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(-) Description

Title :  FLUORIDE-INHIBITED SUBSTRATE COMPLEX OF SACCHAROMYCES CEREVISIAE INORGANIC PYROPHOSPHATASE
 
Authors :  P. Heikinheimo, V. Tuominen, A. -K. Ahonen, A. Teplyakov, B. S. Cooperman, A. A. Baykov, R. Lahti, A. Goldman
Date :  09 Aug 00  (Deposition) - 19 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphoryl Transfer, Hydrolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Heikinheimo, V. Tuominen, A. -K. Ahonen, A. Teplyakov, B. S. Cooperman, A. A. Baykov, R. Lahti, A. Goldman
Toward A Quantum-Mechanical Description Of Metal- Assisted Phosphoryl Transfer In Pyrophosphatase
Proc. Natl. Acad. Sci. Usa V. 98 3121 2001
PubMed-ID: 11248042  |  Reference-DOI: 10.1073/PNAS.061612498

(-) Compounds

Molecule 1 - INORGANIC PYROPHOSPHATASE
    Cellular LocationCYTOPLASM
    ChainsA, B
    EC Number3.6.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainXL2-BLUEB
    Expression System Taxid562
    GenePPA1
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymPPASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1F2Ligand/IonFLUORIDE ION
2MN8Ligand/IonMANGANESE (II) ION
3NA1Ligand/IonSODIUM ION
4PO42Ligand/IonPHOSPHATE ION
5POP2Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:115 , ASP A:120 , ASP A:152 , MN A:2002 , MN A:2004 , HOH A:2334 , POP A:3001 , F A:4001 , NA A:4740BINDING SITE FOR RESIDUE MN A2001
02AC2SOFTWAREASP A:120 , MN A:2001 , HOH A:2335 , HOH A:2336 , HOH A:2337 , POP A:3001 , F A:4001BINDING SITE FOR RESIDUE MN A2002
03AC3SOFTWAREGLU A:58 , HOH A:2338 , HOH A:2339 , HOH A:2340 , POP A:3001 , NA A:4740BINDING SITE FOR RESIDUE MN A2003
04AC4SOFTWAREASP A:147 , ASP A:152 , MN A:2001 , HOH A:2341 , HOH A:2342 , POP A:3001BINDING SITE FOR RESIDUE MN A2004
05AC5SOFTWAREASP A:115 , ASP A:117 , ASP A:120 , MN A:2001 , MN A:2002 , HOH A:2336 , POP A:3001 , NA A:4740BINDING SITE FOR RESIDUE F A4001
06AC6SOFTWAREASP A:115 , ASP A:117 , MN A:2001 , MN A:2003 , HOH A:2165 , HOH A:2339 , POP A:3001 , F A:4001BINDING SITE FOR RESIDUE NA A4740
07AC7SOFTWAREASP B:1115 , ASP B:1120 , ASP B:1152 , MN B:2006 , MN B:2008 , HOH B:2294 , POP B:3002 , PO4 B:3004 , F B:4010BINDING SITE FOR RESIDUE MN B2005
08AC8SOFTWAREASP B:1120 , MN B:2005 , HOH B:2295 , HOH B:2296 , HOH B:2297 , POP B:3002 , PO4 B:3004 , F B:4010BINDING SITE FOR RESIDUE MN B2006
09AC9SOFTWAREGLU B:1058 , HOH B:2298 , HOH B:2299 , HOH B:2300 , POP B:3002 , PO4 B:3003 , PO4 B:3004BINDING SITE FOR RESIDUE MN B2007
10BC1SOFTWAREASP B:1147 , ASP B:1152 , MN B:2005 , HOH B:2301 , HOH B:2302 , POP B:3002 , PO4 B:3003 , PO4 B:3004BINDING SITE FOR RESIDUE MN B2008
11BC2SOFTWARELYS B:1056 , GLU B:1058 , TYR B:1093 , ASP B:1115 , ASP B:1117 , ASP B:1120 , ASP B:1152 , MN B:2005 , MN B:2006 , MN B:2007 , MN B:2008 , HOH B:2096 , HOH B:2297 , HOH B:2301 , HOH B:2302 , POP B:3002 , PO4 B:3003 , F B:4010BINDING SITE FOR RESIDUE PO4 B3004
12BC3SOFTWAREASP B:1115 , ASP B:1117 , ASP B:1120 , MN B:2005 , MN B:2006 , HOH B:2294 , HOH B:2295 , HOH B:2297 , POP B:3002 , PO4 B:3004BINDING SITE FOR RESIDUE F B4010
13BC4SOFTWARELYS A:56 , GLU A:58 , ARG A:78 , TYR A:93 , ASP A:115 , ASP A:117 , ASP A:120 , ASP A:147 , ASP A:152 , TYR A:192 , LYS A:193 , MN A:2001 , MN A:2002 , MN A:2003 , MN A:2004 , HOH A:2145 , HOH A:2335 , HOH A:2339 , HOH A:2340 , HOH A:2341 , F A:4001 , NA A:4740BINDING SITE FOR RESIDUE POP A3001
14BC5SOFTWARELYS B:1056 , GLU B:1058 , ARG B:1078 , TYR B:1093 , ASP B:1115 , ASP B:1117 , ASP B:1120 , ASP B:1147 , ASP B:1152 , TYR B:1192 , LYS B:1193 , MN B:2005 , MN B:2006 , MN B:2007 , MN B:2008 , HOH B:2096 , HOH B:2297 , HOH B:2300 , HOH B:2301 , HOH B:2303 , PO4 B:3003 , PO4 B:3004 , F B:4010BINDING SITE FOR RESIDUE POP B3002
15BC6SOFTWARELYS B:1056 , GLU B:1058 , ARG B:1078 , ASP B:1147 , TYR B:1192 , LYS B:1193 , MN B:2007 , MN B:2008 , HOH B:2300 , HOH B:2301 , HOH B:2303 , POP B:3002 , PO4 B:3004BINDING SITE FOR RESIDUE PO4 B3003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E6A)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:84 -Pro A:85
2Phe B:1084 -Pro B:1085

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E6A)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPASEPS00387 Inorganic pyrophosphatase signature.IPYR_YEAST116-122
 
  2A:115-121
B:1115-1121

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBR011C1YBR011C.1II:257973-257110864IPYR_YEAST1-2872872A:1-284
B:1001-1282
284
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:284
 aligned with IPYR_YEAST | P00817 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:284
                                    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 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASPKADAPIDKSIDKWFFISG  285
               SCOP domains d1e6aa_ A: Inorganic pyrophosphatase                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1e6aA00 A:1-284 Inorganic Pyrophosphatase                                                                                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........eeeeee..eee...........hhh.eeeeeeee.......eee........eee.....................eeeee.......................eeee..........eeeeeeeeee..........eeeeee....hhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh.......hhh.eeehhhhhhhhhhhhhhhhhhhh.......................hhhhhh............hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------PPASE  ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-284 UniProt: 1-287 [INCOMPLETE]                                                                                                                                                                                                                                           Transcript 1
                1e6a A    1 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASLKADAPIDKSIDKWFFISG  284
                                    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 d1e6ab_ B: Inorganic pyrophosphatase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1e6aB00 B:1001-1282 Inorganic Pyrophosphatase                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........eeeeee..eee...............eeeeeeee.......eee........eee.....................eeeee.......................eeee..........eeeeeeeeee..........eeeeee....hhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhh.......hhh.eeehhhhhhhhhhhhhhhhhhhh.......................hhhhhhh...........hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------PPASE  ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1001-1282 UniProt: 1-287 [INCOMPLETE]                                                                                                                                                                                                                                     Transcript 1
                1e6a B 1001 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASLKADAPIDKSIDKWFFI 1282
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280  

   Legend:   → Mismatch (orange background)
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    → 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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E6A)

(-) 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 | P00817117e 1e9g 1huj 1huk 1m38 1pyp 1wgi 1wgj 1ypp 2ihp 2ik0 2ik1 2ik2 2ik4 2ik6 2ik7 2ik9 8prk

(-) Related Entries Specified in the PDB File

117e THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISIAE SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL STUDIES AND MECHANISTIC IMPLICATIONS
1huj REFINED STRUCTURE OF YEAST INORGANIC PYROPHOSPHATASE AND ITS K61R MUTANT
1huk REFINED STRUCTURE OF YEAST INORGANIC PYROPHOSPHATASE AND ITS K61R MUTANT
1wgi STRUCTURE OF INORGANIC PYROPHOSPHATASE
1wgj STRUCTURE OF INORGANIC PYROPHOSPHATASE
1ypp ACID ANHYDRIDE HYDROLASE
8prk THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISIAE SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL STUDIES AND MECHANISTIC IMPLICATIONS