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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PROTEIN PHOSPHATASE 1A (PPM1A) BOUND WITH PHOSPHATE AT 1 MM OF MN2+
 
Authors :  T. Hu, L. Wang, K. Wang, H. Jiang, X. Shen
Date :  21 Jan 09  (Deposition) - 26 Jan 10  (Release) - 26 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphatase, Alternative Splicing, Hydrolase, Magnesium, Manganese, Metal-Binding, Phosphoprotein, Protein Phosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Hu, L. Wang, K. Wang, J. Chen, H. Jiang, X. Shen
Structural Basis For The Mn2+-Dependent Activation Of Human Ppm1A
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN PHOSPHATASE 1A
    ChainsA
    EC Number3.1.3.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-24A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPPM1A, PROTEIN PHOSPHATASE 2C ISOFORM ALPHA, PP2C- ALPHA, IA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:60 , ASP A:239 , ASP A:282 , HOH A:435 , HOH A:554 , HOH A:620BINDING SITE FOR RESIDUE MN A 391
2AC2SOFTWAREASP A:60 , GLY A:61 , HOH A:402 , HOH A:416 , HOH A:553 , HOH A:554BINDING SITE FOR RESIDUE MN A 392
3AC3SOFTWAREARG A:33 , HOH A:485 , HOH A:553 , HOH A:554 , HOH A:596 , HOH A:597 , HOH A:620BINDING SITE FOR RESIDUE PO4 A 393
4AC4SOFTWAREASN A:188 , ASP A:201 , TYR A:202 , LEU A:214BINDING SITE FOR RESIDUE PO4 A 394

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FXO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FXO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FXO)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPM_2PS51746 PPM-type phosphatase domain profile.PPM1A_HUMAN23-291  1A:23-291
2PPM_1PS01032 PPM-type phosphatase domain signature.PPM1A_HUMAN55-63  1A:55-63

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003950762bENSE00001871344chr14:60715986-60716395410PPM1A_HUMAN-00--
1.9fENST000003950769fENSE00001642202chr14:60749402-60750255854PPM1A_HUMAN1-2782781A:2-278277
1.10aENST0000039507610aENSE00001228994chr14:60752342-60752459118PPM1A_HUMAN279-318401A:279-31840
1.11ENST0000039507611ENSE00001094885chr14:60756524-60756632109PPM1A_HUMAN318-354371A:318-354 (gaps)37
1.12ENST0000039507612ENSE00001094888chr14:60758115-6075817258PPM1A_HUMAN354-373201A:354-36815
1.13eENST0000039507613eENSE00001818583chr14:60759171-607658056635PPM1A_HUMAN374-38290--

(-) 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:363
 aligned with PPM1A_HUMAN | P35813 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:367
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       
          PPM1A_HUMAN     2 GAFLDKPKMEKHNAQGQGNGLRYGLSSMQGWRVEMEDAHTAVIGLPSGLESWSFFAVYDGHAGSQVAKYCCEHLLDHITNNQDFKGSAGAPSVENVKNGIRTGFLEIDEHMRVMSEKKHGADRSGSTAVGVLISPQHTYFINCGDSRGLLCRNRKVHFFTQDHKPSNPLEKERIQNAGGSVMIQRVNGSLAVSRALGDFDYKCVHGKGPTEQLVSPEPEVHDIERSEEDDQFIILACDGIWDVMGNEELCDFVRSRLEVTDDLEKVCNEVVDTCLYKGSRDNMSVILICFPNAPKVSPEAVKKEAELDKYLECRVEEIIKKQGEGVPDLVHVMRTLASENIPSLPPGGELASKRNVIEAVYNRLNPY 368
               SCOP domains d3fxoa1 A:2-296 automated matches                                                                                                                                                                                                                                                                      d3fxoa2 A:297-368 automat    ed matches                                  SCOP domains
               CATH domains 3fxoA01 A:2-295 Phosphatase 2c; Domain 1                                                                                                                                                                                                                                                              3fxoA02 A:296-368 Phosphat    ase 2C; domain 2                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee..eeeeeeee.eee....eeeeeeeee...eeeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh......ee.eeeeee...eeeeeee...eeeeee..eeeee.......hhhhhhhhhhh...ee..ee.........ee.hhhh.....hhhhh......eeeeee.....eeeeeeehhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhh.----...hhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------PPM_2  PDB: A:23-291 UniProt: 23-291                                                                                                                                                                                                                                         ----------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------PPM_1    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.9f  PDB: A:2-278 UniProt: 1-278 [INCOMPLETE]                                                                                                                                                                                                                                  Exon 1.10a  PDB: A:279-318              -----------------------------------Exon 1.12       Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.11  PDB: A:318-354 (gaps)     -------------- Transcript 1 (2)
                 3fxo A   2 GAFLDKPKMEKHNAQGQGNGLRYGLSSMQGWRVEMEDAHTAVIGLPSGLESWSFFAVYDGHAGSQVAKYCCEHLLDHITNNQDFKGSAGAPSVENVKNGIRTGFLEIDEHMRVMSEKKHGADRSGSTAVGVLISPQHTYFINCGDSRGLLCRNRKVHFFTQDHKPSNPLEKERIQNAGGSVMIQRVNGSLAVSRALGDFDYKCVHGKGPTEQLVSPEPEVHDIERSEEDDQFIILACDGIWDVMGNEELCDFVRSRLEVTDDLEKVCNEVVDTCLYKGSRDNMSVILICFPNAPKVSPEAVKKEAELDKYLECRVEEIIK----GVPDLVHVMRTLASENIPSLPPGGELASKRNVIEAVYNRLNPY 368
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321    |  331       341       351       361       
                                                                                                                                                                                                                                                                                                                                                         321  326                                          

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FXO)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PPM1A_HUMAN | P35813)
molecular function
    GO:0070412    R-SMAD binding    Interacting selectively and non-covalently with a receptor-regulated SMAD signaling protein.
    GO:0033192    calmodulin-dependent protein phosphatase activity    Catalysis of the reaction: protein serine/threonine phosphate + H2O = protein serine/threonine + phosphate, dependent on the presence of calcium-bound calmodulin.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0043169    cation binding    Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge.
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004722    protein serine/threonine phosphatase activity    Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0006499    N-terminal protein myristoylation    The covalent attachment of a myristoyl group to the N-terminal amino acid residue of a protein.
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0071560    cellular response to transforming growth factor beta stimulus    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 a transforming growth factor beta stimulus.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0030514    negative regulation of BMP signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway.
    GO:0043124    negative regulation of I-kappaB kinase/NF-kappaB signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of -kappaB kinase/NF-kappaB signaling.
    GO:0042347    negative regulation of NF-kappaB import into nucleus    Any process that stops, prevents, or reduces the frequency, rate or extent of the transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0010991    negative regulation of SMAD protein complex assembly    Any process that decreases the rate, frequency, or extent of SMAD protein complex assembly. SMAD protein complex assembly is the aggregation, arrangement and bonding together of a set of components to form a protein complex that contains SMAD proteins.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0030512    negative regulation of transforming growth factor beta receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
    GO:0035970    peptidyl-threonine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-L-threonine to form peptidyl-threonine.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0030177    positive regulation of Wnt signaling pathway    Any process that activates or increases the frequency, rate or extent of Wnt signal transduction.
    GO:0046827    positive regulation of protein export from nucleus    Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPM1A_HUMAN | P358131a6q 3fxj 3fxk 3fxl 3fxm 4ra2 4raf 4rag

(-) Related Entries Specified in the PDB File

3fxj 3fxk 3fxl 3fxm