3EA1 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE Y247S/Y251S MUTANT OF PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM BACILLUS THURINGIENSIS

Authors :   X. Shi, C. Shao, X. Zhang, C. Zambonelli, A. G. Redfied, J. F. Head, B. A. Seaton, M. F. Roberts

Date :   24 Aug 08 (Deposition) - 14 Apr 09 (Release) - 09 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Phosphatidylinositol-Specific Phospholipase C, Pi-Plc, Dimer, Interfacially Impaired, Membrane Binding, Tim Barrel, Lipid Degradation, Lyase, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Shi, C. Shao, X. Zhang, C. Zambonelli, A. G. Redfield, J. F. Head, B. A. Seaton, M. F. Roberts
Modulation Of Bacillus Thuringiensis Phosphatidylinositol-Specific Phospholipase C Activity By Mutations In The Putative Dimerization Interface.
J. Biol. Chem. V. 284 15607 2009
PubMed-ID: 19369255 | Reference-DOI: 10.1074/JBC.M901601200
(for further references see the PDB file header)

Molecule 1 - 1-PHOSPHATIDYLINOSITOL PHOSPHODIESTERASE
	Chains	:	A, B
	EC Number	:	4.6.1.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS THURINGIENSIS
	Organism Taxid	:	1428
	Synonym	:	PHOSPHATIDYLINOSITOL DIACYLGLYCEROL-LYASE, PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C, PI-PLC

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:224 , HIS A:227 , HOH A:315 , HOH A:635 , HOH A:646	BINDING SITE FOR RESIDUE ZN A 299
2	AC2	SOFTWARE	TYR A:57 , HIS A:61 , GLU A:278 , ASP B:75	BINDING SITE FOR RESIDUE ZN A 300
3	AC3	SOFTWARE	GLU A:93 , HOH A:636 , HOH A:637 , HOH B:474	BINDING SITE FOR RESIDUE ZN A 301
4	AC4	SOFTWARE	ASP A:74 , ASP A:75 , HOH A:309 , HOH A:465 , ASP B:54	BINDING SITE FOR RESIDUE ZN A 302
5	AC5	SOFTWARE	HOH A:441 , HOH A:462 , HOH A:472 , TYR B:57 , HIS B:61 , GLU B:278	BINDING SITE FOR RESIDUE ZN B 299
6	AC6	SOFTWARE	ASP B:224 , HIS B:227 , HOH B:743 , HOH B:748 , HOH B:749	BINDING SITE FOR RESIDUE ZN B 300

(no "SS Bond" information available for 3EA1)

Asymmetric Unit

No.	Residues
1	Ser A:281	-	Pro A:282
2	Ser B:281	-	Pro B:282

(no "SAP(SNP)/Variant" information available for 3EA1)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PIPLC_X_DOMAIN	PS50007	Phosphatidylinositol-specific phospholipase X-box domain profile.	PLC_BACTU	51-194	2	A:20-163 B:20-163

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PIPLC_X_DOMAIN	PS50007	Phosphatidylinositol-specific phospholipase X-box domain profile.	PLC_BACTU	51-194	1	A:20-163 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PIPLC_X_DOMAIN	PS50007	Phosphatidylinositol-specific phospholipase X-box domain profile.	PLC_BACTU	51-194	1	- B:20-163

(no "Exon" information available for 3EA1)

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:296
 aligned with PLC_BACTU | P08954 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:296
                                    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      
            PLC_BACTU    32 ASSVNELENWSKWMQPIPDNIPLARISIPGTHDSGTFKLQNPIKQVWGMTQEYDFRYQMDHGARIFDIRGRLTDDNTIVLHHGPLYLYVTLHEFINEAKQFLKDNPSETIIMSLKKEYEDMKGAEGSFSSTFEKNYFVDPIFLKTEGNIKLGDARGKIVLLKRYSGSNESGGYNNFYWPDNETFTTTVNQNVNVTVQDKYKVNYDEKVKSIKDTMDETMNNSEDLNHLYINFTSLSSGGTAWNSPYYYASYINPEIANDIKQKNPTRVGWVIQDYINEKWSPLLYQEVIRANKSLI 327
               SCOP domains d3ea1a_ A: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3ea1A00 A:1-296 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..................eeee.........hhhhhhhhh....hhhhhhhh...eeeeeeee.....eeeee..eeeeeehhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhh.............hhhhhh..eeeeee...................eeeee.....eeeee.....hhhhhhhhhhhhhhhhhh......eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------PIPLC_X_DOMAIN  PDB: A:20-163 UniProt: 51-194                                                                                                   ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ea1 A   1 ASSVNELENWSKWMQPIPDNIPLARISIPGTHDSGTFKLQNPIKQVWGMTQEYDFRYQMDHGARIFDIRGRLTDDNTIVLHHGPLYLYVTLHEFINEAKQFLKDNPSETIIMSLKKEYEDMKGAEGSFSSTFEKNYFVDPIFLKTEGNIKLGDARGKIVLLKRYSGSNESGGYNNFYWPDNETFTTTVNQNVNVTVQDKYKVNYDEKVKSIKDTMDETMNNSEDLNHLYINFTSLSSGGTAWNSPYSYASSINPEIANDIKQKNPTRVGWVIQDYINEKWSPLLYQEVIRANKSLI 296
                                    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

Chain B from PDB  Type:PROTEIN  Length:296
 aligned with PLC_BACTU | P08954 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:296
                                    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      
            PLC_BACTU    32 ASSVNELENWSKWMQPIPDNIPLARISIPGTHDSGTFKLQNPIKQVWGMTQEYDFRYQMDHGARIFDIRGRLTDDNTIVLHHGPLYLYVTLHEFINEAKQFLKDNPSETIIMSLKKEYEDMKGAEGSFSSTFEKNYFVDPIFLKTEGNIKLGDARGKIVLLKRYSGSNESGGYNNFYWPDNETFTTTVNQNVNVTVQDKYKVNYDEKVKSIKDTMDETMNNSEDLNHLYINFTSLSSGGTAWNSPYYYASYINPEIANDIKQKNPTRVGWVIQDYINEKWSPLLYQEVIRANKSLI 327
               SCOP domains d3ea1b_ B: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3ea1B00 B:1-296 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..................eeee...hhhhh.hhhhhhhhh....hhhhhhhh...eeeeeeee.....eeeee..eeeeeehhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhh.............hhhhhh..eeeeee..................eeeeeee...eeeeeee....hhhhhhhhhhhhhhhhhh......eeeeee...........hhhhhhhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------PIPLC_X_DOMAIN  PDB: B:20-163 UniProt: 51-194                                                                                                   ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ea1 B   1 ASSVNELENWSKWMQPIPDNIPLARISIPGTHDSGTFKLQNPIKQVWGMTQEYDFRYQMDHGARIFDIRGRLTDDNTIVLHHGPLYLYVTLHEFINEAKQFLKDNPSETIIMSLKKEYEDMKGAEGSFSSTFEKNYFVDPIFLKTEGNIKLGDARGKIVLLKRYSGSNESGGYNNFYWPDNETFTTTVNQNVNVTVQDKYKVNYDEKVKSIKDTMDETMNNSEDLNHLYINFTSLSSGGTAWNSPYSYASSINPEIANDIKQKNPTRVGWVIQDYINEKWSPLLYQEVIRANKSLI 296
                                    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

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: PLC-like phosphodiesterases (46)

Family: Bacterial PLC (16)

Protein domain: automated matches (5)

Bacillus thuringiensis [TaxId: 1428] (5)

1a	d3ea1a_	A:
1b	d3ea1b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Phosphatidylinositol (PI) phosphodiesterase (37)

Bacillus thuringiensis. Organism_taxid: 1428. (5)

1a	3ea1A00	A:1-296
1b	3ea1B00	B:1-296

(no "Pfam Domain" information available for 3EA1)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PLC_BACTU | P08954)

molecular function
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0004436	phosphatidylinositol diacylglycerol-lyase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol = D-myo-inositol 1,2-cyclic phosphate + diacylglycerol.
	GO:0008081	phosphoric diester hydrolase activity	Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
	GO:0016042	lipid catabolic process	The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	Cis Peptide Bonds
		Ser A:281 - Pro A:282	[ RasMol ]
		Ser B:281 - Pro B:282	[ RasMol ]

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	PLC_BACTU \| P08954	:	1t6m 2or2 3ea2 3ea3

Description

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Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (0, 0)

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