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(-) Description

Title :  1.3A CRYSTAL STRUCTURE OF RV3628, MYCOBACTERIUM TUBERCULOSIS INORGANIC PYROPHOSPHATASE (PPASE) AT PH5.0
 
Authors :  S. Benini, K. S. Wilson
Date :  31 Mar 04  (Deposition) - 12 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Mycobacterium Tuberculosis, Structural Genomics, Inorganic Pyrophosphatase, Ppase, , Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Benini, K. S. Wilson
Mycobacterium Tuberculosis Rv3628, Yet Another Inorganic Pyrophosphatase Or A Possible Drug Target?
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INORGANIC PYROPHOSPHATASE
    Chains: A
    EC Number: 3.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PPA, RV3628, MT3730, MTCY15C10.24, MB3652
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: PYROPHOSPHATE PHOSPHO- HYDROLASE, PPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1GOL18Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:16 , GLU A:18 , ASP A:29 , ARG A:30 , HIS A:86 , TYR A:126 , LYS A:127 , HOH A:473BINDING SITE FOR RESIDUE SO4 A 304
2AC2SOFTWAREHIS A:104 , ALA A:113 , PHE A:114 , HOH A:460BINDING SITE FOR RESIDUE GOL A 301
3AC3SOFTWARETRP A:102 , HIS A:104 , HOH A:401 , HOH A:480 , HOH A:511 , HOH A:535BINDING SITE FOR RESIDUE GOL A 302
4AC4SOFTWAREPRO A:10 , GLN A:13 , VAL A:66 , PHE A:67 , HOH A:384 , HOH A:495 , HOH A:532BINDING SITE FOR RESIDUE GOL A 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPASEPS00387 Inorganic pyrophosphatase signature.IPYR_MYCTU52-58  1A:52-58
IPYR_MYCTO52-58  1A:52-58
Biological Unit 1 (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPASEPS00387 Inorganic pyrophosphatase signature.IPYR_MYCTU52-58  6A:52-58
IPYR_MYCTO52-58  6A:52-58

(-) Exons   (0, 0)

(no "Exon" information available for 1SXV)

(-) 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:160
 aligned with IPYR_MYCTO | P9WI54 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:160
                             1                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
           IPYR_MYCTO     - -MQFDVTIEIPKGQRNKYEVDHETGRVRLDRYLYTPMAYPTDYGFIEDTLGDDGDPLDALVLLPQPVFPGVLVAARPVGMFRMVDEHGGDDKVLCVPAGDPRWDHVQDIGDVPAFELDAIKHFFVHYKDLEPGKFVKAADWVDRAEAEAEVQRSVERFKA 159
               SCOP domains d1sxva_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains 1sxvA00 A:0-159 Inorganic Pyrophosphatase                                                                                                                        CATH domains
               Pfam domains ----Pyrophosphatase-1sxvA01 A:4-159                                                                                                                              Pfam domains
         Sec.struct. author ...eeeeeee.....eeeee......eeeeee.........eeeee...........eeee..........eeeeeeeeeeeeee..ee..eeeeee..hhhhh...hhhhhhhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------PPASE  ----------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sxv A   0 HMQFDVTIEIPKGQRNKYEVDHETGRVRLDRYLYTPMAYPTDYGFIEDTLGDDGDPLDALVLLPQPVFPGVLVAARPVGMFRMVDEHGGDDKVLCVPAGDPRWDHVQDIGDVPAFELDAIKHFFVHYKDLEPGKFVKAADWVDRAEAEAEVQRSVERFKA 159
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159


Chain A from PDB  Type:PROTEIN  Length:160
 aligned with IPYR_MYCTU | P9WI55 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:160
                             1                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
           IPYR_MYCTU     - -MQFDVTIEIPKGQRNKYEVDHETGRVRLDRYLYTPMAYPTDYGFIEDTLGDDGDPLDALVLLPQPVFPGVLVAARPVGMFRMVDEHGGDDKVLCVPAGDPRWDHVQDIGDVPAFELDAIKHFFVHYKDLEPGKFVKAADWVDRAEAEAEVQRSVERFKA 159
               SCOP domains d1sxva_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains 1sxvA00 A:0-159 Inorganic Pyrophosphatase                                                                                                                        CATH domains
               Pfam domains ----Pyrophosphatase-1sxvA01 A:4-159                                                                                                                              Pfam domains
         Sec.struct. author ...eeeeeee.....eeeee......eeeeee.........eeeee...........eeee..........eeeeeeeeeeeeee..ee..eeeeee..hhhhh...hhhhhhhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------PPASE  ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sxv A   0 HMQFDVTIEIPKGQRNKYEVDHETGRVRLDRYLYTPMAYPTDYGFIEDTLGDDGDPLDALVLLPQPVFPGVLVAARPVGMFRMVDEHGGDDKVLCVPAGDPRWDHVQDIGDVPAFELDAIKHFFVHYKDLEPGKFVKAADWVDRAEAEAEVQRSVERFKA 159
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Pyrophosphatase] (19)

(-) Gene Ontology  (8, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (IPYR_MYCTU | P9WI55)
molecular function
    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:0004427    inorganic diphosphatase activity    Catalysis of the reaction: diphosphate + H(2)O = H(+) + 2 phosphate.
    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.
biological process
    GO:0006796    phosphate-containing compound metabolic process    The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
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: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   (IPYR_MYCTO | P9WI54)
molecular function
    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:0004427    inorganic diphosphatase activity    Catalysis of the reaction: diphosphate + H(2)O = H(+) + 2 phosphate.
    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.
biological process
    GO:0006796    phosphate-containing compound metabolic process    The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IPYR_MYCTO | P9WI54: 1wcf 2uxs
        IPYR_MYCTU | P9WI55: 1wcf 2uxs 4z70 4z71 4z72 4z73 4z74 5kde 5kdf

(-) Related Entries Specified in the PDB File

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