1N9K - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE BROMIDE ADDUCT OF APHA CLASS B ACID PHOSPHATASE/PHOSPHOTRANSFERASE FROM E. COLI AT 2.2 A RESOLUTION

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

Date :   25 Nov 02 (Deposition) - 03 Feb 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Class B Acid Phosphatase, Dddd Acid Phosphatase, Metallo-Enzyme Bromide Mad, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Calderone, C. Forleo, M. Benvenuti, M. C. Thaller, G. M. Rossolini, S. Mangani
The First Structure Of A Bacterial Class B Acid Phosphatase Reveals Further Structural Heterogeneity Among Phosphatases Of The Haloacid Dehalogenase Fold.
J. Mol. Biol. V. 335 761 2004
PubMed-ID: 14687572 | Reference-DOI: 10.1016/J.JMB.2003.10.050
(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
	Gene	:	APHA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	APHA CLASS B ACID PHOSPHATASE/PHOSPHOTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 17)

No.	Name	Count	Type	Full Name
1	BR	15	Ligand/Ion	BROMIDE ION
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:44 , ASP A:46 , ASP A:167 , HOH A:1277 , HOH A:1296 , HOH A:1395	BINDING SITE FOR RESIDUE MG A 1213
02	AC2	SOFTWARE	ASP B:44 , ASP B:46 , ASP B:167 , HOH B:1293 , HOH B:1380	BINDING SITE FOR RESIDUE MG B 1214
03	AC3	SOFTWARE	LEU A:196 , HOH A:1254 , HOH B:1281	BINDING SITE FOR RESIDUE BR A 213
04	AC4	SOFTWARE	THR A:151 , LYS A:152	BINDING SITE FOR RESIDUE BR A 214
05	AC5	SOFTWARE	PHE A:63 , TYR A:70 , ASN A:73	BINDING SITE FOR RESIDUE BR A 215
06	AC6	SOFTWARE	ASP A:169 , HOH A:1269	BINDING SITE FOR RESIDUE BR A 216
07	AC7	SOFTWARE	SER A:64 , PRO A:65 , GLU A:66	BINDING SITE FOR RESIDUE BR A 217
08	AC8	SOFTWARE	GLN A:28 , ASN A:31 , HOH A:1324	BINDING SITE FOR RESIDUE BR A 218
09	AC9	SOFTWARE	GLN A:96	BINDING SITE FOR RESIDUE BR A 219
10	BC1	SOFTWARE	GLN B:96	BINDING SITE FOR RESIDUE BR B 220
11	BC2	SOFTWARE	LEU B:196 , HOH B:1243	BINDING SITE FOR RESIDUE BR B 221
12	BC3	SOFTWARE	GLY B:144 , THR B:151 , LYS B:152 , HOH B:1283	BINDING SITE FOR RESIDUE BR B 222
13	BC4	SOFTWARE	ASP B:169 , PRO B:197 , HOH B:1278	BINDING SITE FOR RESIDUE BR B 223
14	BC5	SOFTWARE	PHE B:63 , TYR B:70 , ASN B:73	BINDING SITE FOR RESIDUE BR B 224
15	BC6	SOFTWARE	SER B:64 , PRO B:65 , GLU B:66	BINDING SITE FOR RESIDUE BR B 225
16	BC7	SOFTWARE	PRO B:116 , ALA B:134 , PHE B:142 , GLN B:149	BINDING SITE FOR RESIDUE BR B 226
17	BC8	SOFTWARE	GLY B:83 , TRP B:84 , HOH B:1332	BINDING SITE FOR RESIDUE BR B 227

(no "SS Bond" information available for 1N9K)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 1N9K)

(no "PROSITE Motif" information available for 1N9K)

(no "Exon" information available for 1N9K)

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:209
 aligned with APHA_ECOLI | P0AE22 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:209
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228         
           APHA_ECOLI    29 SPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d1n9ka_ A: Class B acid phosphatase, AphA                                                                                                                                                                         SCOP domains
               CATH domains 1n9kA00 A:4-212  [code=3.40.50.1000, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh....eeehhhhhhhhh......eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh..........ee........hhhhhhhhh.eeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n9k A   4 SPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 212
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Chain A from PDB  Type:PROTEIN  Length:209
 aligned with APHA_SHIFL | P0AE23 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:209
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228         
           APHA_SHIFL    29 SPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d1n9ka_ A: Class B acid phosphatase, AphA                                                                                                                                                                         SCOP domains
               CATH domains 1n9kA00 A:4-212  [code=3.40.50.1000, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh....eeehhhhhhhhh......eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh..........ee........hhhhhhhhh.eeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n9k A   4 SPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 212
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with APHA_ECOLI | P0AE22 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:209
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228         
           APHA_ECOLI    29 SPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d1n9kb_ B: Class B acid phosphatase, AphA                                                                                                                                                                         SCOP domains
               CATH domains 1n9kB00 B:4-212  [code=3.40.50.1000, no name defined]                                                                                                                                                             CATH domains
           Pfam domains (1) Acid_phosphat_B-1n9kB01 B:4-196                                                                                                                                                                  ---------------- Pfam domains (1)
           Pfam domains (2) Acid_phosphat_B-1n9kB02 B:4-196                                                                                                                                                                  ---------------- Pfam domains (2)
         Sec.struct. author .......hhhhhhh....eeehhhhhhhhh......eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh..........ee........hhhhhhhhhheeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n9k B   4 SPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 212
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with APHA_SHIFL | P0AE23 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:209
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228         
           APHA_SHIFL    29 SPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d1n9kb_ B: Class B acid phosphatase, AphA                                                                                                                                                                         SCOP domains
               CATH domains 1n9kB00 B:4-212  [code=3.40.50.1000, no name defined]                                                                                                                                                             CATH domains
           Pfam domains (1) Acid_phosphat_B-1n9kB01 B:4-196                                                                                                                                                                  ---------------- Pfam domains (1)
           Pfam domains (2) Acid_phosphat_B-1n9kB02 B:4-196                                                                                                                                                                  ---------------- Pfam domains (2)
         Sec.struct. author .......hhhhhhh....eeehhhhhhhhh......eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh..........ee........hhhhhhhhhheeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n9k B   4 SPLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 212
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

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	d1n9ka_	A:
1b	d1n9kb_	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	1n9kA00	A:4-212
1b	1n9kB00	B:4-212

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: Acid_phosphat_B (11)

Escherichia coli (strain K12) (5)

1a	Acid_phosphat_B-1n9kB01	B:4-196
1b	Acid_phosphat_B-1n9kB02	B:4-196

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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