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(-) Description

Title :  CRYSTAL STRUCTURE OF METHANOCOCCUS JANNASCHII PUTATIVE FAMILY II INORGANIC PYROPHOSPHATASE
 
Authors :  A. Shimada, S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/P Initiative (Rsgi)
Date :  05 Feb 07  (Deposition) - 07 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dhh Domain, Dhha2 Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Shimada, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Methanococcus Jannaschii Inorganic Pyrophosphatase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MJ0608
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: DSM 2661
    Synonym: PUTATIVE FAMILY II INORGANIC PYROPHOSPHATASE, PYROPHOSPHATE PHOSPHO-HYDROLASE, PPASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:7 , ASP A:11 , ASP A:66 , LYS A:204 , MN A:502 , HOH A:662BINDING SITE FOR RESIDUE MN A 501
2AC2SOFTWAREASP A:13 , ASP A:66 , HIS A:88 , ASP A:147 , MN A:501 , HOH A:662BINDING SITE FOR RESIDUE MN A 502
3AC3SOFTWAREASP B:13 , ASP B:66 , HIS B:88 , ASP B:147 , MN B:504 , HOH B:669BINDING SITE FOR RESIDUE MN B 503
4AC4SOFTWAREHIS B:7 , ASP B:11 , ASP B:66 , MN B:503BINDING SITE FOR RESIDUE MN B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EB0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EB0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EB0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EB0)

(-) Exons   (0, 0)

(no "Exon" information available for 2EB0)

(-) 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:304
 aligned with PPAC_METJA | Q58025 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:307
                                    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_METJA     1 MRYVVGHKNPDTDSIASAIVLAYFLDCYPARLGDINPETEFVLRKFGVMEPELIESAKGKEIILVDHSEKSQSFDDLEEGKLIAIIDHHKVGLTTTEPILYYAKPVGSTATVIAELYFKDAIDLIGGKKKELKPDLAGLLLSAIISDTVLFKSPTTTDLDKEMAKKLAEIAGISNIEEFGMEILKAKSVVGKLKPEEIINMDFKNFDFNGKKVGIGQVEVIDVSEVESKKEDIYKLLEEKLKNEGYDLIVFLITDIMKEGSEALVVGNKEMFEKAFNVKVEGNSVFLEGVMSRKKQVVPPLERAYNG 307
               SCOP domains d2eb0a_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2eb0A01 A:1-188 inorganic pyrophosphatase (n-terminal core)                                                                                                                                 ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhh....ee.......eeeee...hhhhh..hhhhheeeeeee............eeee....hhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeehhhhhhhhh---....eeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eb0 A   1 MRYVVGHKNPDTDSIASAIVLAYFLDCYPARLGDINPETEFVLRKFGVMEPELIESAKGKEIILVDHSEKSQSFDDLEEGKLIAIIDHHKVGLTTTEPILYYAKPVGSTATVIAELYFKDAIDLIGGKKKELKPDLAGLLLSAIISDTVLFKSPTTTDLDKEMAKKLAEIAGISNIEEFGMEILKAKSVVGKLKPEEIINMDFKNFDFNGKKVGIGQVEVIDVSEVESKKEDIYKLLEEKLKNEGYDLIVFLITDIMKEGSEALVVGNKEMFEKAF---VEGNSVFLEGVMSRKKQVVPPLERAYNG 307
                                    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       
                                                                                                                                                                                                                                                                                                             276 280                           


Chain B from PDB  Type:PROTEIN  Length:307
 aligned with PPAC_METJA | Q58025 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:307
                                    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_METJA     1 MRYVVGHKNPDTDSIASAIVLAYFLDCYPARLGDINPETEFVLRKFGVMEPELIESAKGKEIILVDHSEKSQSFDDLEEGKLIAIIDHHKVGLTTTEPILYYAKPVGSTATVIAELYFKDAIDLIGGKKKELKPDLAGLLLSAIISDTVLFKSPTTTDLDKEMAKKLAEIAGISNIEEFGMEILKAKSVVGKLKPEEIINMDFKNFDFNGKKVGIGQVEVIDVSEVESKKEDIYKLLEEKLKNEGYDLIVFLITDIMKEGSEALVVGNKEMFEKAFNVKVEGNSVFLEGVMSRKKQVVPPLERAYNG 307
               SCOP domains d2eb0b_ B: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2eb0B01 B:1-188 inorganic pyrophosphatase (n-terminal core)                                                                                                                                 ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhh.....ee.......eeeee...hhhhh..hhhhheeeeeee............eeee....hhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeehhhhhhhhh.......eeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eb0 B   1 MRYVVGHKNPDTDSIASAIVLAYFLDCYPARLGDINPETEFVLRKFGVMEPELIESAKGKEIILVDHSEKSQSFDDLEEGKLIAIIDHHKVGLTTTEPILYYAKPVGSTATVIAELYFKDAIDLIGGKKKELKPDLAGLLLSAIISDTVLFKSPTTTDLDKEMAKKLAEIAGISNIEEFGMEILKAKSVVGKLKPEEIINMDFKNFDFNGKKVGIGQVEVIDVSEVESKKEDIYKLLEEKLKNEGYDLIVFLITDIMKEGSEALVVGNKEMFEKAFNVKVEGNSVFLEGVMSRKKQVVPPLERAYNG 307
                                    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)
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  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 2EB0)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PPAC_METJA | Q58025)
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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