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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 :  16 Sep 98  (Deposition) - 23 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme Mechanism, Iorganic Pyrophosphatase, Mutant 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
    Synonym: PPASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1MN6Ligand/IonMANGANESE (II) ION
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:1115 , ASP B:1120 , ASP B:1152 , MN B:2008 , PO4 B:3004 , HOH B:4008BINDING SITE FOR RESIDUE MN B 2005
02AC2SOFTWAREASP A:147 , ASP A:152 , PO4 A:3002BINDING SITE FOR RESIDUE MN A 2004
03AC3SOFTWAREASP B:1147 , ASP B:1152 , MN B:2005 , PO4 B:3004 , HOH B:4012BINDING SITE FOR RESIDUE MN B 2008
04AC4SOFTWAREASP B:1120 , PO4 B:3004 , HOH B:4009 , HOH B:4010 , HOH B:4011BINDING SITE FOR RESIDUE MN B 2006
05AC5SOFTWAREASP A:120 , PO4 A:3002 , HOH A:4002 , HOH A:4003 , HOH A:4004BINDING SITE FOR RESIDUE MN A 2002
06AC6SOFTWAREASP A:115 , ASP A:120 , ASP A:152 , PO4 A:3002 , HOH A:4001BINDING SITE FOR RESIDUE MN A 2001
07AC7SOFTWARELYS A:56 , TYR A:93 , ASP A:115 , ASP A:117 , ASP A:120 , ASP A:152 , LYS A:154 , MN A:2001 , MN A:2002 , MN A:2004 , HOH A:4021 , HOH A:4262BINDING SITE FOR RESIDUE PO4 A 3002
08AC8SOFTWARELYS B:1056 , TYR B:1093 , ASP B:1115 , ASP B:1117 , ASP B:1120 , ASP B:1152 , LYS B:1154 , MN B:2005 , MN B:2006 , MN B:2008 , HOH B:4012 , HOH B:4202BINDING SITE FOR RESIDUE PO4 B 3004
09MN1AUTHORASP A:117 , ASP A:152 , ASP A:115 , ASP A:120METAL 1 BINDING SITE
10MN2AUTHORASP A:117 , TYR A:93 , ASP A:120METAL 2 BINDING SITE
11MN4AUTHORASP A:152 , ASP A:147METAL 4 BINDING SITE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 8PRK)

(-) 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 8PRK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 8PRK)

(-) Exons   (0, 0)

(no "Exon" information available for 8PRK)

(-) 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
                                                                                                                                                                                                                                                                                                                           
               SCOP domains d8prka_ A: Inorganic pyrophosphatase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 8prkA00 A:1-282 Inorganic Pyrophosphatase                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........eeeeee..eee...........hhh.eeeeeeee.......eee........eee.....................eeeee.......................eeee..........eeeeeeeeeeeeee..eeeeeeeeee.....hhh...hhhhhhh...hhhhhhhhhhh..hhh.......hhhh.eeehhhhhhhhhhhhhhhhhhh...........................................hhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                8prk A    1 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLKFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASLKADAPIDKSIDKWFFI  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
                                                                                                                                                                                                                                                                                                                           
               SCOP domains d8prkb_ B: Inorganic pyrophosphatase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 8prkB00 B:1001-1282 Inorganic Pyrophosphatase                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee......eeeeee..eee...............eeeeeeee.......eee........eee.....................eeeee.......................eeee..........eeeeeeeeee..........eeeeee.....hhh...hhhhhhh...hhhhhhhhhhh..hhh.......hhhh.eeehhhhhhhhhhhhhhhhhhh........................hhhhh.....eee......hhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                8prk B 1001 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLKFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASLKADAPIDKSIDKWFFI 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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  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 8PRK)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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    Phe A:84 - Pro A:85   [ RasMol ]  
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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 1wgj 1ypp 2ihp 2ik0 2ik1 2ik2 2ik4 2ik6 2ik7 2ik9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 8PRK)