1Y6V - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF E. COLI ALKALINE PHOSPHATASE IN PRESENCE OF COBALT AT 1.60 A RESOLUTION

Authors :   J. Wang, K. Stieglitz, E. R. Kantrowitz

Date :   07 Dec 04 (Deposition) - 21 Jun 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Metal Specificity, X-Ray Crystallography, High-Spin/Low- Spin Configurations, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Wang, K. A. Stieglitz, E. R. Kantrowitz
Metal Specificity Is Correlated With Two Crucial Active Site Residues In Escherichia Coli Alkaline Phosphatase(, ).
Biochemistry V. 44 8378 2005
PubMed-ID: 15938627 | Reference-DOI: 10.1021/BI050155P
(for further references see the PDB file header)

Molecule 1 - ALKALINE PHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.1.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEK154
	Expression System Strain	:	SM547
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PHOA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	APASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	CO	6	Ligand/Ion	COBALT (II) ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:327 , HIS A:331 , HIS A:412 , PO4 A:856	BINDING SITE FOR RESIDUE CO A 850
02	AC2	SOFTWARE	ASP A:51 , SER A:102 , ASP A:327 , ASP A:369 , HIS A:370 , PO4 A:856	BINDING SITE FOR RESIDUE CO A 851
03	AC3	SOFTWARE	ASP A:51 , THR A:155 , GLU A:322 , HOH A:888 , HOH A:1242 , HOH A:1265	BINDING SITE FOR RESIDUE CO A 852
04	AC4	SOFTWARE	ASP A:51 , ASP A:101 , SER A:102 , ARG A:166 , ASP A:327 , HIS A:331 , HIS A:370 , HIS A:412 , CO A:850 , CO A:851 , HOH A:888 , HOH A:987 , HOH A:1228	BINDING SITE FOR RESIDUE PO4 A 856
05	AC5	SOFTWARE	ARG A:267 , TRP A:268 , ARG A:292 , HOH A:859 , HOH A:902 , HOH A:1218 , LYS B:449	BINDING SITE FOR RESIDUE SO4 A 858
06	AC6	SOFTWARE	ASP B:327 , HIS B:331 , HIS B:412 , PO4 B:956	BINDING SITE FOR RESIDUE CO B 950
07	AC7	SOFTWARE	ASP B:51 , SER B:102 , ASP B:369 , HIS B:370 , PO4 B:956	BINDING SITE FOR RESIDUE CO B 951
08	AC8	SOFTWARE	ASP B:51 , ASP B:153 , THR B:155 , GLU B:322 , HOH B:970 , HOH B:1022 , HOH B:1262	BINDING SITE FOR RESIDUE CO B 952
09	AC9	SOFTWARE	ASP B:51 , ASP B:101 , SER B:102 , ARG B:166 , ASP B:327 , HIS B:331 , HIS B:370 , HIS B:412 , CO B:950 , CO B:951 , HOH B:1022 , HOH B:1024 , HOH B:1168	BINDING SITE FOR RESIDUE PO4 B 956
10	BC1	SOFTWARE	ARG B:267 , TRP B:268 , ARG B:292 , HOH B:1109	BINDING SITE FOR RESIDUE SO4 B 958

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 1Y6V)

(no "SAP(SNP)/Variant" information available for 1Y6V)

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 1Y6V)

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
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462         
            PPB_ECOLI    23 TPEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK 471
               SCOP domains d1y6va_ A: Alkaline phosphatase                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1y6vA00 A:1-449 Alkaline Phosphatase, subunit A                                                                                                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................hhhhhhhh.......eeeeeee...hhhhhhhhhhhhh.......hhhhh.eeeeee..ee......ee...hhhhhhhhhhhh..................hhhhhhhhh..eeeeeeeee..hhhhhh...........hhhhhhhhh...hhhhh...hhhhhhhhhh..eeeee.hhhhhh..........hhhhhhhhh..eee.hhhhhhhh........eeee.........ee....eehhhhhh.....ee.........hhhhhhhhhhhhhh.....eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.......eee........eeeeee.....eeeeee..............eeeeee..hhhhhheeeehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------ALKALINE_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y6v A   1 TPEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK 449
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440

Chain B from PDB  Type:PROTEIN  Length:449
 aligned with PPB_ECOLI | P00634 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:449
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462         
            PPB_ECOLI    23 TPEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK 471
               SCOP domains d1y6vb_ B: Alkaline phosphatase                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1y6vB00 B:1-449 Alkaline Phosphatase, subunit A                                                                                                                                                                                                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Alk_phosphatase-1y6vB01 B:405-448           - Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Alk_phosphatase-1y6vB02 B:405-448           - Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Alk_phosphatase-1y6vB03 B:405-448           - Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Alk_phosphatase-1y6vB04 B:405-448           - Pfam domains (4)
         Sec.struct. author ............................hhhhhhhhh......eeeeeee...hhhhhhhhhhhhh.......hhhhh.eeeeee..ee......ee...hhhhhhhhhhhh..................hhhhhhhhh..eeeeeeeee..hhhhhh...........hhhhhhhhh...hhhhh...hhhhhhhhhh..eeeeehhhhhhh..........hhhhhhhhh..eee.hhhhhh..........eeee.........ee....eehhhhhh.....ee.........hhhhhhhhhhhhhh.....eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......eee........eeeeee.....eeeeee..............eeeeee..hhhhhheeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------ALKALINE_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y6v B   1 TPEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK 449
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440

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 [TaxId: 562] (41)

1a	d1y6va_	A:
1b	d1y6vb_	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. Organism_taxid: 562. (8)

1a	1y6vA00	A:1-449
1b	1y6vB00	B:1-449

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Alk_phosphatase (47)

Family: Alk_phosphatase (22)

Escherichia coli (strain K12) (10)

1a	Alk_phosphatase-1y6vB01	B:405-448
1b	Alk_phosphatase-1y6vB02	B:405-448
1c	Alk_phosphatase-1y6vB03	B:405-448
1d	Alk_phosphatase-1y6vB04	B:405-448

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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	1y6v
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1ed8	THE SAME PROTEIN COMPLEXED WITH COBALT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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