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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL CORE 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 :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inorganic Pyrophosphatase, 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
    Fragment: N-TERMINAL DOMAIN
    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
1MN4Ligand/IonMANGANESE (II) ION
2SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:9 , ASP A:13 , ASP A:75 , MN A:602 , HOH A:704 , HOH A:772BINDING SITE FOR RESIDUE MN A 601
2AC2SOFTWAREASP A:15 , ASP A:75 , HIS A:97 , ASP A:149 , MN A:601 , HOH A:704BINDING SITE FOR RESIDUE MN A 602
3AC3SOFTWAREHIS B:9 , ASP B:13 , ASP B:75 , MN B:604 , HOH B:605 , HOH B:665BINDING SITE FOR RESIDUE MN B 603
4AC4SOFTWAREASP B:15 , ASP B:75 , HIS B:97 , ASP B:149 , MN B:603 , HOH B:605BINDING SITE FOR RESIDUE MN B 604
5AC5SOFTWAREGLN A:90 , VAL A:91 , THR A:105 , ALA A:106 , GLU A:107 , HOH A:717 , HOH A:802 , HOH A:813 , HOH A:881BINDING SITE FOR RESIDUE SO4 A 701
6AC6SOFTWAREGLN A:47 , GLU A:56 , SER A:57 , HOH A:722 , HOH A:899BINDING SITE FOR RESIDUE SO4 A 702
7AC7SOFTWAREARG A:38 , GLN A:41 , HOH A:746 , HOH A:806BINDING SITE FOR RESIDUE SO4 A 703

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WPN)

(-) 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:187
 aligned with PPAC_BACSU | P37487 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       
           PPAC_BACSU     2 EKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAG 188
               SCOP domains d1wpna_ A: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                        SCOP domains
               CATH domains 1wpnA00 A:2-188 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.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wpn A   2 EKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAG 188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       


Chain B from PDB  Type:PROTEIN  Length:187
 aligned with PPAC_BACSU | P37487 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       
           PPAC_BACSU     2 EKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAG 188
               SCOP domains d1wpnb_ B: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                        SCOP domains
               CATH domains 1wpnB00 B:2-188 inorganic pyrophosphatase (n-terminal core)                                                                                                                                 CATH domains
           Pfam domains (1) DHH-1wpnB03 B:2-147                                                                                                                               ---------------------------------DHHA2-1w Pfam domains (1)
           Pfam domains (2) DHH-1wpnB04 B:2-147                                                                                                                               ---------------------------------DHHA2-1w Pfam domains (2)
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.....ee.........eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wpn B   2 EKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAG 188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DHHA2] (7)
(-)
Family: DHHA2 (7)
(-)
Bacillus subtilis (2)
1aDHHA2-1wpnB01B:181-188
1bDHHA2-1wpnB02B:181-188
(-)
Clan: no clan defined [family: DHH] (7)
(-)
Family: DHH (7)
(-)
Bacillus subtilis (2)
2aDHH-1wpnB03B:2-147
2bDHH-1wpnB04B:2-147

(-) 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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  3.6.1.1
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1wpm B. SUBTILIS PPASE WITHOUT METALS
1wpp STREPTOCOCCUS GORDONII PPASE COMPLEXED WITH ZINC