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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS SERINE/THREONINE PHOSPHATASE PSTP/PPP AT 1.95 A.
 
Authors :  K. E. Pullen, H. L. Ng, P. Y. Sung, M. C. Good, S. M. Smith, T. Alber, Tb Str Genomics Consortium (Tbsgc)
Date :  05 Jul 04  (Deposition) - 23 Nov 04  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Putative Bacterial Enzyme, Serine/Threonine Protein Phosphatases, Pstp/Ppp, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. E. Pullen, H. L. Ng, P. Y. Sung, M. C. Good, S. M. Smith, T. Alber
An Alternate Conformation And A Third Metal In Pstp/Ppp, Th M. Tuberculosis Pp2C-Family Ser/Thr Protein Phosphatase.
Structure V. 12 1947 2004
PubMed-ID: 15530359  |  Reference-DOI: 10.1016/J.STR.2004.09.008

(-) Compounds

Molecule 1 - PUTATIVE BACTERIAL ENZYME
    ChainsA, B
    EC Number3.1.3.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24B
    Expression System StrainBL21-CODONPLUS (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    SynonymSERINE/THREONINE PROTEIN PHOSPHATASES, PSTP/PPP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1MN6Ligand/IonMANGANESE (II) ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:38 , ASP A:191 , ASP A:229 , HOH A:705 , HOH A:726 , HOH A:831BINDING SITE FOR RESIDUE MN A 700
2AC2SOFTWAREASP A:38 , GLY A:39 , HOH A:715 , HOH A:723 , HOH A:724 , HOH A:831BINDING SITE FOR RESIDUE MN A 701
3AC3SOFTWAREASP A:118 , SER A:160 , ASP A:191 , HOH A:707 , HOH A:832BINDING SITE FOR RESIDUE MN A 702
4AC4SOFTWAREASP B:38 , GLY B:39 , HOH B:718 , HOH B:725 , HOH B:726 , HOH B:799BINDING SITE FOR RESIDUE MN B 703
5AC5SOFTWAREASP B:38 , ASP B:191 , ASP B:229 , HOH B:799 , HOH B:800 , HOH B:805BINDING SITE FOR RESIDUE MN B 704
6AC6SOFTWAREASP B:118 , SER B:160 , ASP B:191 , HOH B:720 , HOH B:798BINDING SITE FOR RESIDUE MN B 705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TXO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TXO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TXO)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPM_2PS51746 PPM-type phosphatase domain profile.PSTP_MYCTO9-238
 
  2A:9-237
B:9-237
PSTP_MYCTU9-238
 
  2A:9-237
B:9-237
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPM_2PS51746 PPM-type phosphatase domain profile.PSTP_MYCTO9-238
 
  1A:9-237
-
PSTP_MYCTU9-238
 
  1A:9-237
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPM_2PS51746 PPM-type phosphatase domain profile.PSTP_MYCTO9-238
 
  1-
B:9-237
PSTP_MYCTU9-238
 
  1-
B:9-237

(-) Exons   (0, 0)

(no "Exon" information available for 1TXO)

(-) 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:235
 aligned with PSTP_MYCTO | P9WHW4 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:235
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235     
           PSTP_MYCTO     6 LVLRYAARSDRGLVRANNEDSVYAGARLLALADGMGGHAAGEVASQLVIAALAHLDDDEPGGDLLAKLDAAVRAGNSAIAAQVEMEPDLEGMGTTLTAILFAGNRLGLVHIGDSRGYLLRDGELTQITKDDTFVQTLVDEGRITPEEAHSHPQRSLIMRALTGHEVEPTLTMREARAGDRYLLCSDGLSDPVSDETILEALQIPEVAESAHRLIELALRGGGPDNVTVVVADVVD 240
               SCOP domains d1txoa_ A: putative serine/threonine phosphatase pstp/ppp                                                                                                                                                                                   SCOP domains
               CATH domains 1txoA00 A:6-240 Phosphatase 2c; Domain 1                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.........eeeee...eeeeeeee...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.eeeeeee..eeeeeee...eeeeee..eeee.....hhhhhhhhh.....hhhhhh.................eeeeee.....eeeeehhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhh.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---PPM_2  PDB: A:9-237 UniProt: 9-238                                                                                                                                                                                                    -- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1txo A   6 LVLRYAARSDRGLVRANNEDSVYAGARLLALADGmGGHAAGEVASQLVIAALAHLDDDEPGGDLLAKLDAAVRAGNSAIAAQVEmEPDLEGmGTTLTAILFAGNRLGLVHIGDSRGYLLRDGELTQITKDDTFVQTLVDEGRITPEEAHSHPQRSLImRALTGHEVEPTLTmREARAGDRYLLCSDGLSDPVSDETILEALQIPEVAESAHRLIELALRGGGPDNVTVVVADLEH 240
                                    15        25        35    |   45        55        65        75        85    |   95 |     105       115       125       135       145       155       165       175 |     185       195       205       215       225       235     
                                                             40-MSE                                            90-MSE 97-MSE                                                           163-MSE       177-MSE                                                           

Chain A from PDB  Type:PROTEIN  Length:235
 aligned with PSTP_MYCTU | P9WHW5 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:235
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235     
           PSTP_MYCTU     6 LVLRYAARSDRGLVRANNEDSVYAGARLLALADGMGGHAAGEVASQLVIAALAHLDDDEPGGDLLAKLDAAVRAGNSAIAAQVEMEPDLEGMGTTLTAILFAGNRLGLVHIGDSRGYLLRDGELTQITKDDTFVQTLVDEGRITPEEAHSHPQRSLIMRALTGHEVEPTLTMREARAGDRYLLCSDGLSDPVSDETILEALQIPEVAESAHRLIELALRGGGPDNVTVVVADVVD 240
               SCOP domains d1txoa_ A: putative serine/threonine phosphatase pstp/ppp                                                                                                                                                                                   SCOP domains
               CATH domains 1txoA00 A:6-240 Phosphatase 2c; Domain 1                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.........eeeee...eeeeeeee...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.eeeeeee..eeeeeee...eeeeee..eeee.....hhhhhhhhh.....hhhhhh.................eeeeee.....eeeeehhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhh.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PPM_2  PDB: A:9-237 UniProt: 9-238                                                                                                                                                                                                    -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1txo A   6 LVLRYAARSDRGLVRANNEDSVYAGARLLALADGmGGHAAGEVASQLVIAALAHLDDDEPGGDLLAKLDAAVRAGNSAIAAQVEmEPDLEGmGTTLTAILFAGNRLGLVHIGDSRGYLLRDGELTQITKDDTFVQTLVDEGRITPEEAHSHPQRSLImRALTGHEVEPTLTmREARAGDRYLLCSDGLSDPVSDETILEALQIPEVAESAHRLIELALRGGGPDNVTVVVADLEH 240
                                    15        25        35    |   45        55        65        75        85    |   95 |     105       115       125       135       145       155       165       175 |     185       195       205       215       225       235     
                                                             40-MSE                                            90-MSE 97-MSE                                                           163-MSE       177-MSE                                                           

Chain B from PDB  Type:PROTEIN  Length:236
 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 d1txob_ B: putative serine/threonine phosphatase pstp/ppp                                                                                                                                                                                    SCOP domains
               CATH domains 1txoB00 B:5-240 Phosphatase 2c; Domain 1                                                                                                                                                                                                     CATH domains
           Pfam domains (1) -----------PP2C_2-1txoB01 B:16-218                                                                                                                                                                                    ---------------------- Pfam domains (1)
           Pfam domains (2) -----------PP2C_2-1txoB02 B:16-218                                                                                                                                                                                    ---------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeeeee.........eeeee...eeeeeeee...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.eeeeeee..eeeeeee...eeeeee..eeee.....hhhhhhhhh...hhhhhh...................eeeeee.....eeeeehhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhh.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----PPM_2  PDB: B:9-237 UniProt: 9-238                                                                                                                                                                                                    -- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1txo B   5 TLVLRYAARSDRGLVRANNEDSVYAGARLLALADGmGGHAAGEVASQLVIAALAHLDDDEPGGDLLAKLDAAVRAGNSAIAAQVEmEPDLEGmGTTLTAILFAGNRLGLVHIGDSRGYLLRDGELTQITKDDTFVQTLVDEGRITPEEAHSHPQRSLImRALTGHEVEPTLTmREARAGDRYLLCSDGLSDPVSDETILEALQIPEVAESAHRLIELALRGGGPDNVTVVVADLEH 240
                                    14        24        34     |  44        54        64        74        84     |  94  |    104       114       124       134       144       154       164       174  |    184       194       204       214       224       234      
                                                              40-MSE                                            90-MSE 97-MSE                                                           163-MSE       177-MSE                                                           

Chain B from PDB  Type:PROTEIN  Length:236
 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 d1txob_ B: putative serine/threonine phosphatase pstp/ppp                                                                                                                                                                                    SCOP domains
               CATH domains 1txoB00 B:5-240 Phosphatase 2c; Domain 1                                                                                                                                                                                                     CATH domains
           Pfam domains (1) -----------PP2C_2-1txoB01 B:16-218                                                                                                                                                                                    ---------------------- Pfam domains (1)
           Pfam domains (2) -----------PP2C_2-1txoB02 B:16-218                                                                                                                                                                                    ---------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeeeee.........eeeee...eeeeeeee...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.eeeeeee..eeeeeee...eeeeee..eeee.....hhhhhhhhh...hhhhhh...................eeeeee.....eeeeehhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhh.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PPM_2  PDB: B:9-237 UniProt: 9-238                                                                                                                                                                                                    -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1txo B   5 TLVLRYAARSDRGLVRANNEDSVYAGARLLALADGmGGHAAGEVASQLVIAALAHLDDDEPGGDLLAKLDAAVRAGNSAIAAQVEmEPDLEGmGTTLTAILFAGNRLGLVHIGDSRGYLLRDGELTQITKDDTFVQTLVDEGRITPEEAHSHPQRSLImRALTGHEVEPTLTmREARAGDRYLLCSDGLSDPVSDETILEALQIPEVAESAHRLIELALRGGGPDNVTVVVADLEH 240
                                    14        24        34     |  44        54        64        74        84     |  94  |    104       114       124       134       144       154       164       174  |    184       194       204       214       224       234      
                                                              40-MSE                                            90-MSE 97-MSE                                                           163-MSE       177-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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PP2C (22)

(-) Gene Ontology  (18, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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,B   (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 | P9WHW42cm1
        PSTP_MYCTU | P9WHW52cm1

(-) Related Entries Specified in the PDB File

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