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(-) Description

Title :  THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISIAE SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL STUDIES AND MECHANISTIC IMPLICATIONS
 
Authors :  V. Tuominen, P. Heikinheimo, T. Kajander, T. Torkkel, T. Hyytia, J. Kapyla, R. Lahti, B. S. Cooperman, A. Goldman
Date :  15 Sep 98  (Deposition) - 23 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme Mechanism, Iorganic Pyrophosphatase, Mutan Structures, 2-Metal Ion Mechanism, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Tuominen, P. Heikinheimo, T. Kajander, T. Torkkel, T. Hyytia, J. Kapyla, R. Lahti, B. S. Cooperman, A. Goldman
The R78K And D117E Active-Site Variants Of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies And Mechanistic Implications.
J. Mol. Biol. V. 284 1565 1998
PubMed-ID: 9878371  |  Reference-DOI: 10.1006/JMBI.1998.2266
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (INORGANIC PYROPHOSPHATASE)
    Cellular Location: CYTOPLASM
    Chains: A, B
    EC Number: 3.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: HB101
    Expression System Taxid: 562
    Gene: PPA1
    Mutation: YES
    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, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1MN8Ligand/IonMANGANESE (II) ION
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:115 , GLU A:117 , ASP A:120 , ASP A:152 , MN A:2002 , PO4 A:3002 , HOH A:4002BINDING SITE FOR RESIDUE MN A 2001
02AC2SOFTWAREGLU A:117 , ASP A:120 , MN A:2001 , PO4 A:3002 , HOH A:4003 , HOH A:4004 , HOH A:4005BINDING SITE FOR RESIDUE MN A 2002
03AC3SOFTWAREPO4 A:3001 , HOH A:4006 , HOH A:4008 , HOH A:4405 , HOH A:4414BINDING SITE FOR RESIDUE MN A 2003
04AC4SOFTWAREASP A:147 , ASP A:152 , PO4 A:3001 , PO4 A:3002 , HOH A:4009 , HOH A:4010BINDING SITE FOR RESIDUE MN A 2004
05AC5SOFTWAREASP B:1115 , GLU B:1117 , ASP B:1120 , ASP B:1152 , MN B:2006 , MN B:2008 , PO4 B:3004 , HOH B:4012BINDING SITE FOR RESIDUE MN B 2005
06AC6SOFTWAREGLU B:1117 , ASP B:1120 , MN B:2005 , PO4 B:3004 , HOH B:4013 , HOH B:4014 , HOH B:4015BINDING SITE FOR RESIDUE MN B 2006
07AC7SOFTWAREGLU B:1058 , GLU B:1117 , PO4 B:3004 , HOH B:4016 , HOH B:4017 , HOH B:4417BINDING SITE FOR RESIDUE MN B 2007
08AC8SOFTWAREASP B:1147 , ASP B:1152 , MN B:2005 , PO4 B:3004 , HOH B:4019 , HOH B:4020 , HOH B:4416BINDING SITE FOR RESIDUE MN B 2008
09AC9SOFTWARELYS A:56 , ARG A:78 , ASP A:147 , TYR A:192 , LYS A:193 , MN A:2003 , MN A:2004 , PO4 A:3002 , HOH A:4006 , HOH A:4182 , HOH A:4414BINDING SITE FOR RESIDUE PO4 A 3001
10BC1SOFTWARELYS A:56 , TYR A:93 , ASP A:115 , GLU A:117 , ASP A:120 , ASP A:152 , MN A:2001 , MN A:2002 , MN A:2004 , PO4 A:3001 , HOH A:4006 , HOH A:4010 , HOH A:4401 , HOH A:4405BINDING SITE FOR RESIDUE PO4 A 3002
11BC2SOFTWARELYS B:1056 , TYR B:1093 , ASP B:1115 , GLU B:1117 , ASP B:1120 , ASP B:1152 , LYS B:1154 , MN B:2005 , MN B:2006 , MN B:2007 , MN B:2008 , HOH B:4017 , HOH B:4020 , HOH B:4056 , HOH B:4409 , HOH B:4416BINDING SITE FOR RESIDUE PO4 B 3004
12MN1AUTHORGLU A:117 , ASP A:152 , ASP A:115 , ASP A:120NULL
13MN2AUTHORGLU A:117 , TYR A:93 , ASP A:120NULL
14MN4AUTHORASP A:152 , ASP A:147NULL
15MN5AUTHORGLU B:1117 , ASP B:1152 , ASP B:1115 , ASP B:1120NULL
16MN6AUTHORGLU B:1117 , TYR B:1093 , ASP B:1120NULL
17MN8AUTHORASP B:1152 , ASP B:1147NULL

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 117E)

(-) 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 117E)

(-) 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:1-282
B:1001-1282		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 d117ea_ A: Inorganic pyrophosphatase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 117eA00 A:1-282 Inorganic Pyrophosphatase                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee......eeeeee..eee...........hhh.eeeeeeee.......eee........eee.....................eeeee.......................eeee..........eeeeeeeeee...hhh....eeeeee.....hhh...hhhhhhh...hhhhhhhhhhh..hhh........hhh.eeehhhhhhhhhhhhhhhhhhh........................hhh.......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
                117e A    1 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNEPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASLKADAPIDKSIDKWFFI  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 d117eb_ B: Inorganic pyrophosphatase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 117eB00 B:1001-1282 Inorganic Pyrophosphatase                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee......eeeeee..eee...............eeeeeeee.......eee........eee.....................eeeee.......................eeee..........eeeeeeeeee..........eeeeee...........hhhhhhh...hhhhhhhhhhh..hhh.......hhhh.eeehhhhhhhhhhhhhhhhhhh........................hhhhhh....eee......hhhh..... 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
                117e B 1001 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNEPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASLKADAPIDKSIDKWFFI 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)
  - → 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  (0, 0)

(no "Pfam Domain" information available for 117E)

(-) 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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  117e
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  3.6.1.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        IPYR_YEAST | P00817: 1e6a 1e9g 1huj 1huk 1m38 1pyp 1wgi 1wgj 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 117E)