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(-) Description

Title :  CRYSTAL STRUCTURE OF S. TYPHIMURIUM APHA COMPLEXED WITH CYCLIC-AMP
 
Authors :  R. D. Makde, V. Kumar
Date :  20 Mar 05  (Deposition) - 21 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Class-B Bacterial Acid Phosphatase, Cyclic-Amp Complex Of Apha Protein, Metalloenzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. D. Makde, G. D. Gupta, V. Kumar
Structure And Function Of Class-B Bacterial Non-Specific Acid Phosphatase: Functional Role Of Invariant Lys154
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - APHA PROTEIN
    Chains: A, B, C, D
    EC Number: 3.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21(A)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: APHA
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CMP4Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2MG4Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:46 , ASP A:48 , ASP A:169 , HOH A:504 , HOH A:505 , HOH A:613BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREASP B:46 , ASP B:48 , ASP B:169 , HOH B:509 , HOH B:619 , HOH B:620BINDING SITE FOR RESIDUE MG B 503
3AC3SOFTWAREASP C:46 , ASP C:48 , ASP C:169 , HOH C:227 , HOH C:470 , HOH C:471BINDING SITE FOR RESIDUE MG C 505
4AC4SOFTWAREASP D:46 , ASP D:48 , ASP D:169 , HOH D:338 , HOH D:473 , HOH D:474BINDING SITE FOR RESIDUE MG D 507
5AC5SOFTWAREASP A:48 , PHE A:58 , ASP A:70 , TYR A:72 , LEU A:73 , GLY A:115 , ARG A:116 , THR A:194 , TYR A:195 , HOH A:503 , HOH A:505 , HOH A:613 , HOH A:614BINDING SITE FOR RESIDUE CMP A 502
6AC6SOFTWAREASP B:48 , PHE B:58 , TYR B:72 , GLY B:115 , ARG B:116 , THR B:194 , TYR B:195 , HOH B:511 , HOH B:512 , HOH B:620 , HOH B:621 , HOH B:622BINDING SITE FOR RESIDUE CMP B 504
7AC7SOFTWAREASP C:48 , PHE C:58 , TYR C:72 , GLY C:115 , ARG C:116 , THR C:194 , TYR C:195 , HOH C:230 , HOH C:231 , HOH C:471 , HOH C:472BINDING SITE FOR RESIDUE CMP C 506
8AC8SOFTWAREASP D:46 , ASP D:48 , PHE D:58 , TYR D:72 , LEU D:73 , GLY D:115 , ARG D:116 , LYS D:154 , THR D:194 , TYR D:195 , HOH D:339 , HOH D:340 , HOH D:430 , HOH D:473 , HOH D:475 , HOH D:476BINDING SITE FOR RESIDUE CMP D 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z5U)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:196 -Pro A:197
2Lys B:196 -Pro B:197
3Lys C:196 -Pro C:197
4Lys D:196 -Pro D:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z5U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z5U)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z5U)

(-) 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:208
 aligned with APHA_SALTM | Q540U1 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:208
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229        
           APHA_SALTM    30 TLNPGTNVAKLAEQAPVHWVSVAQIENSLTGRPPMAVGFDIDDTVLFSSPGFWRGKKTYSPDSDDYLKNPAFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDSIYFVTGRSQTKTETVSKTLADNFHIPAANMNPVIFAGDKPEQNTKVQWLQEKNMRIFYGDSDNDITAARDCGIRGIRILRAANSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d1z5ua_ A: Class B acid phosphatase, AphA                                                                                                                                                                        SCOP domains
               CATH domains 1z5uA00 A:7-214  [code=3.40.50.1000, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh....eeehhhhhhhhh......eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh..........ee........hhhhhhhhh.eeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z5u A   7 TLNPGTNVAKLAEQAPVHWVSVAQIENSLTGRPPMAVGFDIDDTVLFSSPGFWRGKKTYSPDSDDYLKNPAFWEKMNNGWDEFSIPKEAARQLIDMHVRRGDSIYFVTGRSQTKTETVSKTLADNFHIPAANMNPVIFAGDKPEQNTKVQWLQEKNMRIFYGDSDNDITAARDCGIRGIRILRAANSTYKPLPQAGAFGEEVIVNSEY 214
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206        


Chain B from PDB  Type:PROTEIN  Length:210
 aligned with APHA_SALTM | Q540U1 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:210
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237
           APHA_SALTM    28 PSTLNPGTNVAKLAEQAPVHWVSVAQIENSLTGRPPMAVGFDIDDTVLFSSPGFWRGKKTYSPDSDDYLKNPAFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDSIYFVTGRSQTKTETVSKTLADNFHIPAANMNPVIFAGDKPEQNTKVQWLQEKNMRIFYGDSDNDITAARDCGIRGIRILRAANSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d1z5ub_ B: Class B acid phosphatase, AphA                                                                                                                                                                          SCOP domains
               CATH domains 1z5uB00 B:5-214  [code=3.40.50.1000, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhh....eeehhhhhhhhhh.....eeeee.....eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhh.........ee........hhhhhhhhh.eeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z5u B   5 PSTLNPGTNVAKLAEQAPVHWVSVAQIENSLTGRPPMAVGFDIDDTVLFSSPGFWRGKKTYSPDSDDYLKNPAFWEKMNNGWDEFSIPKEAARQLIDMHVRRGDSIYFVTGRSQTKTETVSKTLADNFHIPAANMNPVIFAGDKPEQNTKVQWLQEKNMRIFYGDSDNDITAARDCGIRGIRILRAANSTYKPLPQAGAFGEEVIVNSEY 214
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214


Chain C from PDB  Type:PROTEIN  Length:208
 aligned with APHA_SALTM | Q540U1 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:208
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229        
           APHA_SALTM    30 TLNPGTNVAKLAEQAPVHWVSVAQIENSLTGRPPMAVGFDIDDTVLFSSPGFWRGKKTYSPDSDDYLKNPAFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDSIYFVTGRSQTKTETVSKTLADNFHIPAANMNPVIFAGDKPEQNTKVQWLQEKNMRIFYGDSDNDITAARDCGIRGIRILRAANSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d1z5uc_ C: Class B acid phosphatase, AphA                                                                                                                                                                        SCOP domains
               CATH domains 1z5uC00 C:7-214  [code=3.40.50.1000, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh....eeehhhhhhhhh......eeeee.....eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhh..........ee........hhhhhhhhh.eeeeee.hhhhhhhhhhhh.eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z5u C   7 TLNPGTNVAKLAEQAPVHWVSVAQIENSLTGRPPMAVGFDIDDTVLFSSPGFWRGKKTYSPDSDDYLKNPAFWEKMNNGWDEFSIPKEAARQLIDMHVRRGDSIYFVTGRSQTKTETVSKTLADNFHIPAANMNPVIFAGDKPEQNTKVQWLQEKNMRIFYGDSDNDITAARDCGIRGIRILRAANSTYKPLPQAGAFGEEVIVNSEY 214
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206        


Chain D from PDB  Type:PROTEIN  Length:210
 aligned with APHA_SALTM | Q540U1 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:210
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237
           APHA_SALTM    28 PSTLNPGTNVAKLAEQAPVHWVSVAQIENSLTGRPPMAVGFDIDDTVLFSSPGFWRGKKTYSPDSDDYLKNPAFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDSIYFVTGRSQTKTETVSKTLADNFHIPAANMNPVIFAGDKPEQNTKVQWLQEKNMRIFYGDSDNDITAARDCGIRGIRILRAANSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d1z5ud_ D: Class B acid phosphatase, AphA                                                                                                                                                                          SCOP domains
               CATH domains 1z5uD00 D:5-214  [code=3.40.50.1000, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhh....eeehhhhhhhh.......eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhh..........ee........hhhhhhhhh.eeeeee.hhhhhhhhhhhh.eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z5u D   5 PSTLNPGTNVAKLAEQAPVHWVSVAQIENSLTGRPPMAVGFDIDDTVLFSSPGFWRGKKTYSPDSDDYLKNPAFWEKMNNGWDEFSIPKEAARQLIDMHVRRGDSIYFVTGRSQTKTETVSKTLADNFHIPAANMNPVIFAGDKPEQNTKVQWLQEKNMRIFYGDSDNDITAARDCGIRGIRILRAANSTYKPLPQAGAFGEEVIVNSEY 214
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Z5U)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (APHA_SALTM | Q540U1)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        APHA_SALTM | Q540U1: 1z5g 1z88 2aut

(-) Related Entries Specified in the PDB File

1z5g CRYSTAL STRUCTURE OF THE NATIVE APHA PROTEIN FROM S. TYPHIMURIUM
1z88 CRYSTAL STRUCTURE OF LYS154ARG MUTANT OF MATURE APHA OF S. TYPHIMURIUM