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(-) Description

Title :  STREPTOCOCCUS MUTANS INORGANIC PYROPHOSPHATASE
 
Authors :  M. C. Merckel, I. P. Fabrichniy, A. Goldman, R. Lahti, A. Salminen
Date :  07 Mar 01  (Deposition) - 06 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Merckel, I. P. Fabrichniy, A. Salminen, N. Kalkkinen, A. A. Baykov, R. Lahti, A. Goldman
Crystal Structure Of Streptococcus Mutans Pyrophosphatase: A New Fold For An Old Mechanism.
Structure V. 9 289 2001
PubMed-ID: 11525166  |  Reference-DOI: 10.1016/S0969-2126(01)00587-1
(for further references see the PDB file header)

(-) 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 Taxid: 562
    Organism Scientific: STREPTOCOCCUS MUTANS
    Organism Taxid: 1309
    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  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MN4Ligand/IonMANGANESE (II) ION
3MSE10Mod. Amino AcidSELENOMETHIONINE
4SO44Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:8 , ASP A:12 , ASP A:75 , MN A:402 , SO4 A:405 , HOH A:406BINDING SITE FOR RESIDUE MN A 401
02AC2SOFTWAREASP A:14 , ASP A:75 , HIS A:97 , ASP A:149 , MN A:401 , SO4 A:405 , HOH A:406BINDING SITE FOR RESIDUE MN A 402
03AC3SOFTWARESO4 A:404 , SO4 A:405 , HOH A:504 , HOH A:507 , HOH A:571 , HOH A:597BINDING SITE FOR RESIDUE MG A 403
04AC4SOFTWARELYS A:205 , ARG A:295 , LYS A:296 , MG A:403 , SO4 A:405 , HOH A:507 , HOH A:509 , HOH A:512 , HOH A:525BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWAREHIS A:8 , ASP A:12 , ASP A:75 , HIS A:97 , HIS A:98 , ASP A:149 , LYS A:205 , MN A:401 , MN A:402 , MG A:403 , SO4 A:404 , HOH A:406 , HOH A:502 , HOH A:504 , HOH A:562BINDING SITE FOR RESIDUE SO4 A 405
06AC6SOFTWAREHIS B:8 , ASP B:12 , ASP B:75 , MN B:402 , SO4 B:1405 , HOH B:1406BINDING SITE FOR RESIDUE MN B 401
07AC7SOFTWAREASP B:14 , ASP B:75 , HIS B:97 , ASP B:149 , MN B:401 , SO4 B:1405 , HOH B:1406BINDING SITE FOR RESIDUE MN B 402
08AC8SOFTWARESO4 B:1405BINDING SITE FOR RESIDUE MG B 1403
09AC9SOFTWAREARG B:295 , LYS B:296 , SO4 B:1405BINDING SITE FOR RESIDUE SO4 B 1404
10BC1SOFTWAREHIS B:8 , ASP B:12 , ASP B:75 , HIS B:97 , HIS B:98 , ASP B:149 , MN B:401 , MN B:402 , HOH B:695 , MG B:1403 , SO4 B:1404 , HOH B:1406BINDING SITE FOR RESIDUE SO4 B 1405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I74)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I74)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I74)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I74)

(-) Exons   (0, 0)

(no "Exon" information available for 1I74)

(-) 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:309
 aligned with PPAC_STRMU | O68579 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:309
                                    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_STRMU     2 SKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVLDYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHRVANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISDTLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQLVDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSDFVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQVVPQLTESFNG 310
               SCOP domains d1i74a_ A: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1i74A01 A:1-190 inorganic pyrophosphatase (n-terminal core)                                                                                                                                   ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhh.................eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhh...eeeeee..eeeeeeeeee.hhhhhh.hhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee.hhhhhhhhhh......eeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i74 A   1 SKILVFGHQNPDSDAIGSSmAYAYLKRQLGVDAQAVALGNPNEETAFVLDYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHRVANFETANPLYmRLEPVGSASSIVYRLYKENGVAIPKEIAGVmLSGLISDTLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAmLKAGTNLASKTAAQLVDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSDFVLmITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQVVPQLTESFNG 309
                                    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         
                                              20-MSE                                                                                    111-MSE                        142-MSE                                   184-MSE                                                              253-MSE                                                    


Chain B from PDB  Type:PROTEIN  Length:309
 aligned with PPAC_STRMU | O68579 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:309
                                    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_STRMU     2 SKILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVALGNPNEETAFVLDYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHRVANFETANPLYMRLEPVGSASSIVYRLYKENGVAIPKEIAGVMLSGLISDTLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAMLKAGTNLASKTAAQLVDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSDFVLMITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQVVPQLTESFNG 310
               SCOP domains d1i74b_ B: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1i74B01 B:1-190 inorganic pyrophosphatase (n-terminal core)                                                                                                                                   ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhh.................eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhh...eeeeee..eeeeeeeeee.hhhhhh.hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee.....hhhhhh......eeee....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i74 B   1 SKILVFGHQNPDSDAIGSSmAYAYLKRQLGVDAQAVALGNPNEETAFVLDYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHRVANFETANPLYmRLEPVGSASSIVYRLYKENGVAIPKEIAGVmLSGLISDTLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLAmLKAGTNLASKTAAQLVDIDAKTFELNGSQVRVAQVNTVDINEVLERQNEIEEAIKASQAANGYSDFVLmITDILNSNSEILALGNNTDKVEAAFNFTLKNNHAFLAGAVSRKKQVVPQLTESFNG 309
                                    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         
                                              20-MSE                                                                                    111-MSE                        142-MSE                                   184-MSE                                                              253-MSE
   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 1I74)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PPAC_STRMU | O68579)
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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