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(-) Description

Title :  CRYSTAL STRUCTURE OF BASILLUS SUBTILIS FAMILY II INORGANIC PYROPHOSPHATASE MUTANT, H98Q, IN COMPLEX WITH PNP
 
Authors :  I. P. Fabrichniy, L. Lehtio, E. Oksanen, A. Goldman
Date :  26 Jun 06  (Deposition) - 07 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Pyrophosphatase, Substrate Complex, Mutant, Manganese, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. P. Fabrichniy, L. Lehtio, M. Tammenkoski, A. B. Zyryanov, E. Oksanen, A. A. Baykov, R. Lahti, A. Goldman
A Trimetal Site And Substrate Distortion In A Family Ii Inorganic Pyrophosphatase.
J. Biol. Chem. V. 282 1422 2007
PubMed-ID: 17095506  |  Reference-DOI: 10.1074/JBC.M513161200

(-) Compounds

Molecule 1 - MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE
    ChainsA, B
    EC Number3.6.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-15B
    Expression System StrainC43 (DE3)
    Expression System Taxid562
    MutationYES
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymINORGANIC PYROPHOSPHATASE, PYROPHOSPHATE PHOSPHO-HYDROLASE, PPASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 19)

Asymmetric/Biological Unit (7, 19)
No.NameCountTypeFull Name
12PN2Ligand/IonIMIDODIPHOSPHORIC ACID
2FE4Ligand/IonFE (III) ION
3GOL2Ligand/IonGLYCEROL
4MG4Ligand/IonMAGNESIUM ION
5MN3Ligand/IonMANGANESE (II) ION
6PG42Ligand/IonTETRAETHYLENE GLYCOL
7SO42Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:9 , ASP A:13 , ASP A:75 , FE A:1310 , MG A:1312 , MN A:1314 , 2PN A:1315 , HOH A:2195BINDING SITE FOR RESIDUE FE A1309
02AC2SOFTWAREASP A:15 , ASP A:75 , HIS A:97 , ASP A:149 , FE A:1309 , MN A:1313 , 2PN A:1315 , HOH A:2195BINDING SITE FOR RESIDUE FE A1310
03AC3SOFTWAREMG A:1312 , 2PN A:1315 , HOH A:2013 , HOH A:2131 , HOH A:2198 , HOH A:2199BINDING SITE FOR RESIDUE MG A1311
04AC4SOFTWAREASP A:13 , ASP A:149 , FE A:1309 , MG A:1311 , MN A:1313 , 2PN A:1315 , HOH A:2105 , HOH A:2195 , HOH A:2199BINDING SITE FOR RESIDUE MG A1312
05AC5SOFTWAREHIS A:9 , ASP A:13 , ASP A:75 , FE A:1310 , MG A:1312 , MN A:1314 , 2PN A:1315 , HOH A:2195BINDING SITE FOR RESIDUE MN A1313
06AC6SOFTWAREASP A:15 , ASP A:75 , HIS A:97 , ASP A:149 , FE A:1309 , MN A:1313 , 2PN A:1315 , HOH A:2195BINDING SITE FOR RESIDUE MN A1314
07AC7SOFTWAREARG A:38 , GLN A:41BINDING SITE FOR RESIDUE SO4 A1316
08AC8SOFTWAREHIS B:9 , ASP B:13 , ASP B:75 , FE B:1312 , MG B:1314 , MN B:1317 , 2PN B:1318 , HOH B:2283BINDING SITE FOR RESIDUE FE B1311
09AC9SOFTWAREASP B:15 , ASP B:75 , HIS B:97 , ASP B:149 , FE B:1311 , 2PN B:1318 , HOH B:2283BINDING SITE FOR RESIDUE FE B1312
10BC1SOFTWAREMG B:1314 , 2PN B:1318 , HOH B:2023 , HOH B:2219 , HOH B:2285 , HOH B:2286BINDING SITE FOR RESIDUE MG B1313
11BC2SOFTWAREASP B:13 , ASP B:149 , FE B:1311 , MG B:1313 , 2PN B:1318 , HOH B:2187 , HOH B:2283 , HOH B:2285BINDING SITE FOR RESIDUE MG B1314
12BC3SOFTWAREASP B:15 , ASP B:75 , HIS B:97 , ASP B:149 , FE B:1311 , 2PN B:1318 , HOH B:2283BINDING SITE FOR RESIDUE MN B1317
13BC4SOFTWAREARG B:38 , GLN B:41 , HOH B:2287BINDING SITE FOR RESIDUE SO4 B1319
14BC5SOFTWAREHIS A:9 , ASP A:13 , ASP A:75 , HIS A:97 , GLN A:98 , ASP A:149 , LYS A:205 , ARG A:295 , LYS A:296 , FE A:1309 , FE A:1310 , MG A:1311 , MG A:1312 , MN A:1313 , MN A:1314 , HOH A:2013 , HOH A:2131 , HOH A:2146 , HOH A:2187 , HOH A:2195 , HOH A:2196 , HOH A:2197 , HOH A:2198 , HOH A:2199BINDING SITE FOR RESIDUE 2PN A1315
15BC6SOFTWARETYR B:23 , LYS B:27 , LEU B:30 , PHE B:32 , GLU B:93 , TYR B:110 , ASN B:130 , HOH B:2135BINDING SITE FOR RESIDUE PG4 B1309
16BC7SOFTWAREMET B:1 , GLU B:2 , LYS B:128 , LYS B:167 , GLU B:168 , GLU B:171 , HOH B:2199BINDING SITE FOR RESIDUE PG4 B1310
17BC8SOFTWAREHIS B:9 , ASP B:13 , ASP B:75 , HIS B:97 , GLN B:98 , ASP B:149 , LYS B:205 , ARG B:295 , LYS B:296 , FE B:1311 , FE B:1312 , MG B:1313 , MG B:1314 , MN B:1317 , HOH B:2023 , HOH B:2137 , HOH B:2219 , HOH B:2234 , HOH B:2275 , HOH B:2283 , HOH B:2284 , HOH B:2285 , HOH B:2286BINDING SITE FOR RESIDUE 2PN B1318
18BC9SOFTWAREASN B:69 , LYS B:133 , GLU B:135 , LYS B:136 , HOH B:2180 , HOH B:2282BINDING SITE FOR RESIDUE GOL B1315
19CC1SOFTWARETHR B:195 , VAL B:196 , GLU B:197 , ARG B:230 , GLU B:233BINDING SITE FOR RESIDUE GOL B1316

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IW4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IW4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IW4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IW4)

(-) Exons   (0, 0)

(no "Exon" information available for 2IW4)

(-) 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:308
 aligned with PPAC_BACSU | P37487 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    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       291       301        
           PPAC_BACSU     2 EKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMAE 309
               SCOP domains d2iw4a_ A: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2iw4A01 A:2-189 inorganic pyrophosphatase (n-terminal core)                                                                                                                                 ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.....ee.........eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhh...eeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeee...hhhhhhhhh......eeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iw4 A   2 EKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHQRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMAE 309
                                    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       291       301        

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with PPAC_BACSU | P37487 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:309
                                    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       290       300         
           PPAC_BACSU     1 MEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMAE 309
               SCOP domains d2iw4b_ B: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2iw4B01 B:1-189 inorganic pyrophosphatase (n-terminal core)                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.....ee.........eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhh...eeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeee...hhhhhhhhh......eeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iw4 B   1 MEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHQRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMAE 309
                                    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       290       300         

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IW4)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PPAC_BACSU | P37487)
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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016462    pyrophosphatase activity    Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments.
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
        PPAC_BACSU | P374871k23 1wpm 1wpn 2haw

(-) Related Entries Specified in the PDB File

1k23 INORGANIC PYROPHOSPHATASE (FAMILY II) FROM BACILLUS SUBTILIS
1wpm STRUCTURE OF BACILLUS SUBTILIS INORGANIC PYROPHOSPHATASE
1wpn CRYSTAL STRUCTURE OF THE N-TERMINAL CORE OF BACILLUSSUBTILIS INORGANIC PYROPHOSPHATASE