1Y6O - JenaLib

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Title :   CRYSTAL STRUCTURE OF DISULFIDE ENGINEERED PORCINE PANCREATIC PHOSPHOLIPASE A2 TO GROUP-X ISOZYME IN COMPLEX WITH INHIBITOR MJ33 AND PHOSPHATE IONS

Authors :   B. Z. Yu, Y. H. Pan, M. J. W. Jassen, B. J. Bahnson, M. K. Jain

Date :   06 Dec 04 (Deposition) - 22 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Hydrolase. Disulfide Engineered Pla2. Porcine Pancratic Isozyme. , Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Z. Yu, Y. H. Pan, M. J. W. Janssen, B. J. Bahnson, M. K. Jain
Kinetic And Structural Properties Of Disulfide Engineered Phospholipase A(2): Insight Into The Role Of Disulfide Bonding Patterns.
Biochemistry V. 44 3369 2005
PubMed-ID: 15736947 | Reference-DOI: 10.1021/BI0482147
(for further references see the PDB file header)

Molecule 1 - PHOSPHOLIPASE A2, MAJOR ISOENZYME
	Chains	:	A, B
	EC Number	:	3.1.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMAR25
	Expression System Strain	:	PC2429
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PLA2G1B
	Mutation	:	YES
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Other Details	:	M8L,M20L, N50C, C-TERMIAL INSERTION KGESDKC (RESIDUES 125 TO 131)
	Synonym	:	PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE, GROUP IB PHOSPHOLIPASE A2

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	MJI	2	Ligand/Ion	1-HEXADECYL-3-TRIFLUOROETHYL-SN-GLYCERO-2-PHOSPHATEMETHANE
3	PO4	8	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MJI	1	Ligand/Ion	1-HEXADECYL-3-TRIFLUOROETHYL-SN-GLYCERO-2-PHOSPHATEMETHANE
3	PO4	5	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MJI	1	Ligand/Ion	1-HEXADECYL-3-TRIFLUOROETHYL-SN-GLYCERO-2-PHOSPHATEMETHANE
3	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (2, 10)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MJI	2	Ligand/Ion	1-HEXADECYL-3-TRIFLUOROETHYL-SN-GLYCERO-2-PHOSPHATEMETHANE
3	PO4	8	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:28 , GLY A:30 , GLY A:32 , ASP A:49 , MJI A:217 , HOH A:218	BINDING SITE FOR RESIDUE CA A 207
02	AC2	SOFTWARE	TYR B:28 , GLY B:30 , GLY B:32 , ASP B:49 , MJI B:218 , HOH B:228	BINDING SITE FOR RESIDUE CA B 208
03	AC3	SOFTWARE	ARG A:6 , HIS A:17 , PRO A:18 , LEU A:19 , LEU A:20 , HOH A:309 , HOH A:312 , ARG B:6	BINDING SITE FOR RESIDUE PO4 A 209
04	AC4	SOFTWARE	ARG A:6 , PO4 A:211 , ARG B:6 , HIS B:17 , PRO B:18 , LEU B:19 , LEU B:20 , HOH B:220 , HOH B:222	BINDING SITE FOR RESIDUE PO4 B 210
05	AC5	SOFTWARE	ARG A:6 , LYS A:10 , LYS A:122 , LYS A:125 , HOH A:321 , ARG B:6 , HIS B:17 , PO4 B:210	BINDING SITE FOR RESIDUE PO4 A 211
06	AC6	SOFTWARE	ARG A:43 , HOH A:277 , HOH A:315	BINDING SITE FOR RESIDUE PO4 A 212
07	AC7	SOFTWARE	ASP A:39 , GLU A:40 , PRO A:110 , ASN A:112 , HOH A:238 , HOH A:286	BINDING SITE FOR RESIDUE PO4 A 213
08	AC8	SOFTWARE	ASP B:39 , GLU B:40 , PRO B:110 , ASN B:112 , HOH B:244 , HOH B:246	BINDING SITE FOR RESIDUE PO4 B 214
09	AC9	SOFTWARE	ASP A:21 , LYS A:62 , PHE A:63 , ASP A:66 , TYR A:111 , HOH A:322 , LYS B:121	BINDING SITE FOR RESIDUE PO4 A 215
10	BC1	SOFTWARE	LYS A:121 , ASP B:21 , LYS B:62 , PHE B:63 , ASP B:66 , TYR B:111 , LYS B:113	BINDING SITE FOR RESIDUE PO4 B 216
11	BC2	SOFTWARE	LEU A:2 , PHE A:5 , PRO A:18 , LEU A:19 , ASN A:23 , TYR A:28 , GLY A:30 , LEU A:31 , ASP A:49 , TYR A:69 , CA A:207 , HOH A:219 , HOH A:285 , MJI B:218	BINDING SITE FOR RESIDUE MJI A 217
12	BC3	SOFTWARE	MJI A:217 , PHE B:5 , ILE B:9 , PRO B:18 , LEU B:19 , ASN B:23 , TYR B:28 , GLY B:30 , LEU B:31 , ASP B:49 , TYR B:69 , CA B:208 , HOH B:309	BINDING SITE FOR RESIDUE MJI B 218

Asymmetric Unit

No.	Residues
1	A:11	-	A:77
2	A:27	-	A:124
3	A:29	-	A:45
4	A:44	-	A:105
5	A:50	-	A:131
6	A:51	-	A:98
7	A:61	-	A:91
8	A:84	-	A:96
9	B:11	-	B:77
10	B:27	-	B:124
11	B:29	-	B:45
12	B:44	-	B:105
13	B:50	-	B:131
14	B:51	-	B:98
15	B:61	-	B:91
16	B:84	-	B:96

(no "Cis Peptide Bond" information available for 1Y6O)

(no "SAP(SNP)/Variant" information available for 1Y6O)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA21B_PIG	66-73	2	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA21B_PIG	117-127	2	A:95-105 B:95-105

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA21B_PIG	66-73	1	A:44-51 -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA21B_PIG	117-127	1	A:95-105 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA21B_PIG	66-73	1	- B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA21B_PIG	117-127	1	- B:95-105

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA21B_PIG	66-73	2	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA21B_PIG	117-127	2	A:95-105 B:95-105

(no "Exon" information available for 1Y6O)

Asymmetric Unit

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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:131
 aligned with PA21B_PIG | P00592 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:131
                                                                                                                                                     146       
                                    32        42        52        62        72        82        92       102       112       122       132       142   |     - 
            PA21B_PIG    23 ALWQFRSMIKCAIPGSHPLMDFNNYGCYCGLGGSGTPVDELDRCCETHDNCYRDAKNLDSCKFLVDNPYTESYSYSCSNTEITCNSKNNACEAFICNCDRNAAICFSKAPYNKEHKNLDTKKYC-------   -
               SCOP domains d1y6oa_ A: Phospholipase A2                                                                                                         SCOP domains
               CATH domains 1y6oA00 A:1-131 Phospholipase A2                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh................hhhhhhhhhhhhhhhhhhh.........hhhhh...eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS -------------------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y6o A   1 ALWQFRSLIKCAIPGSHPLLDFNNYGCYCGLGGSGTPVDELDRCCETHDCCYRDAKNLDSCKFLVDNPYTESYSYSCSNTEITCNSKNNACEAFICNCDRNAAICFSKAPYNKEHKNLDTKKYCKGESDKC 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with PA21B_PIG | P00592 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:131
                                                                                                                                                     146       
                                    32        42        52        62        72        82        92       102       112       122       132       142   |     - 
            PA21B_PIG    23 ALWQFRSMIKCAIPGSHPLMDFNNYGCYCGLGGSGTPVDELDRCCETHDNCYRDAKNLDSCKFLVDNPYTESYSYSCSNTEITCNSKNNACEAFICNCDRNAAICFSKAPYNKEHKNLDTKKYC-------   -
               SCOP domains d1y6ob_ B: Phospholipase A2                                                                                                         SCOP domains
               CATH domains 1y6oB00 B:1-131 Phospholipase A2                                                                                                    CATH domains
           Pfam domains (1) Phospholip_A2_1-1y6oB01 B:1-124                                                                                             ------- Pfam domains (1)
           Pfam domains (2) Phospholip_A2_1-1y6oB02 B:1-124                                                                                             ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhh...hhhhhhh...............hhhhhhhhhhhhhhhhhhh.........hhhhh...eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS -------------------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y6o B   1 ALWQFRSLIKCAIPGSHPLLDFNNYGCYCGLGGSGTPVDELDRCCETHDCCYRDAKNLDSCKFLVDNPYTESYSYSCSNTEITCNSKNNACEAFICNCDRNAAICFSKAPYNKEHKNLDTKKYCKGESDKC 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Legend:		→ Mismatch	(orange background)
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	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( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Phospholipase A2, PLA2 (282)

Superfamily: Phospholipase A2, PLA2 (282)

Family: Vertebrate phospholipase A2 (271)

Protein domain: Phospholipase A2 (72)

Pig (Sus scrofa), pancreas [TaxId: 9823] (21)

1a	d1y6oa_	A:
1b	d1y6ob_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Phospholipase A2 (241)

Homologous Superfamily: Phospholipase A2 (241)

Pig (Sus scrofa) (24)

1a	1y6oA00	A:1-131
1b	1y6oB00	B:1-131

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Phospholip_A2_1] (33)

Family: Phospholip_A2_1 (33)

Sus scrofa (Pig) (12)

1a	Phospholip_A2_1-1y6oB01	B:1-124
1b	Phospholip_A2_1-1y6oB02	B:1-124

Asymmetric Unit(hide GO term definitions)

Chain A,B (PA21B_PIG | P00592)

molecular function
	GO:0032052	bile acid binding	Interacting selectively and non-covalently with bile acids, any of a group of steroid carboxylic acids occurring in bile.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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:0004623	phospholipase A2 activity	Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	GO:0050482	arachidonic acid secretion	The controlled release of arachidonic acid from a cell or a tissue.
	GO:0032869	cellular response to insulin stimulus	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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
	GO:0006633	fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
	GO:0015758	glucose transport	The directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0032612	interleukin-1 production	The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
	GO:0032637	interleukin-8 production	The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0019370	leukotriene biosynthetic process	The chemical reactions and pathways resulting in the formation of leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid.
	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.
	GO:0030593	neutrophil chemotaxis	The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
	GO:0002446	neutrophil mediated immunity	Any process involved in the carrying out of an immune response by a neutrophil.
	GO:0045740	positive regulation of DNA replication	Any process that activates or increases the frequency, rate or extent of DNA replication.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:0010524	positive regulation of calcium ion transport into cytosol	Any process that increases the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components.
	GO:0048146	positive regulation of fibroblast proliferation	Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
	GO:0050778	positive regulation of immune response	Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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1fxf	CRYSTAL STRUCTURE OF PORCINE PANCRATIC PHOSPHOLIPASE A2 (GROUP 1B) IN COMPLEX WITH INHIBITOR MJ33 AND PHOSPHATE IONS
1le6	CRYSTAL STRUCTURE OF HUMAN GROUP X SECRETED PHOSPHOLIPASE A2 (SPLA2)
1y6p	CRYSTAL STRUCTURE OF DISULFIDE ENGINEERED PORCINE PANCRATIC PHOSPHOLIPASE A2 GROUP X ISOZYME

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (16, 16)

Cis Peptide Bonds (0, 0)

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