1RMQ - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF APHA CLASS B ACID PHOSPHATASE/PHOSPHOTRANSFERASE WITH OSMIATE MIMICKING THE CATALYTIC INTERMEDIATE

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

Date :   28 Nov 03 (Deposition) - 14 Dec 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   V. Calderone, C. Forleo, M. Benvenuti, G. M. Rossolini, M. C. Thaller, S. Mangani
Insights In The Catalytic Mechanism Of Apha From Escherichi Coli
To Be Published
PubMed: search
(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 Plasmid	:	PATAC
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	APHA, NAPA, B4055, SF4149, S3580
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CO	2	Ligand/Ion	COBALT (II) ION
2	OS	4	Ligand/Ion	OSMIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	OS	-1	Ligand/Ion	OSMIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:44 , ASP A:46 , ASP A:167 , OS A:402 , HOH A:408 , HOH A:428	BINDING SITE FOR RESIDUE CO A 401
2	AC2	SOFTWARE	ASP A:44 , CO A:401 , HOH A:442	BINDING SITE FOR RESIDUE OS A 402
3	AC3	SOFTWARE	ASP B:44 , ASP B:46 , ASP B:167 , OS B:404 , HOH B:495 , HOH B:551	BINDING SITE FOR RESIDUE CO B 403
4	AC4	SOFTWARE	ASP B:44 , CO B:403 , HOH B:442 , HOH B:548 , HOH B:549	BINDING SITE FOR RESIDUE OS B 404
5	AC5	SOFTWARE	HIS A:22	BINDING SITE FOR RESIDUE OS A 405
6	AC6	SOFTWARE	HIS B:22	BINDING SITE FOR RESIDUE OS B 406

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

Asymmetric Unit

No.	Residues
1	Pro A:147	-	Gly A:148
2	Lys A:194	-	Pro A:195
3	Lys B:194	-	Pro B:195

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

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

(no "Exon" information available for 1RMQ)

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 d1rmqa_ A: Class B acid phosphatase, AphA                                                                                                                                                                         SCOP domains
               CATH domains 1rmqA00 A:4-212  [code=3.40.50.1000, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh....eeehhhhhhhhh......eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhheehhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhh.........ee.........hhhhhhhhheeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rmq 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 d1rmqa_ A: Class B acid phosphatase, AphA                                                                                                                                                                         SCOP domains
               CATH domains 1rmqA00 A:4-212  [code=3.40.50.1000, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh....eeehhhhhhhhh......eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhheehhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhh.........ee.........hhhhhhhhheeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rmq 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:208
 aligned with APHA_ECOLI | P0AE22 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_ECOLI    30 PLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d1rmqb_ B: Class B acid phosphatase, AphA                                                                                                                                                                        SCOP domains
               CATH domains 1rmqB00 B:5-212  [code=3.40.50.1000, no name defined]                                                                                                                                                            CATH domains
           Pfam domains (1) Acid_phosphat_B-1rmqB01 B:5-196                                                                                                                                                                 ---------------- Pfam domains (1)
           Pfam domains (2) Acid_phosphat_B-1rmqB02 B:5-196                                                                                                                                                                 ---------------- Pfam domains (2)
         Sec.struct. author ......hhhhhhh....eeehhhhhhhhhh.....eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhheehhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhh.........ee........hhhhhhhhhheeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rmq B   5 PLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 212
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204

Chain B from PDB  Type:PROTEIN  Length:208
 aligned with APHA_SHIFL | P0AE23 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_SHIFL    30 PLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 237
               SCOP domains d1rmqb_ B: Class B acid phosphatase, AphA                                                                                                                                                                        SCOP domains
               CATH domains 1rmqB00 B:5-212  [code=3.40.50.1000, no name defined]                                                                                                                                                            CATH domains
           Pfam domains (1) Acid_phosphat_B-1rmqB01 B:5-196                                                                                                                                                                 ---------------- Pfam domains (1)
           Pfam domains (2) Acid_phosphat_B-1rmqB02 B:5-196                                                                                                                                                                 ---------------- Pfam domains (2)
         Sec.struct. author ......hhhhhhh....eeehhhhhhhhhh.....eeee......eehhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhheehhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhh.........ee........hhhhhhhhhheeeeee.hhhhhhhhhhh..eeee....................eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rmq B   5 PLNPGTNVARLAEQAPIHWVSVAQIENSLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSPTKTETVSKTLADNFHIPATNMNPVIFAGDKPGQNTKSQWLQDKNIRIFYGDSDNDITAARDVGARGIRILRASNSTYKPLPQAGAFGEEVIVNSEY 212
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204

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	d1rmqa_	A:
1b	d1rmqb_	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	1rmqB00	B:5-212
1b	1rmqA00	A:4-212

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: Acid_phosphat_B (11)

Escherichia coli (strain K12) (5)

1a	Acid_phosphat_B-1rmqB01	B:5-196
1b	Acid_phosphat_B-1rmqB02	B:5-196

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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	Cis Peptide Bonds
		Lys A:194 - Pro A:195	[ RasMol ]
		Lys B:194 - Pro B:195	[ RasMol ]
		Pro A:147 - Gly A:148	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1rmq
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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
1rm7	CRYSTAL STRUCTURE OF APHA CLASS B ACID PHOSPHATASE/ PHOSPHOTRANSFERASE TERNARY COMPLEX WITH ADENOSINE AND PHOSPHATE AT 2 A RESOLUTION
1rmt	CRYSTAL STRUCTURE OF APHA CLASS B ACID PHOSPHATASE/ PHOSPHOTRANSFERASE COMPLEXED WITH ADENOSINE
1rmw	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
1rmy	CRYSTAL STRUCTURE OF APHA CLASS B ACID PHOSPHATASE/ PHOSPHOTRANSFERASE TERNARY COMPLEX WITH DEOXYCYTOSINE AND PHOSPHATE BOUND TO THE CATALYTIC METAL

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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