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Title :   CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 4.5 (NO LIGAND BOUND)

Authors :   D. Lim, S. Golovan, C. W. Forsberg, Z. Jia

Date :   08 Dec 99 (Deposition) - 03 Aug 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Histidine Acid Phosphatase Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Lim, S. Golovan, C. W. Forsberg, Z. Jia
Crystal Structures Of Escherichia Coli Phytase And Its Complex With Phytate.
Nat. Struct. Biol. V. 7 108 2000
PubMed-ID: 10655611 | Reference-DOI: 10.1038/72371
(for further references see the PDB file header)

Molecule 1 - PHYTASE
	Chains	:	A, B
	EC Number	:	3.1.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PH 2.5 ACID PHOSPHATASE

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1DKL)

(no "Site" information available for 1DKL)

Asymmetric Unit

No.	Residues
1	A:77	-	A:108
2	A:133	-	A:408
3	A:178	-	A:188
4	A:382	-	A:391
5	B:77	-	B:108
6	B:133	-	B:408
7	B:178	-	B:188
8	B:382	-	B:391

Asymmetric Unit

No.	Residues
1	Leu A:293	-	Pro A:294
2	Leu B:293	-	Pro B:294

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIS_ACID_PHOSPHAT_1	PS00616	Histidine acid phosphatases phosphohistidine signature.	PPA_ECOLI	30-44	2	A:8-22 B:8-22
2	HIS_ACID_PHOSPHAT_2	PS00778	Histidine acid phosphatases active site signature.	PPA_ECOLI	319-335	2	A:297-313 B:297-313

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIS_ACID_PHOSPHAT_1	PS00616	Histidine acid phosphatases phosphohistidine signature.	PPA_ECOLI	30-44	1	A:8-22 -
2	HIS_ACID_PHOSPHAT_2	PS00778	Histidine acid phosphatases active site signature.	PPA_ECOLI	319-335	1	A:297-313 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIS_ACID_PHOSPHAT_1	PS00616	Histidine acid phosphatases phosphohistidine signature.	PPA_ECOLI	30-44	1	- B:8-22
2	HIS_ACID_PHOSPHAT_2	PS00778	Histidine acid phosphatases active site signature.	PPA_ECOLI	319-335	1	- B:297-313

(no "Exon" information available for 1DKL)

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:404
 aligned with PPA_ECOLI | P07102 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:409
                                    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         
            PPA_ECOLI    24 SEPELKLESVVIVSRHGVRAPTKATQLMQDVTPDAWPTWPVKLGWLTPRGGELIAYLGHYQRQRLVADGLLAKKGCPQSGQVAIIADVDERTRKTGEAFAAGLAPDCAITVHTQADTSSPDPLFNPLKTGVCQLDNANVTDAILSRAGGSIADFTGHRQTAFRELERVLNFPQSNLCLKREKQDESCSLTQALPSELKVSADNVSLTGAVSLASMLTEIFLLQQAQGMPEPGWGRITDSHQWNTLLSLHNAQFYLLQRTPEVARSRATPLLDLIKTALTPHPPQKQAYGVTLPTSVLFIAGHDTNLANLGGALELNWTLPGQPDNTPPGGELVFERWRRLSDNSQWIQVSLVFQTLQQMRDKTPLSLNTPPGEVKLTLAGCEERNAQGMCSLAGFTQIVNEARIPACSL 432
               SCOP domains d1dkla_ A: Phytase (myo-inositol-hexakisphosphate-3-phosphohydrolase)                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1dklA01 A:2-134,A:259-410 Phosphoglycerate mutase-like                                                                               1dklA02 A:135-258 Phosphoglycerate mutase-like                                                                              1dklA01 A:2-134,A:259-410 Phosphoglycerate mutase-like                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee.........hhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh.............eeeee..hhhhhhhhhhhhhhhh......ee........hhhhh.........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----..hhhhhh...eeee..eeeehhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....ee.hhh.ee...eeeeeehhhhhhhhhhhhh................eeeeeeeee.....eeeeeeeee.hhhhhhh..........eeee..............eehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HIS_ACID_PHOSPH----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HIS_ACID_PHOSPHAT------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dkl A   2 SEPELKLESVVIVSRHGVRAPTKATQLMQDVTPDAWPTWPVKLGWLTPRGGELIAYLGHYQRQRLVADGLLAKKGCPQSGQVAIIADVDERTRKTGEAFAAGLAPDCAITVHTQADTSSPDPLFNPLKTGVCQLDNANVTDAILSRAGGSIADFTGHRQTAFRELERVLNFPQSNLCLKR-----SCSLTQALPSELKVSADNVSLTGAVSLASMLTEIFLLQQAQGMPEPGWGRITDSHQWNTLLSLHNAQFYLLQRTPEVARSRATPLLDLIKTALTPHPPQKQAYGVTLPTSVLFIAGHDTNLANLGGALELNWTLPGQPDNTPPGGELVFERWRRLSDNSQWIQVSLVFQTLQQMRDKTPLSLNTPPGEVKLTLAGCEERNAQGMCSLAGFTQIVNEARIPACSL 410
                                    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         
                                                                                                                                                                                                             181   187

Chain B from PDB  Type:PROTEIN  Length:402
 aligned with PPA_ECOLI | P07102 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:407
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       
            PPA_ECOLI    26 PELKLESVVIVSRHGVRAPTKATQLMQDVTPDAWPTWPVKLGWLTPRGGELIAYLGHYQRQRLVADGLLAKKGCPQSGQVAIIADVDERTRKTGEAFAAGLAPDCAITVHTQADTSSPDPLFNPLKTGVCQLDNANVTDAILSRAGGSIADFTGHRQTAFRELERVLNFPQSNLCLKREKQDESCSLTQALPSELKVSADNVSLTGAVSLASMLTEIFLLQQAQGMPEPGWGRITDSHQWNTLLSLHNAQFYLLQRTPEVARSRATPLLDLIKTALTPHPPQKQAYGVTLPTSVLFIAGHDTNLANLGGALELNWTLPGQPDNTPPGGELVFERWRRLSDNSQWIQVSLVFQTLQQMRDKTPLSLNTPPGEVKLTLAGCEERNAQGMCSLAGFTQIVNEARIPACSL 432
               SCOP domains d1dklb_ B: Phytase (myo-inositol-hexakisphosphate-3-phosphohydrolase)                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1dklB01 B:4-134,B:259-410 Phosphoglycerate mutase-like                                                                             1dklB02 B:135-258 Phosphoglycerate mutase-like                                                                              1dklB01 B:4-134,B:259-410 Phosphoglycerate mutase-like                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.........hhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh.............eeeee..hhhhhhhhhhhhhhhh......ee........hhhhh.........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----..hhhhhh...eee....eeehhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....ee.hhh.ee...eeeeeehhhhhhhhhhhhh................eeeeeeeee.....eeeeeeeee.hhhhhhh..........eeeee.............eehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----HIS_ACID_PHOSPH----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HIS_ACID_PHOSPHAT------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dkl B   4 PELKLESVVIVSRHGVRAPTKATQLMQDVTPDAWPTWPVKLGWLTPRGGELIAYLGHYQRQRLVADGLLAKKGCPQSGQVAIIADVDERTRKTGEAFAAGLAPDCAITVHTQADTSSPDPLFNPLKTGVCQLDNANVTDAILSRAGGSIADFTGHRQTAFRELERVLNFPQSNLCLKR-----SCSLTQALPSELKVSADNVSLTGAVSLASMLTEIFLLQQAQGMPEPGWGRITDSHQWNTLLSLHNAQFYLLQRTPEVARSRATPLLDLIKTALTPHPPQKQAYGVTLPTSVLFIAGHDTNLANLGGALELNWTLPGQPDNTPPGGELVFERWRRLSDNSQWIQVSLVFQTLQQMRDKTPLSLNTPPGEVKLTLAGCEERNAQGMCSLAGFTQIVNEARIPACSL 410
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       | -   |   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       
                                                                                                                                                                                                           181   187

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: Phosphoglycerate mutase-like (103)

Superfamily: Phosphoglycerate mutase-like (103)

Family: Histidine acid phosphatase (24)

Protein domain: Phytase (myo-inositol-hexakisphosphate-3-phosphohydrolase) (15)

Escherichia coli [TaxId: 562] (6)

1a	d1dkla_	A:
1b	d1dklb_	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: Phosphoglycerate mutase-like (91)

Escherichia coli. Organism_taxid: 562. (8)

1a	1dklB01	B:4-134,B:259-410
1b	1dklA02	A:135-258
1c	1dklB02	B:135-258
1d	1dklA01	A:2-134,A:259-410

(no "Pfam Domain" information available for 1DKL)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PPA_ECOLI | P07102)

molecular function
	GO:0008707	4-phytase activity	Catalysis of the reaction: myo-inositol hexakisphosphate + H2O = 1-myo-inositol 1,2,3,4,5-pentakisphosphate + phosphate.
	GO:0003993	acid phosphatase activity	Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid 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: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.
biological process
	GO:0071454	cellular response to anoxia	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating a decline in oxygen levels to trace amounts, <0.1%.
	GO:0016036	cellular response to phosphate starvation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of phosphate.
	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.
cellular component
	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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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1dkl)

	Sites
(no "Sites" information available for 1dkl)

	Cis Peptide Bonds
		Leu A:293 - Pro A:294	[ RasMol ]
		Leu B:293 - Pro B:294	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	1dkl
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	3.1.3.2
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UniProtKB/Swiss-Prot
	PPA_ECOLI \| P07102	:	1dkm 1dkn 1dko 1dkp 1dkq 4tsr

1dkl	PHYTASE AT PH 4.5 (NO LIGAND BOUND)
1dkm	PHYTASE AT PH 6.6 (HG2+ ACTING AS AN INTERMOLECULAR BRIDGE)
1dkn	PHYTASE AT PH 5.0 (HG2+ ACTING AS AN INTERMOLECULAR BRIDGE)
1dko	PHYTASE AT PH 6.6 (TUNGSTATE BOUND AT THE ACTIVE SITE, HG2+ ACTING AS AN INTERMOLECULAR BRIDGE)
1dkp	PHYTASE AT PH 6.6 (PHYTATE BOUND IN ACTIVE SITE, HG2+ ACTING AS AN INTERMOLECULAR BRIDGE)
1dkq	PHYTASE AT PH 5.0 (PHYTATE BOUND IN ACTIVE SITE, HG2+ ACTING AS AN INTERMOLECULAR BRIDGE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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