Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THE CYANOBACTERIAL PP2C-LIKE PHOSPHATASE TPPHA REQUIRES THREE METALS IN THE CATALYTIC CENTER FOR EFFICIENT CATALYSIS
 
Authors :  C. Schlicker, S. Jiyong, K. Forchhammer
Date :  01 Dec 10  (Deposition) - 09 Feb 11  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Pp2C Family Phosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Su, C. Schlicker, K. Forchhammer
A Third Metal Is Required For Catalytic Activity Of The Signal-Transducing Protein Phosphatase M Tppha.
J. Biol. Chem. V. 286 13481 2011
PubMed-ID: 21310952  |  Reference-DOI: 10.1074/JBC.M109.036467

(-) Compounds

Molecule 1 - PROTEIN SERIN-THREONIN PHOSPHATASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
    Organism Taxid: 32046

 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
1CA2Ligand/IonCALCIUM ION
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:34 , GLY A:35 , HOH A:2018 , HOH A:2034 , HOH A:2037 , HOH A:2108 , HOH A:2110BINDING SITE FOR RESIDUE CA A1241
2AC2SOFTWAREASP A:34 , ASP A:193 , ASP A:231 , HOH A:2085 , HOH A:2108 , HOH A:2111BINDING SITE FOR RESIDUE CA A1242
3AC3SOFTWAREGLU A:183 , HOH A:2030 , HOH A:2032BINDING SITE FOR RESIDUE MG A1243
4AC4SOFTWAREGLU A:198 , HIS A:227 , HOH A:2092 , HOH A:2093BINDING SITE FOR RESIDUE MG A1244

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y09)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y09)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y09)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y09)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y09)

(-) 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:236
 aligned with Q8DGS1_THEEB | Q8DGS1 from UniProtKB/TrEMBL  Length:240

    Alignment length:240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
         Q8DGS1_THEEB     1 MDVAGLTDCGLIRKSNQDAFYIDEKHQRFFIVADGMGGHAGGEEASRLAVDHIRQYLETHLEDLQHDPVTLLRQAFLAANHAIVEQQRQNSARADMGTTAVVILLDEKGDRAWCAHVGDSRIYRWRKDQLQQITSDHTWIAQAVQLGSLTIEQARQHPWRHVLSQCLGREDLSQIDIQPIDLEPGDRLLLCSDGLTEELTDDVISIYLSEPNVQKAAAALVDAAKTHGGRDNVTVVVISV 240
               SCOP domains d2y09a_ A: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------PP2C_2-2y09A01 A:12-234                                                                                                                                                                                                        ------ Pfam domains
         Sec.struct. author .eeeeeee.........eeeee......eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.eeeeee.....eeeeeee...eeeeee..eeee.....hhhhhhhhh...----......................eeeeee.....eeeeehhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y09 A   1 MDVAGLTDCGLIRKSNQDAFYIDEKHQRFFIVADGMGGHAGGEEASRLAVDHIRQYLETHLEDLQHDPVTLLRQAFLAANHAIVEQQRQNSARADMGTTAVVILLDEKGDRAWCAHVGASRIYRWRKDQLQQITSDHTWIAQAVQLGSL----ARQHPWRHVLSQCLGREDLSQIDIQPIDLEPGDRLLLCSDGLTEELTDDVISIYLSEPNVQKAAAALVDAAKTHGGRDNVTVVVISV 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        |-   |   160       170       180       190       200       210       220       230       240
                                                                                                                                                                              149  154
   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) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y09)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PP2C (22)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8DGS1_THEEB | Q8DGS1)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2y09)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2y09
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8DGS1_THEEB | Q8DGS1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q8DGS1_THEEB | Q8DGS1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8DGS1_THEEB | Q8DGS1: 2j82 2j86 2xzv 5d2u 5iti

(-) Related Entries Specified in the PDB File

2j82 STRUCTURAL ANALYSIS OF THE PP2C FAMILY PHOSPHATASE TPPHA FROM THERMOSYNECHOCOCCUS ELONGATUS
2j86 STRUCTURAL ANALYSIS OF THE PP2C FAMILY PHOSPHATASE TPPHA OF THERMOSYNECHOCOCCUS ELONGATUS
2xzv THE CYANOBACTERIAL PP2C-LIKE PHOSPHATASE TPPHA REQUIRES THREE METALS IN THE CATALYTIC CENTER FOR EFFICIENT CATALYSIS