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(-) Description

Title :  STRUCTURE OF STREPTOCOCCUS GORDONII INORGANIC PYROPHOSPHATASE
 
Authors :  I. P. Fabrichniy, L. Lehtio, A. Salminen, A. A. Baykov, R. Lahti, A. Gold
Date :  09 Sep 04  (Deposition) - 23 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inorganic Pyrophosphatase, Metal Binding, Inhibition, 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

(-) Compounds

Molecule 1 - PROBABLE MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: C43(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOCOCCUS GORDONII
    Organism Taxid: 29390
    Strain: STR. CHALLIS
    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  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2SO46Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:9 , ASP A:13 , ASP A:77 , ZN A:602 , HOH A:807 , HOH A:852BINDING SITE FOR RESIDUE ZN A 601
02AC2SOFTWAREASP A:15 , ASP A:77 , HIS A:99 , ASP A:151 , ZN A:601 , HOH A:807BINDING SITE FOR RESIDUE ZN A 602
03AC3SOFTWAREHIS B:9 , ASP B:13 , ASP B:77 , ZN B:604 , HOH B:902 , HOH B:1007BINDING SITE FOR RESIDUE ZN B 603
04AC4SOFTWAREASP B:15 , ASP B:77 , HIS B:99 , ASP B:151 , ZN B:603 , HOH B:902BINDING SITE FOR RESIDUE ZN B 604
05AC5SOFTWAREARG A:297 , LYS A:298 , HOH A:816 , HOH A:854 , HOH A:1003 , HOH A:1067BINDING SITE FOR RESIDUE SO4 A 801
06AC6SOFTWAREARG B:297 , LYS B:298 , HOH B:945 , HOH B:979BINDING SITE FOR RESIDUE SO4 B 802
07AC7SOFTWAREGLU A:92 , VAL A:93 , THR A:107 , ALA A:108 , SER A:109 , HOH A:819 , HOH A:830 , HOH A:1001BINDING SITE FOR RESIDUE SO4 A 803
08AC8SOFTWAREGLU B:92 , VAL B:93 , THR B:107 , ALA B:108 , SER B:109 , HOH B:906 , HOH B:943 , HOH B:1006 , HOH B:1112BINDING SITE FOR RESIDUE SO4 B 804
09AC9SOFTWAREGLN B:82 , GLN B:83 , LYS B:207 , HOH B:1049BINDING SITE FOR RESIDUE SO4 B 805
10BC1SOFTWAREGLN A:82 , GLN A:83 , LYS A:207 , HOH A:987 , HOH A:995BINDING SITE FOR RESIDUE SO4 A 806
11BC2SOFTWAREARG B:101 , LYS B:298BINDING SITE FOR RESIDUE CL B 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WPP)

(-) 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:310
 aligned with PPAC_STRGC | P95765 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    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       311
           PPAC_STRGC     2 SKILVFGHQNPDSDAIGSSYAFAYLAREAYGLDTEAVALGEPNEETAFVLDYFGVAAPRVITSAKAEGAEQVILTDHNEFQQSVADIAEVEVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKEHSVAVSKEIAGLMLSGLISDTLLLKSPTTHPTDKAIAPELAELAGVNLEEYGLAMLKAGTNLASKSAEELIDIDAKTFELNGNNVRVAQVNTVDIAEVLERQAEIEAAIEKAIADNGYSDFVLMITDIINSNSEILAIGSNMDKVEAAFNFVLENNHAFLAGAVSRKKQVVPQLTESFNA 311
               SCOP domains d1wppa_ A: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1wppA01 A:2-191 inorganic pyrophosphatase (n-terminal core)                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh................eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhh...eeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee.hhhhhhhhhh......eeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wpp A   2 SKILVFGHQNPDSDAIGSSYAFAYLAREAYGLDTEAVALGEPNEETAFVLDYFGVAAPRVITSAKAEGAEQVILTDHNEFQQSVADIAEVEVYGVVDHHRVANFETASPLYMRLEPVGSASSIVYRMFKEHGVAVPKEIAGLMLSGLISDTLLLKSPTTHPTDKVIAPELAELAGVNLEEYGLAMLKAGTNLASKSAEELIDIDAKTFELNGNNVRVAQVNTVDIAEVLERQAEIEAAIEKAIADNGYSDFVLMITDIINSNSEILAIGSNMDKVEAAFNFVLENNHAFLAGAVSRKKQVVPQLTESFNA 311
                                    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       311


Chain B from PDB  Type:PROTEIN  Length:310
 aligned with PPAC_STRGC | P95765 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    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       311
           PPAC_STRGC     2 SKILVFGHQNPDSDAIGSSYAFAYLAREAYGLDTEAVALGEPNEETAFVLDYFGVAAPRVITSAKAEGAEQVILTDHNEFQQSVADIAEVEVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKEHSVAVSKEIAGLMLSGLISDTLLLKSPTTHPTDKAIAPELAELAGVNLEEYGLAMLKAGTNLASKSAEELIDIDAKTFELNGNNVRVAQVNTVDIAEVLERQAEIEAAIEKAIADNGYSDFVLMITDIINSNSEILAIGSNMDKVEAAFNFVLENNHAFLAGAVSRKKQVVPQLTESFNA 311
               SCOP domains d1wppb_ B: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1wppB01 B:2-191 inorganic pyrophosphatase (n-terminal core)                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) DHH-1wppB03 B:2-149                                                                                                                                 ---------------------------------DHHA2-1wppB01 B:183-309                                                                                                        -- Pfam domains (1)
           Pfam domains (2) DHH-1wppB04 B:2-149                                                                                                                                 ---------------------------------DHHA2-1wppB02 B:183-309                                                                                                        -- Pfam domains (2)
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh................eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhh...eeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee.hhhhhhhhhh......eeeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wpp B   2 SKILVFGHQNPDSDAIGSSYAFAYLAREAYGLDTEAVALGEPNEETAFVLDYFGVAAPRVITSAKAEGAEQVILTDHNEFQQSVADIAEVEVYGVVDHHRVANFETASPLYMRLEPVGSASSIVYRMFKEHGVAVPKEIAGLMLSGLISDTLLLKSPTTHPTDKVIAPELAELAGVNLEEYGLAMLKAGTNLASKSAEELIDIDAKTFELNGNNVRVAQVNTVDIAEVLERQAEIEAAIEKAIADNGYSDFVLMITDIINSNSEILAIGSNMDKVEAAFNFVLENNHAFLAGAVSRKKQVVPQLTESFNA 311
                                    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       311
   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)
(-)
Clan: no clan defined [family: DHH] (7)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PPAC_STRGC | P95765)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        PPAC_STRGC | P95765: 1k20

(-) Related Entries Specified in the PDB File

1wpm STRUCTURE OF B. SUBTILIS PPASE WITHOUT METALS
1wpn STRUCTURE OF N-TERMINAL CORE OF B. SUBTILIS PPASE