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(-) Description

Title :  STRUCTURE OF BACILLUS SUBTILIS INORGANIC PYROPHOSPHATASE
 
Authors :  I. P. Fabrichniy, L. Lehtio, A. Salminen, A. A. Baykov, R. Lahti, A. Goldman
Date :  09 Sep 04  (Deposition) - 23 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inorganic Pyrophosphatase, Ppase, Metal Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. P. Fabrichniy, L. Lehtio, A. Salminen, A. B. Zyryanov, A. A. Baykov, R. Lahti, A. Goldman
Structural Studies Of Metal Ions In Family Ii Pyrophosphatases: The Requirement For A Janus Ion
Biochemistry V. 43 14403 2004
PubMed-ID: 15533045  |  Reference-DOI: 10.1021/BI0484973
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: PYROPHOSPHATE PHOSPHO-HYDROLASE, PPASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1PG43Ligand/IonTETRAETHYLENE GLYCOL
2SO44Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:98 , LYS A:205 , ARG A:295 , LYS A:296 , HOH A:714 , HOH A:723 , HOH A:757 , HOH A:785 , HOH A:786BINDING SITE FOR RESIDUE SO4 A 701
2AC2SOFTWAREHIS B:98 , LYS B:205 , ARG B:295 , LYS B:296 , HOH B:736 , HOH B:767 , HOH B:779 , HOH B:831 , HOH B:833BINDING SITE FOR RESIDUE SO4 B 702
3AC3SOFTWAREARG A:38 , GLN A:41 , LEU A:60BINDING SITE FOR RESIDUE SO4 A 703
4AC4SOFTWAREARG B:38 , HOH B:763 , HOH B:1019 , HOH B:1029BINDING SITE FOR RESIDUE SO4 B 704
5AC5SOFTWARETYR B:23 , LYS B:27 , LEU B:30 , PHE B:32 , GLU B:93 , TYR B:110 , ASN B:130 , HOH B:850 , HOH B:984BINDING SITE FOR RESIDUE PG4 B 601
6AC6SOFTWAREMET B:1 , ASN B:33 , GLU B:168 , GLU B:171 , HOH B:874 , HOH B:964BINDING SITE FOR RESIDUE PG4 B 602
7AC7SOFTWARETYR A:23 , LYS A:27 , PHE A:32 , GLU A:93 , TYR A:110 , HOH A:866BINDING SITE FOR RESIDUE PG4 A 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WPM)

(-) Exons   (0, 0)

(no "Exon" information available for 1WPM)

(-) 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:307
 aligned with PPAC_BACSU | P37487 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:307
                                    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       
           PPAC_BACSU     2 EKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMA 308
               SCOP domains d1wpma_ A: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1wpmA01 A:2-189 inorganic pyrophosphatase (n-terminal core)                                                                                                                                 ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh.....ee.........eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhh...eeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeee....hhhhhhhh......eeee....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wpm A   2 EKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMA 308
                                    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       


Chain B from PDB  Type:PROTEIN  Length:308
 aligned with PPAC_BACSU | P37487 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
           PPAC_BACSU     1 MEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMA 308
               SCOP domains d1wpmb_ B: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1wpmB01 B:1-189 inorganic pyrophosphatase (n-terminal core)                                                                                                                                  ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.....ee.........eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhh.eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeee...hhhhhhhhh......eeee....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wpm B   1 MEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMA 308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WPM)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PPAC_BACSU | P37487)
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: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:0016462    pyrophosphatase activity    Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments.
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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  1wpm
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 Related Entries

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

UniProtKB/Swiss-Prot
        PPAC_BACSU | P37487: 1k23 1wpn 2haw 2iw4

(-) Related Entries Specified in the PDB File

1wpn N-TERMINAL CORE OF B. SUBTILIS PPASE
1wpp STREPTOCOCCUS GORDONII PPASE COMPLEXED WITH ZINC