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(-) Description

Title :  STRUCTURE OF INORGANIC PYROPHOSPHATASE
 
Authors :  V. Yu. Oganessyan, E. H. Harutyunyan, S. M. Avaeva, N. N. Oganessyan, T. R. Huber
Date :  09 Oct 96  (Deposition) - 04 Sep 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Hydrolase, Magnesium, Metal Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. H. Harutyunyan, V. Y. Oganessyan, N. N. Oganessyan, S. M. Avaeva, T. I. Nazarova, N. N. Vorobyeva, S. A. Kurilova, R. Huber, T. Mather
Crystal Structure Of Holo Inorganic Pyrophosphatase From Escherichia Coli At 1. 9 A Resolution. Mechanism Of Hydrolysis.
Biochemistry V. 36 7754 1997
PubMed-ID: 9201917  |  Reference-DOI: 10.1021/BI962637U
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INORGANIC PYROPHOSPHATASE
    Chains: A, B, C
    EC Number: 3.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: PYROPHOSPHATASE FROM ESCHERICHIA COLI
    Expression System Plasmid: PUC19
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: JM109
    Synonym: PYROPHOSPHATE HYDROLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1MG7Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:65 , ASP A:70 , ASP A:102 , HOH A:198 , HOH A:200 , HOH A:202BINDING SITE FOR RESIDUE MG A 176
2AC2SOFTWAREHOH C:187 , HOH C:200 , HOH C:232BINDING SITE FOR RESIDUE MG C 176
3AC3SOFTWAREASP C:65 , ASP C:70 , ASP C:102 , HOH C:195 , HOH C:218 , HOH C:254BINDING SITE FOR RESIDUE MG C 177
4AC4SOFTWAREHOH A:201 , HOH A:203 , HOH A:209 , HOH B:194 , HOH B:201 , HOH B:213BINDING SITE FOR RESIDUE MG A 177
5AC5SOFTWAREASP B:65 , ASP B:70 , ASP B:102 , HOH B:209 , HOH B:242 , HOH B:253BINDING SITE FOR RESIDUE MG B 176
6AC6SOFTWAREASP A:70 , HOH A:213 , HOH A:217 , HOH A:224 , HOH A:225 , HOH A:242BINDING SITE FOR RESIDUE MG A 178
7AC7SOFTWAREASP B:70 , HOH B:206 , HOH B:211 , HOH B:233 , HOH B:237 , HOH B:239BINDING SITE FOR RESIDUE MG B 177

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:11 -Pro A:12
2Leu B:11 -Pro B:12
3Leu C:11 -Pro C:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPASEPS00387 Inorganic pyrophosphatase signature.IPYR_ECOLI66-72
 
 		  3A:65-71
B:65-71
C:65-71
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPASEPS00387 Inorganic pyrophosphatase signature.IPYR_ECOLI66-72
 
 		  6A:65-71
B:65-71
C:65-71

(-) Exons   (0, 0)

(no "Exon" information available for 1OBW)

(-) Sequences/Alignments

Asymmetric 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:175
 aligned with IPYR_ECOLI | P0A7A9 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
           IPYR_ECOLI     2 SLLNVPAGKDLPEDIYVVIEIPANADPIKYEIDKESGALFVDRFMSTAMFYPCNYGYINHTLSLDGDPVDVLVPTPYPLQPGSVIRCRPVGVLKMTDEAGEDAKLVAVPHSKLSKEYDHIKDVNDLPELLKAQIAHFFEHYKDLEKGKWVKVEGWENAEAAKAEIVASFERAKNK 176
               SCOP domains d1obwa_ A: Inorganic pyrophosphatase                                                                                                                                            SCOP domains
               CATH domains 1obwA00 A:1-175 Inorganic Pyrophosphatase                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh..........eeeeeee......eeeee......eeeeee.........eeee............eeee..........eeeeeeeeeeeeee......eeeeee.............hhh..hhhhhhhhhhhhh.........eeeeeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------PPASE  -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1obw A   1 SLLNVPAGKDLPEDIYVVIEIPANADPIKYEIDKESGALFVDRFMSTAMFYPCNYGYINHTLSLDGDPVDVLVPTPYPLQPGSVTRCRPVGVLKMTDEAGEDAKLVAVPHSKLSKEYDHIKDVNDLPELLKAQIAHFFEHYKDLEKGKWVKVEGWENAEAAKAEIVASFERAKNK 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain B from PDB  Type:PROTEIN  Length:175
 aligned with IPYR_ECOLI | P0A7A9 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
           IPYR_ECOLI     2 SLLNVPAGKDLPEDIYVVIEIPANADPIKYEIDKESGALFVDRFMSTAMFYPCNYGYINHTLSLDGDPVDVLVPTPYPLQPGSVIRCRPVGVLKMTDEAGEDAKLVAVPHSKLSKEYDHIKDVNDLPELLKAQIAHFFEHYKDLEKGKWVKVEGWENAEAAKAEIVASFERAKNK 176
               SCOP domains d1obwb_ B: Inorganic pyrophosphatase                                                                                                                                            SCOP domains
               CATH domains 1obwB00 B:1-175 Inorganic Pyrophosphatase                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh..........eeeeeee......eeeee......eeeeee.........eeee............eeee..........eeeeeeeeeeeee.......eeeeee.............hhh..hhhhhhhhhhhhh..........eeeeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------PPASE  -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1obw B   1 SLLNVPAGKDLPEDIYVVIEIPANADPIKYEIDKESGALFVDRFMSTAMFYPCNYGYINHTLSLDGDPVDVLVPTPYPLQPGSVTRCRPVGVLKMTDEAGEDAKLVAVPHSKLSKEYDHIKDVNDLPELLKAQIAHFFEHYKDLEKGKWVKVEGWENAEAAKAEIVASFERAKNK 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain C from PDB  Type:PROTEIN  Length:175
 aligned with IPYR_ECOLI | P0A7A9 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
           IPYR_ECOLI     2 SLLNVPAGKDLPEDIYVVIEIPANADPIKYEIDKESGALFVDRFMSTAMFYPCNYGYINHTLSLDGDPVDVLVPTPYPLQPGSVIRCRPVGVLKMTDEAGEDAKLVAVPHSKLSKEYDHIKDVNDLPELLKAQIAHFFEHYKDLEKGKWVKVEGWENAEAAKAEIVASFERAKNK 176
               SCOP domains d1obwc_ C: Inorganic pyrophosphatase                                                                                                                                            SCOP domains
               CATH domains 1obwC00 C:1-175 Inorganic Pyrophosphatase                                                                                                                                       CATH domains
           Pfam domains (1) ---------------Pyrophosphatase-1obwC01 C:16-174                                                                                                                               - Pfam domains (1)
           Pfam domains (2) ---------------Pyrophosphatase-1obwC02 C:16-174                                                                                                                               - Pfam domains (2)
           Pfam domains (3) ---------------Pyrophosphatase-1obwC03 C:16-174                                                                                                                               - Pfam domains (3)
         Sec.struct. author .hhh..........eeeeeee......eeeee......eeeeee.........eeee............eeee..........eeeeeeeeeeeeee......eeeeee.............hhh..hhhhhhhhhhhhh.........eeeeeee.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------PPASE  -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1obw C   1 SLLNVPAGKDLPEDIYVVIEIPANADPIKYEIDKESGALFVDRFMSTAMFYPCNYGYINHTLSLDGDPVDVLVPTPYPLQPGSVTRCRPVGVLKMTDEAGEDAKLVAVPHSKLSKEYDHIKDVNDLPELLKAQIAHFFEHYKDLEKGKWVKVEGWENAEAAKAEIVASFERAKNK 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Pyrophosphatase] (19)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (IPYR_ECOLI | P0A7A9)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0050355    triphosphatase activity    Catalysis of the reaction: H(2)O + triphosphate = diphosphate + phosphate.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006796    phosphate-containing compound metabolic process    The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IPYR_ECOLI | P0A7A9: 1faj 1i40 1i6t 1igp 1ino 1ipw 1jfd 1mjw 1mjx 1mjy 1mjz 2au6 2au7 2au8 2au9 2auu 2eip 4um4

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