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(-) Description

Title :  CRYSTAL STRUCTURE OF APHA CLASS B ACID PHOSPHATASE/PHOSPHOTRANSFERASE TERNARY COMPLEX WITH ADENOSINE AND PHOSPHATE BOUND TO THE CATALYTIC METAL AT 1.2 A RESOLUTION
 
Authors :  V. Calderone, C. Forleo, M. Benvenuti, M. C. Thaller, G. M. Rossolini, S
Date :  06 Oct 05  (Deposition) - 29 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Class B Acid Phosphatase; Dddd Acid Phosphatase; Metallo-Enzyme; Amp, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Calderone, C. Forleo, M. Benvenuti, M. C. Thaller, G. M. Rossolini, S. Mangani
A Structure-Based Proposal For The Catalytic Mechanism Of The Bacterial Acid Phosphatase Apha Belonging To The Dddd Superfamily Of Phosphohydrolases
J. Mol. Biol. V. 355 708 2006
PubMed-ID: 16330049  |  Reference-DOI: 10.1016/J.JMB.2005.10.068
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLASS B ACID PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APHA, NAPA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: APHA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ADN2Ligand/IonADENOSINE
2MG2Ligand/IonMAGNESIUM ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1ADN4Ligand/IonADENOSINE
2MG-1Ligand/IonMAGNESIUM ION
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:44 , ASP A:46 , ASP A:167 , PO4 A:1004 , HOH A:1436 , HOH A:1449BINDING SITE FOR RESIDUE MG A 1013
2AC2SOFTWAREASP B:44 , ASP B:46 , ASP B:167 , PO4 B:1005 , HOH B:1425 , HOH B:1433BINDING SITE FOR RESIDUE MG B 1014
3AC3SOFTWAREASP A:44 , ILE A:45 , ASP A:46 , THR A:112 , GLY A:113 , LYS A:152 , ADN A:1001 , MG A:1013 , HOH A:1436 , HOH A:1449BINDING SITE FOR RESIDUE PO4 A 1004
4AC4SOFTWAREASP B:44 , ILE B:45 , ASP B:46 , THR B:112 , GLY B:113 , LYS B:152 , ADN B:1002 , MG B:1014 , HOH B:1054 , HOH B:1425 , HOH B:1433BINDING SITE FOR RESIDUE PO4 B 1005
5AC5SOFTWAREPHE A:56 , LYS A:60 , GLU A:68 , TYR A:70 , LEU A:71 , GLY A:113 , ASP A:145 , THR A:192 , TYR A:193 , LYS A:194 , PO4 A:1004 , HOH A:1045 , HOH A:1247BINDING SITE FOR RESIDUE ADN A 1001
6AC6SOFTWAREPHE B:56 , GLU B:68 , TYR B:70 , LEU B:71 , TRP B:77 , GLY B:113 , THR B:192 , TYR B:193 , LYS B:194 , PO4 B:1005 , HOH B:1051 , HOH B:1170 , HOH B:1254 , HOH B:1345 , HOH B:1434BINDING SITE FOR RESIDUE ADN B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B82)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:194 -Pro A:195
2Ser B:2 -Pro B:3
3Lys B:194 -Pro B:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B82)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B82)

(-) Exons   (0, 0)

(no "Exon" information available for 2B82)

(-) 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:211
 aligned with APHA_ECOLI | P0AE22 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:211
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 
           APHA_ECOLI    27 SPSPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d2b82a_ A: Class B acid phosphatase, AphA                                                                                                                                                                           SCOP domains
               CATH domains 2b82A00 A:2-212  [code=3.40.50.1000, no name defined]                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh....eeehhhhhhhhh......eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhh..........ee.........hhhhhhhh.eeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b82 A   2 SPSPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 


Chain A from PDB  Type:PROTEIN  Length:211
 aligned with APHA_SHIFL | P0AE23 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:211
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 
           APHA_SHIFL    27 SPSPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d2b82a_ A: Class B acid phosphatase, AphA                                                                                                                                                                           SCOP domains
               CATH domains 2b82A00 A:2-212  [code=3.40.50.1000, no name defined]                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh....eeehhhhhhhhh......eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhh..........ee.........hhhhhhhh.eeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b82 A   2 SPSPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 


Chain B from PDB  Type:PROTEIN  Length:211
 aligned with APHA_ECOLI | P0AE22 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:211
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 
           APHA_ECOLI    27 SPSPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d2b82b_ B: Class B acid phosphatase, AphA                                                                                                                                                                           SCOP domains
               CATH domains 2b82B00 B:2-212  [code=3.40.50.1000, no name defined]                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh....eeehhhhhhhhh......eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhh..........ee.........hhhhhhhh.eeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b82 B   2 SPSPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 


Chain B from PDB  Type:PROTEIN  Length:211
 aligned with APHA_SHIFL | P0AE23 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:211
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 
           APHA_SHIFL    27 SPSPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d2b82b_ B: Class B acid phosphatase, AphA                                                                                                                                                                           SCOP domains
               CATH domains 2b82B00 B:2-212  [code=3.40.50.1000, no name defined]                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh....eeehhhhhhhhh......eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhh..........ee.........hhhhhhhh.eeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b82 B   2 SPSPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B82)

(-) Gene Ontology  (8, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (APHA_SHIFL | P0AE23)
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).

Chain A,B   (APHA_ECOLI | P0AE22)
molecular function
    GO:0003993    acid phosphatase activity    Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
    GO:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    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.
    GO:0004647    phosphoserine phosphatase activity    Catalysis of the reaction: L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate.
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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  2b82
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  APHA_SHIFL | P0AE23
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  3.1.3.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        APHA_ECOLI | P0AE22: 1n8n 1n9k 1rmq 1rmt 1rmy 2b8j 2g1a 2heg 2hf7 3cz4
        APHA_SHIFL | P0AE23: 1n8n 1n9k 1rmq 1rmt 1rmy 2b8j

(-) Related Entries Specified in the PDB File

1n8n CRYSTAL STRUCTURE OF THE AU3+ COMPLEX OF APHA CLASS B ACID PHOSPHATASE/PHOSPHOTRANSFERASE FROM E. COLI AT 1.7 A RESOLUTION
1n9k CRYSTAL STRUCTURE OF THE BROMIDE ADDUCT OF APHA CLASS B ACID PHOSPHATASE/PHOSPHOTRANSFERASE FROM E. COLI AT 2.2 A RESOLUTION
2b8j