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Title :   STRUCTURE OF E.COLI ALKALINE PHOSPHATASE MUTANT IN COMPLEX WITH A PHOSPHORYLATED PEPTIDE

Authors :   W. H. Wang, T. Jiang

Date :   07 Jul 08 (Deposition) - 16 Jun 09 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Alkaline Phosphatase, Complex Structure, Protein Kinase, Hydrolase, Magnesium, Metal-Binding, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Li, L. Bi, W. Wang, Y. Li, Y. Zhou, H. Wei, T. Jiang, L. Bai, Y. Chen, Z. Zhang, X. Yuan, J. Xiao, X. -E. Zhang
Development Of A Universal Phosphorylated Peptide-Binding Protein For Simultaneous Assay Of Kinases
Biosens. Bioelectron. V. 24 2871 2009
PubMed-ID: 19349157 | Reference-DOI: 10.1016/J.BIOS.2009.02.020

Molecule 1 - ALKALINE PHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.1.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PASK75
	Expression System Strain	:	SM547
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PHOA, B0383, JW0374
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	APASE

Molecule 2 - PHOSPHORYLATED PEPTIDE
	Chains	:	C
	Engineered	:	YES
	Other Details	:	THIS SEQUENCE IS CHEMICALLY SYNTHESIZED
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION
2	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE
3	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:102 , ARG A:166 , HIS A:412 , HOH A:484	BINDING SITE FOR RESIDUE PO4 A 456
2	AC2	SOFTWARE	ALA A:11 , GLU A:66 , GLY A:70 , PHE A:71 , LYS A:393 , HOH A:549	BINDING SITE FOR RESIDUE TRS A 457

Asymmetric/Biological Unit

No.	Residues
1	A:168	-	A:178
2	A:286	-	A:336
3	B:168	-	B:178
4	B:286	-	B:336

(no "Cis Peptide Bond" information available for 3DPC)

(no "SAP(SNP)/Variant" information available for 3DPC)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALKALINE_PHOSPHATASE	PS00123	Alkaline phosphatase active site.	PPB_ECOLI	121-129	2	A:99-107 B:99-107

(no "Exon" information available for 3DPC)

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:449
 aligned with PPB_ECOLI | P00634 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         471 
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       | 
            PPB_ECOLI    24 PEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK-   -
               SCOP domains d3dpca_ A: Alkaline phosphatase                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3dpcA00 A:2-450 Alkaline Phosphatase, subunit A                                                                                                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................hhhhhhh........eeeeeee...hhhhhhhhhhhhh.......hhhhh.eeeeee..ee......ee...hhhhhhhhhhhh..................hhhhhhhhh..eeeeeeeee..hhhhhh...........hhhhhhhhh...hhhhh...hhhhhhhhhh..eeeee..hhhhh..........hhhhhhhhh..eee.hhhhhhh.........eeee.........ee....eehhhhhh.....ee.........hhhhhhhhhhhhhh.....eeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...ee..eee........eeeeee.....eeeee..........ee...eeeeee..hhhhhheeeehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------ALKALINE_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dpc A   2 PEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDLAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLKH 450
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441

Chain B from PDB  Type:PROTEIN  Length:448
 aligned with PPB_ECOLI | P00634 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:448
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463        
            PPB_ECOLI    24 PEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK 471
               SCOP domains d3dpcb_ B: Alkaline phosphatase                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3dpcB00 B:2-449 Alkaline Phosphatase, subunit A                                                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................hhhhhhhhh......eeeeeee...hhhhhhhhhhhhh.............eeeeee..ee......ee...hhhhhhhhhhhh..................hhhhhhhh...eeeeeeeee..hhhhhh...........hhhhhhhhh...hhhhh...hhhhhhhhhh..eeeee.hhhhhh..........hhhhhhhhh..eee.hhhhhhh.........eeee.........ee....eehhhhhh.....ee.........hhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.......eee........eeeeee.....eeeeee..............eeeeee..hhhhhheeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------ALKALINE_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dpc B   2 PEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDLAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK 449
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441

Chain C from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 3dpc C   1 HAtPPKKEAD  10
                              |     10
                              3-TPO

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Alkaline phosphatase-like (78)

Superfamily: Alkaline phosphatase-like (78)

Family: Alkaline phosphatase (56)

Protein domain: Alkaline phosphatase (47)

Escherichia coli K-12 [TaxId: 83333] (2)

1a	d3dpca_	A:
1b	d3dpcb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Alkaline Phosphatase, subunit A (66)

Homologous Superfamily: Alkaline Phosphatase, subunit A (66)

Escherichia coli k12. Organism_taxid: 83333. Strain: k12. (1)

1a	3dpcB00	B:2-449
1b	3dpcA00	A:2-450

(no "Pfam Domain" information available for 3DPC)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PPB_ECOLI | P00634)

molecular function
	GO:0004035	alkaline phosphatase activity	Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0033748	hydrogenase (acceptor) activity	Catalysis of the reaction: H2 + A = AH2.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0030613	oxidoreductase activity, acting on phosphorus or arsenic in donors	Catalysis of an oxidation-reduction (redox) reaction in which a phosphorus- or arsenic-containing group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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/Biological Unit
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Description

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Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

SS Bonds (4, 4)

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