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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF SERINE THREONINE PROTEIN PHOSPHATASE PSTP IN COMPLEX WITH 2 MANGANESE IONS.
 
Authors :  A. Wehenkel, A. Villarino, M. Bellinzoni, P. M. Alzari
Date :  03 May 06  (Deposition) - 12 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Ser/Thr Protein Phosphatase Pstp, Hydrolase Hypothetical Protein, Mycobacterium Tuberculosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Wehenkel, M. Bellinzoni, F. Schaeffer, A. Villarino, P. M. Alzari
Structural And Binding Studies Of The Three-Metal Center In Two Mycobacterial Ppm Ser/Thr Protein Phosphatases.
J. Mol. Biol. V. 374 890 2007
PubMed-ID: 17961594  |  Reference-DOI: 10.1016/J.JMB.2007.09.076

(-) Compounds

Molecule 1 - SERINE THREONINE PROTEIN PHOSPHATASE PSTP
    ChainsA
    EC Number3.1.3.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentCATALYTIC DOMAIN, RESIDUES 1-240
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid83332
    Other Details2 MANGANESE IONS BOUND IN THE ACTIVE SITE
    StrainH37RV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:38 , ASP A:191 , ASP A:229 , HOH A:2136 , HOH A:2137 , HOH A:2138BINDING SITE FOR RESIDUE MN A 301
2AC2SOFTWAREASP A:38 , GLY A:39 , HOH A:2136 , HOH A:2139 , HOH A:2140 , HOH A:2141BINDING SITE FOR RESIDUE MN A 302
3AC3SOFTWAREASP A:15 , GLY A:17 , PHE A:138 , THR A:141 , ARG A:164 , HOH A:2142 , HOH A:2143BINDING SITE FOR RESIDUE GOL A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CM1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:65 -Gly A:66

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CM1)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPM_2PS51746 PPM-type phosphatase domain profile.PSTP_MYCTO9-238  1A:9-238
PSTP_MYCTU9-238  1A:9-238

(-) Exons   (0, 0)

(no "Exon" information available for 2CM1)

(-) 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:230
 aligned with PSTP_MYCTO | P9WHW4 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:236
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      
           PSTP_MYCTO     5 TLVLRYAARSDRGLVRANNEDSVYAGARLLALADGMGGHAAGEVASQLVIAALAHLDDDEPGGDLLAKLDAAVRAGNSAIAAQVEMEPDLEGMGTTLTAILFAGNRLGLVHIGDSRGYLLRDGELTQITKDDTFVQTLVDEGRITPEEAHSHPQRSLIMRALTGHEVEPTLTMREARAGDRYLLCSDGLSDPVSDETILEALQIPEVAESAHRLIELALRGGGPDNVTVVVADVVD 240
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2cm1A00 A:5-240 Phosphatase 2c; Domain 1                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.........eeeee...eeeeeeee....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.eeeeeee..eeeeeee...eeeeee..eeee.....hhhhhhhhh.........------.............eeeeee.....eeeeehhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhh.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PPM_2  PDB: A:9-238 UniProt: 9-238                                                                                                                                                                                                    -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cm1 A   5 TLVLRYAARSDRGLVRANNEDSVYAGARLLALADGMGGHAAGEVASQLVIAALAHLDDDEPGGDLLAKLDAAVRAGNSAIAAQVEMEPDLEGMGTTLTAILFAGNRLGLVHIGDSRGYLLRDGELTQITKDDTFVQTLVDEGRITPEEAH------LIMRALTGHEVEPTLTMREARAGDRYLLCSDGLSDPVSDETILEALQIPEVAESAHRLIELALRGGGPDNVTVVVADVVD 240
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154      |164       174       184       194       204       214       224       234      
                                                                                                                                                                               154    161                                                                               

Chain A from PDB  Type:PROTEIN  Length:230
 aligned with PSTP_MYCTU | P9WHW5 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:236
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      
           PSTP_MYCTU     5 TLVLRYAARSDRGLVRANNEDSVYAGARLLALADGMGGHAAGEVASQLVIAALAHLDDDEPGGDLLAKLDAAVRAGNSAIAAQVEMEPDLEGMGTTLTAILFAGNRLGLVHIGDSRGYLLRDGELTQITKDDTFVQTLVDEGRITPEEAHSHPQRSLIMRALTGHEVEPTLTMREARAGDRYLLCSDGLSDPVSDETILEALQIPEVAESAHRLIELALRGGGPDNVTVVVADVVD 240
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2cm1A00 A:5-240 Phosphatase 2c; Domain 1                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.........eeeee...eeeeeeee....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.eeeeeee..eeeeeee...eeeeee..eeee.....hhhhhhhhh.........------.............eeeeee.....eeeeehhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhh.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----PPM_2  PDB: A:9-238 UniProt: 9-238                                                                                                                                                                                                    -- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cm1 A   5 TLVLRYAARSDRGLVRANNEDSVYAGARLLALADGMGGHAAGEVASQLVIAALAHLDDDEPGGDLLAKLDAAVRAGNSAIAAQVEMEPDLEGMGTTLTAILFAGNRLGLVHIGDSRGYLLRDGELTQITKDDTFVQTLVDEGRITPEEAH------LIMRALTGHEVEPTLTMREARAGDRYLLCSDGLSDPVSDETILEALQIPEVAESAHRLIELALRGGGPDNVTVVVADVVD 240
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154      |164       174       184       194       204       214       224       234      
                                                                                                                                                                               154    161                                                                               

   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  (0, 0)

(no "SCOP Domain" information available for 2CM1)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CM1)

(-) Gene Ontology  (18, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PSTP_MYCTO | P9WHW4)
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: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: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: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.
cellular component
    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: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.

Chain A   (PSTP_MYCTU | P9WHW5)
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: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:0004647    phosphoserine phosphatase activity    Catalysis of the reaction: L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate.
    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:0043392    negative regulation of DNA binding    Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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:0005887    integral component of plasma membrane    The component of the plasma 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: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.

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 Related Entries

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

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        PSTP_MYCTO | P9WHW41txo
        PSTP_MYCTU | P9WHW51txo

(-) Related Entries Specified in the PDB File

1txo CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS SERINE/THREONINE PHOSPHATASE PSTP/ PPP AT 1.95 A.