2B8J - JenaLib

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Title :   CRYSTAL STRUCTURE OF APHA CLASS B ACID PHOSPHATASE/PHOSPHOTRANSFERASE TERNARY COMPLEX WITH ADENOSINE AND PHOSPHATE AT 2 A RESOLUTION

Authors :   V. Calderone, C. Forleo, M. Benvenuti, M. C. Thaller, G. M. Rossolini, S

Date :   07 Oct 05 (Deposition) - 29 Nov 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.03

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)

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

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 7)

No.	Name	Count	Type	Full Name
1	ADN	1	Ligand/Ion	ADENOSINE
3	AU	1	Ligand/Ion	GOLD ION
2	AU3	1	Ligand/Ion	GOLD 3+ ION
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	PO4	1	Ligand/Ion	PHOSPHATE ION
6	SPM	1	Ligand/Ion	SPERMINE

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	ADN	2	Ligand/Ion	ADENOSINE
3	AU	-1	Ligand/Ion	GOLD ION
2	AU3	2	Ligand/Ion	GOLD 3+ ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	PO4	2	Ligand/Ion	PHOSPHATE ION
6	SPM	2	Ligand/Ion	SPERMINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:44 , ASP A:46 , ASP A:167 , HOH A:670 , HOH A:737 , HOH A:757	BINDING SITE FOR RESIDUE MG A 311
2	AC2	SOFTWARE	ASP B:44 , ASP B:46 , ASP B:167 , HOH B:348 , HOH B:350 , HOH B:352	BINDING SITE FOR RESIDUE MG B 312
3	AC3	SOFTWARE	ASP A:46 , PHE A:56 , LYS A:60 , TYR A:70 , GLY A:113 , THR A:192 , TYR A:193 , PO4 A:301 , AU A:320 , HOH A:696	BINDING SITE FOR RESIDUE SPM A 653
4	AC4	SOFTWARE	ASP A:44 , GLY A:113 , ASP A:145 , LYS A:152 , ASN A:170 , SPM A:653 , HOH A:660 , HOH A:670 , HOH A:737	BINDING SITE FOR RESIDUE PO4 A 301
5	AC5	SOFTWARE	SPM A:653	BINDING SITE FOR RESIDUE AU A 320
6	AC6	SOFTWARE	ASP B:46 , SER B:53 , PHE B:56 , TYR B:70 , TRP B:77 , GLY B:113 , ARG B:114 , THR B:192 , TYR B:193 , HOH B:336	BINDING SITE FOR RESIDUE ADN B 331

(no "SS Bond" information available for 2B8J)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 2B8J)

(no "PROSITE Motif" information available for 2B8J)

(no "Exon" information available for 2B8J)

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 d2b8ja_ A: Class B acid phosphatase, AphA                                                                                                                                                                           SCOP domains
               CATH domains 2b8jA00 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
                 2b8j 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 d2b8ja_ A: Class B acid phosphatase, AphA                                                                                                                                                                           SCOP domains
               CATH domains 2b8jA00 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
                 2b8j 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 d2b8jb_ B: Class B acid phosphatase, AphA                                                                                                                                                                           SCOP domains
               CATH domains 2b8jB00 B:2-212  [code=3.40.50.1000, no name defined]                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh....eeehhhhhhhhhh.....eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhh..........ee........hhhhhhhhh.eeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b8j 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 d2b8jb_ B: Class B acid phosphatase, AphA                                                                                                                                                                           SCOP domains
               CATH domains 2b8jB00 B:2-212  [code=3.40.50.1000, no name defined]                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh....eeehhhhhhhhhh.....eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhh..........ee........hhhhhhhhh.eeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b8j 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: Class B acid phosphatase, AphA (15)

Protein domain: Class B acid phosphatase, AphA (15)

Escherichia coli [TaxId: 562] (11)

1a	d2b8ja_	A:
1b	d2b8jb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1000, no name defined] (211)

Escherichia coli. Organism_taxid: 562. (14)

1a	2b8jA00	A:2-212
1b	2b8jB00	B:2-212

(no "Pfam Domain" information available for 2B8J)

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).

Asymmetric Unit
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	Cis Peptide Bonds
		Lys A:194 - Pro A:195	[ RasMol ]
		Lys B:194 - Pro B:195	[ RasMol ]
		Ser B:2 - Pro B:3	[ RasMol ]

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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
2b82

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Ligands, Modified Residues, Ions (6, 7)

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