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(-) Description

Title :  CRYSTAL STRUCTURE OF A MUTANT OF ACID PHOSPHATASE FROM ESCHERICHIA BLATTAE (G74D/I153T)
 
Authors :  K. Ishikawa, Y. Mihara, N. Shimba, N. Ohtsu, H. Kawasaki, E. Suzuki, Y. Asano
Date :  22 Apr 02  (Deposition) - 11 Sep 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  All Alpha, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ishikawa, Y. Mihara, N. Shimba, N. Ohtsu, H. Kawasaki, E. Suzuki, Y. Asano
Enhancement Of Nucleoside Phosphorylation Activity In An Acid Phosphatase
Protein Eng. V. 15 539 2002
PubMed-ID: 12200535  |  Reference-DOI: 10.1093/PROTEIN/15.7.539
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACID PHOSPHATASE
    Chains: A, B, C, D, E, F
    EC Number: 3.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC118
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-231
    Mutation: YES
    Organism Scientific: ESCHERICHIA BLATTAE
    Organism Taxid: 563

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:115 , ARG A:122 , SER A:148 , GLY A:149 , HIS A:150 , HIS A:189BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWARELYS B:115 , ARG B:122 , GLY B:149 , HIS B:150 , HIS B:189BINDING SITE FOR RESIDUE SO4 B 1002
3AC3SOFTWARELYS C:115 , ARG C:122 , SER C:148 , GLY C:149 , HIS C:150 , HIS C:189BINDING SITE FOR RESIDUE SO4 C 1003
4AC4SOFTWARELYS D:115 , ARG D:122 , GLY D:149 , HIS D:150 , HIS D:189BINDING SITE FOR RESIDUE SO4 D 1004
5AC5SOFTWARELYS E:115 , ARG E:122 , GLY E:149 , HIS E:150 , HIS E:189BINDING SITE FOR RESIDUE SO4 E 1005
6AC6SOFTWARELYS F:115 , ARG F:122 , SER F:148 , GLY F:149 , HIS F:150 , HIS F:189BINDING SITE FOR RESIDUE SO4 F 1006

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:132 -A:186
2B:132 -B:186
3C:132 -C:186
4D:132 -D:186
5E:132 -E:186
6F:132 -F:186

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Tyr A:146 -Pro A:147
2Tyr B:146 -Pro B:147
3Tyr C:146 -Pro C:147
4Tyr D:146 -Pro D:147
5Tyr E:146 -Pro E:147
6Tyr F:146 -Pro F:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IW8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IW8)

(-) Exons   (0, 0)

(no "Exon" information available for 1IW8)

(-) 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:217
 aligned with Q9S1A6_SHIBL | Q9S1A6 from UniProtKB/TrEMBL  Length:249

    Alignment length:222
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244  
         Q9S1A6_SHIBL    25 GNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGGVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCNTTEQDKLSKNGSYPSGHTSIGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQH 246
               SCOP domains d1iw8a_ A: Bacterial acid phosphatase                                                                                                                                                                                          SCOP domains
               CATH domains 1iw8A00 A:7-228 Vanadium-containing Chloroperoxidase, domain 1                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhh.hhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhh......-----.........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1iw8 A   7 GNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGDVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCN-----KLSKNGSYPSGHTSTGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQH 228
                                    16        26        36        46        56        66        76        86        96       106       116       126      |  -  |    146       156       166       176       186       196       206       216       226  
                                                                                                                                                        133   139                                                                                         


Chain B from PDB  Type:PROTEIN  Length:219
 aligned with Q9S1A6_SHIBL | Q9S1A6 from UniProtKB/TrEMBL  Length:249

    Alignment length:225
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243     
         Q9S1A6_SHIBL    24 TGNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGGVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCNTTEQDKLSKNGSYPSGHTSIGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQHQK 248
               SCOP domains d1iw8b_ B: Bacterial acid phosphatase                                                                                                                                                                                             SCOP domains
               CATH domains 1iw8B00 B:6-230 Vanadium-containing Chloroperoxidase, domain 1                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh.hhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhh......------.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iw8 B   6 TGNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGDVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCNT------SKNGSYPSGHTSTGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQHQK 230
                                    15        25        35        45        55        65        75        85        95       105       115       125        |-     | 145       155       165       175       185       195       205       215       225     
                                                                                                                                                          134    141                                                                                         


Chain C from PDB  Type:PROTEIN  Length:216
 aligned with Q9S1A6_SHIBL | Q9S1A6 from UniProtKB/TrEMBL  Length:249

    Alignment length:222
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243  
         Q9S1A6_SHIBL    24 TGNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGGVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCNTTEQDKLSKNGSYPSGHTSIGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQ 245
               SCOP domains d1iw8c_ C: Bacterial acid phosphatase                                                                                                                                                                                          SCOP domains
               CATH domains 1iw8C00 C:6-227 Vanadium-containing Chloroperoxidase, domain 1                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhh.hhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhh......------.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1iw8 C   6 TGNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGDVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCNT------SKNGSYPSGHTSTGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQ 227
                                    15        25        35        45        55        65        75        85        95       105       115       125        |-     | 145       155       165       175       185       195       205       215       225  
                                                                                                                                                          134    141                                                                                      


Chain D from PDB  Type:PROTEIN  Length:215
 aligned with Q9S1A6_SHIBL | Q9S1A6 from UniProtKB/TrEMBL  Length:249

    Alignment length:222
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244  
         Q9S1A6_SHIBL    25 GNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGGVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCNTTEQDKLSKNGSYPSGHTSIGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQH 246
               SCOP domains d1iw8d_ D: Bacterial acid phosphatase                                                                                                                                                                                          SCOP domains
               CATH domains 1iw8D00 D:7-228 Vanadium-containing Chloroperoxidase, domain 1                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhh.hhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhh.....-------.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1iw8 D   7 GNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGDVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCN-------SKNGSYPSGHTSTGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQH 228
                                    16        26        36        46        56        66        76        86        96       106       116       126      |  -    |  146       156       166       176       186       196       206       216       226  
                                                                                                                                                        133     141                                                                                       


Chain E from PDB  Type:PROTEIN  Length:214
 aligned with Q9S1A6_SHIBL | Q9S1A6 from UniProtKB/TrEMBL  Length:249

    Alignment length:221
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244 
         Q9S1A6_SHIBL    25 GNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGGVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCNTTEQDKLSKNGSYPSGHTSIGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQ 245
               SCOP domains d1iw8e_ E: Bacterial acid phosphatase                                                                                                                                                                                         SCOP domains
               CATH domains 1iw8E00 E:7-227 Vanadium-containing Chloroperoxidase, domain 1                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh.hhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhh.....-------.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iw8 E   7 GNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGDVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCN-------SKNGSYPSGHTSTGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQ 227
                                    16        26        36        46        56        66        76        86        96       106       116       126      |  -    |  146       156       166       176       186       196       206       216       226 
                                                                                                                                                        133     141                                                                                      


Chain F from PDB  Type:PROTEIN  Length:217
 aligned with Q9S1A6_SHIBL | Q9S1A6 from UniProtKB/TrEMBL  Length:249

    Alignment length:223
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
         Q9S1A6_SHIBL    24 TGNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGGVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCNTTEQDKLSKNGSYPSGHTSIGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQH 246
               SCOP domains d1iw8f_ F: Bacterial acid phosphatase                                                                                                                                                                                           SCOP domains
               CATH domains 1iw8F00 F:6-228 Vanadium-containing Chloroperoxidase, domain 1                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh.hhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhh......------.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iw8 F   6 TGNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGDVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCNT------SKNGSYPSGHTSTGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQH 228
                                    15        25        35        45        55        65        75        85        95       105       115       125        |-     | 145       155       165       175       185       195       205       215       225   
                                                                                                                                                          134    141
   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, 6)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IW8)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q9S1A6_SHIBL | Q9S1A6)
molecular function
    GO:0003993    acid phosphatase activity    Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
    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.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

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  1iw8
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  Q9S1A6_SHIBL | Q9S1A6
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  3.1.3.2
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 Related Entries

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

UniProtKB/TrEMBL
        Q9S1A6_SHIBL | Q9S1A6: 1d2t 1eoi

(-) Related Entries Specified in the PDB File

1d2t 1D2T CONTAINS THE WILD-TYPE OF THE SAME PROTEIN.
1eoi 1EOI CONTAINS THE WILD-TYPE OF THE SAME PROTEIN COMPLEXED WITH MOLYBDATE.