural Genomics Of Protein Phosphatases.
J. Struct. Funct. Genom. V. 8 121 2007
PubMed-ID: 18058037  |  Reference-DOI: 10.1007/S10969-007-9036-1

(-) Compounds

Molecule 1 - PYRIDOXAL PHOSPHATE PHOSPHATASE
    ChainsA
    EC Number3.1.3.74
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidBC-PSGX3(BC)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePDXP, PLP, PLPP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPLP PHOSPHATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:25 , ASP A:27 , ASP A:238 , PLP A:306 , HOH A:335 , HOH A:343BINDING SITE FOR RESIDUE CA A 305
2AC2SOFTWAREASP A:25 , CYS A:26 , ASP A:27 , SER A:58 , ASN A:59 , ASN A:60 , TYR A:150 , ASP A:179 , HIS A:182 , LYS A:213 , CA A:305 , HOH A:326 , HOH A:350BINDING SITE FOR RESIDUE PLP A 306

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:91 -A:221

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:213 -Pro A:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P69)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P69)

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002159041ENSE00000653968chr22:38054734-38055363630PLPP_HUMAN1-1921921A:1-192 (gaps)192
1.3bENST000002159043bENSE00001788029chr22:38061562-380629411380PLPP_HUMAN192-2961051A:192-294103

(-) Sequences/Alignments

Asymmetric 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:288
 aligned with PLPP_HUMAN | Q96GD0 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:295
                             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_HUMAN     - -MARCERLRGAALRDVLGRAQGVLFDCDGVLWNGERAVPGAPELLERLARAGKAALFVSNNSRRARPELALRFARLGFGGLRAEQLFSSALCAARLLRQRLPGPPDAPGAVFVLGGEGLRAELRAAGLRLAGDPSAGDGAAPRVRAVLVGYDEHFSFAKLREACAHLRDPECLLVATDRDPWHPLSDGSRTPGTGSLAAAVETASGRQALVVGKPSPYMFECITENFSIDPARTLMVGDRLETDILFGHRCGMTTVLTLTGVSRLEEAQAYLAAGQHDLVPHYYVESIADLTEGL 294
               SCOP domains d2p69a_ A: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2p69A01 A:0-87,A:213-294  [code=3.40.50.1000, no name defined]                          -----------------------------------------------------------------------------------------------------------------------------2p69A01 A:0-87,A:213-294  [code=3.40.50.1000, no name defined]                     CATH domains
               Pfam domains ----------------------Hydrolase_6-2p69A01 A:22-128                                                                               --------   ----------------------------------------------------------------------Hydrolase_like-2p69A02 A:210-290                                                 ---- Pfam domains
         Sec.struct. author .....ee.hhhhhhhhhhhh.eeee......ee..ee..hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh.....hhh.eeehhhhhhhhhhhhh....----.eeee.hhhhhhhhhhh...........---.....eeee......hhhhhhhhhhhhhh...eeee.....eee.....eeehhhhhhhhhhhhhh...ee....hhhhhhhhh.....hhh.eeeee....hhhhhhhhh..eeeee.....hhhhhhhhhhh.hhhhh..eee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -Exon 1.1  PDB: A:1-192 (gaps) UniProt: 1-192                                                                                                                                                    ------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3b  PDB: A:192-294 UniProt: 192-296 [INCOMPLETE]                                                 Transcript 1 (2)
                 2p69 A   0 SLARCERLRGAALRDVLGRAQGVLFDCDGVLWNGERAVPGAPELLERLARAGKAALFVSNNSRRARPELALRFARLGFGGLRAEQLFSSALCAARLLRQRLPGPP----AVFVLGGEGLRAELRAAGLRLAGDPSAG---APRVRAVLVGYDEHFSFAKLREACAHLRDPECLLVATDRDPWHPLSDGSRTPGTGSLAAAVETASGRQALVVGKPSPYmFECITENFSIDPARTLmVGDRLETDILFGHRCGmTTVLTLTGVSRLEEAQAYLAAGQHDLVPHYYVESIADLTEGL 294
                                     9        19        29        39        49        59        69        79        89        99    |  109       119       129      |  -|      149       159       169       179       189       199       209       219       229     | 239       249  |    259       269       279       289     
                                                                                                                                  104  109                        136 140                                                                           218-MSE          235-MSE          252-MSE                                      

   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 Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A   (PLPP_HUMAN | Q96GD0)
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: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: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_HUMAN | Q96GD02cfr 2cfs 2cft 2oyc 2p27

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2P69)