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(-) Description

Title :  INORGANIC PYROPHOSPHATASE (FAMILY II) FROM BACILLUS SUBTILIS
 
Authors :  S. Ahn, A. J. Milner, K. Futterer, M. Konopka, M. Ilias, T. W. Young, S. A. White
Date :  26 Sep 01  (Deposition) - 31 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Inorganic Pyrophosphatase, Manganese, Binuclear Metal Centre, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ahn, A. J. Milner, K. Futterer, M. Konopka, M. Ilias, T. W. Young, S. A. White
The "Open" And "Closed" Structures Of The Type-C Inorganic Pyrophosphatases From Bacillus Subtilis And Streptococcus Gordonii.
J. Mol. Biol. V. 313 797 2001
PubMed-ID: 11697905  |  Reference-DOI: 10.1006/JMBI.2001.5070
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE
    Chains: A, B, C, D
    EC Number: 3.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: PYROPHOSPHATE PHOSPHO-HYDROLASE, PPASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 28)

Asymmetric Unit (2, 28)
No.NameCountTypeFull Name
1MN8Ligand/IonMANGANESE (II) ION
2MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:9 , ASP A:13 , ASP A:75 , HOH A:403BINDING SITE FOR RESIDUE MN A 401
2AC2SOFTWAREASP A:15 , ASP A:75 , HIS A:97 , THR A:119 , ASP A:149 , HOH A:403BINDING SITE FOR RESIDUE MN A 402
3AC3SOFTWAREHIS B:9 , ASP B:13 , ASP B:75 , HOH B:405BINDING SITE FOR RESIDUE MN B 403
4AC4SOFTWAREASP B:15 , ASP B:75 , HIS B:97 , THR B:119 , ASP B:149 , HOH B:405BINDING SITE FOR RESIDUE MN B 404
5AC5SOFTWAREHIS C:9 , ASP C:13 , ASP C:75 , HOH C:407BINDING SITE FOR RESIDUE MN C 405
6AC6SOFTWAREASP C:15 , ASP C:75 , HIS C:97 , THR C:119 , ASP C:149 , HOH C:407BINDING SITE FOR RESIDUE MN C 406
7AC7SOFTWAREHIS D:9 , ASP D:13 , ASP D:75 , MN D:408 , HOH D:410BINDING SITE FOR RESIDUE MN D 407
8AC8SOFTWAREASP D:15 , ASP D:75 , HIS D:97 , THR D:119 , ASP D:149 , MN D:407 , HOH D:410BINDING SITE FOR RESIDUE MN D 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K23)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K23)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K23)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K23)

(-) Exons   (0, 0)

(no "Exon" information available for 1K23)

(-) Sequences/Alignments

Asymmetric 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:307
 aligned with PPAC_BACSU | P37487 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:307
                                    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 MEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAM 307
               SCOP domains d1k23a_ A: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                SCOP domains
               CATH domains -1k23A01 A:2-189 inorganic pyrophosphatase (n-terminal core)                                                                                                                                 ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh.....ee.........eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhhhheeeeehhhhh.eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee...hhhhhhh.......eeee.........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k23 A   1 mEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKmYKENNVKIEKEIAGLmLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNmLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAm 307
                            |       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      |
                            |                                                                                                                          126-MSE         142-MSE                                   184-MSE                                                                                                                    307-MSE
                            1-MSE                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:307
 aligned with PPAC_BACSU | P37487 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:307
                                    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 MEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAM 307
               SCOP domains d1k23b_ B: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                SCOP domains
               CATH domains -1k23B01 B:2-189 inorganic pyrophosphatase (n-terminal core)                                                                                                                                 ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh.....ee.........eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhh..eeeeehhhhh.eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee...hhhhhhh.......eeee.........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k23 B   1 mEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKmYKENNVKIEKEIAGLmLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNmLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAm 307
                            |       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      |
                            |                                                                                                                          126-MSE         142-MSE                                   184-MSE                                                                                                                    307-MSE
                            1-MSE                                                                                                                                                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:308
 aligned with PPAC_BACSU | P37487 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    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 MEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMA 308
               SCOP domains d1k23c_ C: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -1k23C01 C:2-189 inorganic pyrophosphatase (n-terminal core)                                                                                                                                 ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh.....ee.........eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhh..eeeeehhhhh.eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee...hhhhhhh.......eeee.........hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k23 C   1 mEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKmYKENNVKIEKEIAGLmLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNmLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAmA 308
                            |       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      | 
                            |                                                                                                                          126-MSE         142-MSE                                   184-MSE                                                                                                                    307-MSE
                            1-MSE                                                                                                                                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:231
 aligned with PPAC_BACSU | P37487 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:307
                                    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 MEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAM 307
               SCOP domains d1k23d_ D: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                SCOP domains
               CATH domains -1k23D01 D:2-190 inorganic pyrophosphatase (n-terminal core)                                                                                                                                  --------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DHH-1k23D05 D:1-147                                                                                                                                ---------------------------------DHHA2-1k23D01                       D:181-307                                                                                   Pfam domains (1)
           Pfam domains (2) DHH-1k23D06 D:1-147                                                                                                                                ---------------------------------DHHA2-1k23D02                       D:181-307                                                                                   Pfam domains (2)
           Pfam domains (3) DHH-1k23D07 D:1-147                                                                                                                                ---------------------------------DHHA2-1k23D03                       D:181-307                                                                                   Pfam domains (3)
           Pfam domains (4) DHH-1k23D08 D:1-147                                                                                                                                ---------------------------------DHHA2-1k23D04                       D:181-307                                                                                   Pfam domains (4)
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh.....ee.........eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhh......----------------------....ee......------------------------...ee......------------------------------.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k23 D   1 mEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKmYKENNVKIEKEIAGLmLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNmLKAGADLSK----------------------IAQVNTVDIEDV------------------------LVITDILENDS------------------------------VSRKKQVVPVLTDAm 307
                            |       10        20        30        40        50        60        70        80        90       100       110       120     | 130       140 |     150       160       170       180   |   190  |      -         -     | 220      |  -         -         - |     260 |       -         -         -  |    300      |
                            |                                                                                                                          126-MSE         142-MSE                                   184-MSE  193                    216        227                      252       262                            293           307-MSE
                            1-MSE
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: no clan defined [family: DHHA2] (7)
(-)
Family: DHHA2 (7)
(-)
Bacillus subtilis (2)
1aDHHA2-1k23D01D:181-307
1bDHHA2-1k23D02D:181-307
1cDHHA2-1k23D03D:181-307
1dDHHA2-1k23D04D:181-307
(-)
Clan: no clan defined [family: DHH] (7)
(-)
Family: DHH (7)
(-)
Bacillus subtilis (2)
2aDHH-1k23D05D:1-147
2bDHH-1k23D06D:1-147
2cDHH-1k23D07D:1-147
2dDHH-1k23D08D:1-147

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  1k23
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  PPAC_BACSU | P37487
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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
        PPAC_BACSU | P37487: 1wpm 1wpn 2haw 2iw4

(-) Related Entries Specified in the PDB File

1k20 INORGANIC PYROPHOSPHATASE (FAMILY II) FROM STREPTOCOCCUS GORDONII