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(-) Description

Title :  STRUCTURE OF INORGANIC PYROPHOSPHATASE
 
Authors :  P. Heikinheimo, J. Lehtonen, A. Goldman
Date :  24 Oct 96  (Deposition) - 19 Nov 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyrophosphate Phosphohydrolase, Hydrolase, Manganese (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Heikinheimo, J. Lehtonen, A. Baykov, R. Lahti, B. S. Cooperman, A. Goldman
The Structural Basis For Pyrophosphatase Catalysis.
Structure V. 4 1491 1996
PubMed-ID: 8994974  |  Reference-DOI: 10.1016/S0969-2126(96)00155-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INORGANIC PYROPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: PPA1
    Expression System Plasmid: PKW9
    Expression System Strain: HB101
    Expression System Taxid: 562
    Gene: PPA1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: PRODUCT COMPLEX
    Synonym: PPASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1MN8Ligand/IonMANGANESE (II) ION
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:115 , ASP A:120 , ASP A:152 , MN A:288 , PO4 A:292 , HOH A:293 , HOH A:294BINDING SITE FOR RESIDUE MN A 287
02AC2SOFTWAREASP A:120 , MN A:287 , PO4 A:292 , HOH A:293 , HOH A:295 , HOH A:296 , HOH A:297BINDING SITE FOR RESIDUE MN A 288
03AC3SOFTWAREGLU A:58 , PO4 A:291 , PO4 A:292 , HOH A:298 , HOH A:299 , HOH A:300BINDING SITE FOR RESIDUE MN A 289
04AC4SOFTWAREASP A:147 , ASP A:152 , PO4 A:291 , PO4 A:292 , HOH A:301 , HOH A:302BINDING SITE FOR RESIDUE MN A 290
05AC5SOFTWARELYS A:56 , GLU A:58 , ARG A:78 , ASP A:147 , TYR A:192 , LYS A:193 , MN A:289 , MN A:290 , PO4 A:292 , HOH A:298 , HOH A:301 , HOH A:351 , HOH A:388BINDING SITE FOR RESIDUE PO4 A 291
06AC6SOFTWARELYS A:56 , GLU A:58 , TYR A:93 , ASP A:115 , ASP A:120 , ASP A:152 , MN A:287 , MN A:288 , MN A:289 , MN A:290 , PO4 A:291 , HOH A:293 , HOH A:295 , HOH A:302 , HOH A:309BINDING SITE FOR RESIDUE PO4 A 292
07AC7SOFTWAREASP B:115 , ASP B:120 , ASP B:152 , MN B:288 , MN B:290 , PO4 B:292 , HOH B:293 , HOH B:294BINDING SITE FOR RESIDUE MN B 287
08AC8SOFTWAREASP B:120 , MN B:287 , PO4 B:292 , HOH B:293 , HOH B:295 , HOH B:296 , HOH B:297BINDING SITE FOR RESIDUE MN B 288
09AC9SOFTWAREGLU B:58 , PO4 B:291 , PO4 B:292 , HOH B:298 , HOH B:299 , HOH B:300BINDING SITE FOR RESIDUE MN B 289
10ASAUNKNOWNGLU A:48 , LYS A:56 , GLU A:58 , ARG A:78 , TYR A:89 , TYR A:93 , ASP A:115 , ASP A:117 , ASP A:120 , ASP A:147 , ASP A:152 , LYS A:154 , TYR A:192 , LYS A:193ACTIVE SITE A.
11ASBUNKNOWNGLU B:48 , LYS B:56 , GLU B:58 , ARG B:78 , TYR B:89 , TYR B:93 , ASP B:115 , ASP B:117 , ASP B:120 , ASP B:147 , ASP B:152 , LYS B:154 , TYR B:192 , LYS B:193ACTIVE SITE B.
12BC1SOFTWAREASP B:147 , ASP B:152 , MN B:287 , PO4 B:291 , PO4 B:292 , HOH B:301 , HOH B:302BINDING SITE FOR RESIDUE MN B 290
13BC2SOFTWARELYS B:56 , GLU B:58 , ARG B:78 , ASP B:147 , TYR B:192 , LYS B:193 , MN B:289 , MN B:290 , PO4 B:292 , HOH B:299 , HOH B:396 , HOH B:417BINDING SITE FOR RESIDUE PO4 B 291
14BC3SOFTWARELYS B:56 , GLU B:58 , TYR B:93 , ASP B:120 , ASP B:152 , MN B:287 , MN B:288 , MN B:289 , MN B:290 , PO4 B:291 , HOH B:293 , HOH B:297 , HOH B:302 , HOH B:310BINDING SITE FOR RESIDUE PO4 B 292

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:84 -Pro A:85
2Phe B:84 -Pro B:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPASEPS00387 Inorganic pyrophosphatase signature.IPYR_YEAST116-122
 		  2A:115-121
B:115-121

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBR011C1YBR011C.1II:257973-257110864IPYR_YEAST1-2872872A:1-282
B:1-282		282
282

(-) 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:282
 aligned with IPYR_YEAST | P00817 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:282
                                    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  
           IPYR_YEAST     2 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASPKADAPIDKSIDKWFFI 283
               SCOP domains d1wgja_ A: Inorganic pyrophosphatase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1wgjA00 A:1-282 Inorganic Pyrophosphatase                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee......eeeeee..eee...........hhh.eeeeeeee.......eee........eee.....................eeeee.......................eeee..........eeeeeeeeee..........eeeeee.....hhh...hhhhhhh...hhhhhhhhhhh..hhh.......hhhh.eeehhhhhhhhhhhhhhhhhhhh.......................hhhhhh....eee......hhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------PPASE  ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-282 UniProt: 1-287 [INCOMPLETE]                                                                                                                                                                                                                                         Transcript 1
                 1wgj A   1 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASLKADAPIDKSIDKWFFI 282
                                    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  


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with IPYR_YEAST | P00817 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:282
                                    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  
           IPYR_YEAST     2 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASPKADAPIDKSIDKWFFI 283
               SCOP domains d1wgjb_ B: Inorganic pyrophosphatase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1wgjB00 B:1-282 Inorganic Pyrophosphatase                                                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) -------------------------------------------Pyrophosphatase-1wgjB01 B:44-228                                                                                                                                                         ------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -------------------------------------------Pyrophosphatase-1wgjB02 B:44-228                                                                                                                                                         ------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeeeeeee......eeeeee..eee...............eeeeeeee.......eee........eee.....................eeeee.......................eeee..........eeeeeeeeee...hhh....eeeeee.....hhh...hhhhhhh...hhhhhhhhhhh..hhh........hhh....hhhhhhhhhhhhhhhhhhhh.......................hhhhhh....eee......hhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------PPASE  ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-282 UniProt: 1-287 [INCOMPLETE]                                                                                                                                                                                                                                         Transcript 1
                 1wgj B   1 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASLKADAPIDKSIDKWFFI 282
                                    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
   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: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IPYR_YEAST | P00817)
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).
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IPYR_YEAST | P00817: 117e 1e6a 1e9g 1huj 1huk 1m38 1pyp 1wgi 1ypp 2ihp 2ik0 2ik1 2ik2 2ik4 2ik6 2ik7 2ik9 8prk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WGJ)