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(-) Description

Title :  INORGANIC PYROPHOSPHATASE (FAMILY II) FROM STREPTOCOCCUS GORDONII AT 1.5 A RESOLUTION
 
Authors :  S. Ahn, A. J. Milner, K. Futterer, M. Konopka, M. Ilias, T. W. Young, S. A.
Date :  26 Sep 01  (Deposition) - 31 Oct 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Family Ii Ppase, Manganese, Binuclear Metal Centre, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ahn, A. J. Milner, K. Futterer, M. Konopka, M. Ilias, T. W. Young, S. A. White
The "Open" And "Closed" Structures Of The Type-C Inorganic Pyrophosphatases From Bacillus Subtilis And Streptococcus Gordonii.
J. Mol. Biol. V. 313 797 2001
PubMed-ID: 11697905  |  Reference-DOI: 10.1006/JMBI.2001.5070

(-) Compounds

Molecule 1 - MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STREPTOCOCCUS GORDONII
    Organism Taxid: 1302
    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
1GOL3Ligand/IonGLYCEROL
2MN4Ligand/IonMANGANESE (II) ION
3SO44Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:9 , ASP A:13 , ASP A:77 , HOH A:711 , HOH A:712BINDING SITE FOR RESIDUE MN A 701
02AC2SOFTWAREASP A:15 , ASP A:77 , HIS A:99 , ASP A:151 , HOH A:711BINDING SITE FOR RESIDUE MN A 702
03AC3SOFTWAREHIS B:9 , ASP B:13 , ASP B:77 , MN B:704 , HOH B:712 , HOH B:713BINDING SITE FOR RESIDUE MN B 703
04AC4SOFTWAREASP B:15 , ASP B:77 , HIS B:99 , ASP B:151 , MN B:703 , HOH B:712BINDING SITE FOR RESIDUE MN B 704
05AC5SOFTWAREHIS A:100 , LYS A:207 , ARG A:297 , LYS A:298 , HOH A:728 , HOH A:735 , HOH A:752 , HOH A:808 , HOH A:1047BINDING SITE FOR RESIDUE SO4 A 705
06AC6SOFTWAREHIS B:100 , LYS B:207 , ARG B:297 , LYS B:298 , HOH B:716 , HOH B:725 , HOH B:768 , HOH B:924BINDING SITE FOR RESIDUE SO4 B 706
07AC7SOFTWAREGLU A:92 , VAL A:93 , THR A:107 , ALA A:108 , ASN A:109 , HOH A:785 , HOH A:799 , HOH A:1011 , HOH A:1063BINDING SITE FOR RESIDUE SO4 A 707
08AC8SOFTWAREGLU B:92 , VAL B:93 , THR B:107 , ALA B:108 , ASN B:109 , HOH B:757 , HOH B:794 , HOH B:975 , HOH B:978 , HOH B:994BINDING SITE FOR RESIDUE SO4 B 708
09AC9SOFTWAREGLY B:190 , ASP B:205 , GLN B:220 , VAL B:221 , ASN B:222 , HOH B:822 , HOH B:888BINDING SITE FOR RESIDUE GOL B 709
10BC1SOFTWAREGLY A:190 , ASP A:205 , VAL A:221 , ASN A:222 , HOH A:782 , HOH A:1054BINDING SITE FOR RESIDUE GOL A 710
11BC2SOFTWAREALA A:238 , ASP B:225 , ILE B:226 , ALA B:227 , ASP B:258 , HOH B:778 , HOH B:972 , HOH B:1003BINDING SITE FOR RESIDUE GOL B 711

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K20)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K20)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K20)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K20)

(-) Exons   (0, 0)

(no "Exon" information available for 1K20)

(-) 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 d1k20a_ A: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1k20A01 A:2-191 inorganic pyrophosphatase (n-terminal core)                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh.........hhhhh..eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhh...eeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee.hhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k20 A   2 SKILVFGHQNPDSDAIGSSYAFAYLAREAYGLDTEAVALGEPNEETAFVLDYFGVAAPRVITSAKAEGAEQVILTDHNEFQQSVADIAEVEVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKEHSVAVSKEIAGLMLSGLISDTLLLKSPTTHPTDKAIAPELAELAGVNLEEYGLAMLKAGTNLASKSAEELIDIDAKTFELNGNNVRVAQVNTVDIAEVLERQAEIEAAIEKAIADNGYSDFVLMITDIINSNSEILAIGSNMDKVEAAFNFVLENNHAFLAGAVSRKKQVVPQLTESFNA 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 d1k20b_ B: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1k20B01 B:2-191 inorganic pyrophosphatase (n-terminal core)                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) DHH-1k20B03 B:2-149                                                                                                                                 ---------------------------------DHHA2-1k20B01 B:183-309                                                                                                        -- Pfam domains (1)
           Pfam domains (2) DHH-1k20B04 B:2-149                                                                                                                                 ---------------------------------DHHA2-1k20B02 B:183-309                                                                                                        -- Pfam domains (2)
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh................eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee.hhhhhhhhhh......eeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k20 B   2 SKILVFGHQNPDSDAIGSSYAFAYLAREAYGLDTEAVALGEPNEETAFVLDYFGVAAPRVITSAKAEGAEQVILTDHNEFQQSVADIAEVEVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKEHSVAVSKEIAGLMLSGLISDTLLLKSPTTHPTDKAIAPELAELAGVNLEEYGLAMLKAGTNLASKSAEELIDIDAKTFELNGNNVRVAQVNTVDIAEVLERQAEIEAAIEKAIADNGYSDFVLMITDIINSNSEILAIGSNMDKVEAAFNFVLENNHAFLAGAVSRKKQVVPQLTESFNA 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: 1wpp

(-) Related Entries Specified in the PDB File

1k23 INORGANIC PYROPHOSPHATASE (FAMILY II) FROM BACILLUS SUBTILIS