3ELO - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN PANCREATIC PROPHOSPHOLIPASE A2

Authors :   W. Xu, L. Yi, Y. Feng, L. Chen, J. Liu

Date :   22 Sep 08 (Deposition) - 14 Apr 09 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Human Pancreatic Prophospholipase A2, Trimeric, Hydrolase, Lipid Degradation, Metal-Binding, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Xu, L. Yi, Y. Feng, L. Chen, J. Liu
Structural Insight Into The Activation Mechanism Of Human Pancreatic Prophospholipase A2
J. Biol. Chem. V. 284 16659 2009
PubMed-ID: 19297324 | Reference-DOI: 10.1074/JBC.M808029200

Molecule 1 - PHOSPHOLIPASE A2
	Chains	:	A
	EC Number	:	3.1.1.4
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPIC9K
	Expression System Strain	:	GS115
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Gene	:	PLA2G1B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE, GROUP IB PHOSPHOLIPASE A2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:3 , ARG A:6 , TYR A:69 , HOH A:174	BINDING SITE FOR RESIDUE SO4 A 127

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:51	-	A:98
6	A:61	-	A:91
7	A:84	-	A:96

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

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011911	D	16	A	PA21B_HUMAN	Polymorphism	5632	A	D	-6	A
2	UniProt	VAR_011913	N	89	K	PA21B_HUMAN	Polymorphism	5636	A	N	67	K
3	UniProt	VAR_011912	N	89	T	PA21B_HUMAN	Polymorphism	5635	A	N	67	T

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011911	D	16	A	PA21B_HUMAN	Polymorphism	5632	A	D	-6	A
2	UniProt	VAR_011913	N	89	K	PA21B_HUMAN	Polymorphism	5636	A	N	67	K
3	UniProt	VAR_011912	N	89	T	PA21B_HUMAN	Polymorphism	5635	A	N	67	T

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011911	D	16	A	PA21B_HUMAN	Polymorphism	5632	A	D	-6	A
2	UniProt	VAR_011913	N	89	K	PA21B_HUMAN	Polymorphism	5636	A	N	67	K
3	UniProt	VAR_011912	N	89	T	PA21B_HUMAN	Polymorphism	5635	A	N	67	T

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA21B_HUMAN	66-73	1	A:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA21B_HUMAN	117-127	1	A: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_HUMAN	66-73	1	A:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA21B_HUMAN	117-127	1	A:95-105

Biological Unit 2 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA21B_HUMAN	66-73	3	A:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA21B_HUMAN	117-127	3	A:95-105

Asymmetric Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000308366	1	ENSE00001208219	chr12:120765592-120765523	70	PA21B_HUMAN	1-12	12	0	-	-
1.2	ENST00000308366	2	ENSE00001129475	chr12:120763823-120763664	160	PA21B_HUMAN	12-65	54	1	A:-6-43	50
1.3	ENST00000308366	3	ENSE00001129471	chr12:120762864-120762737	128	PA21B_HUMAN	65-108	44	1	A:43-86	44
1.4	ENST00000308366	4	ENSE00001667458	chr12:120760120-120759915	206	PA21B_HUMAN	108-148	41	1	A:86-126	41

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:133
 aligned with PA21B_HUMAN | P04054 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:133
                                    25        35        45        55        65        75        85        95       105       115       125       135       145   
          PA21B_HUMAN    16 DSGISPRAVWQFRKMIKCVIPGSDPFLEYNNYGCYCGLGGSGTPVDELDKCCQTHDNCYDQAKKLDSCKFLLDNPYTHTYSYSCSGSAITCSSKNKECEAFICNCDRNAAICFSKAPYNKAHKNLDTKKYCQS 148
               SCOP domains d3eloa_ A: Phospholipase A2                                                                                                           SCOP domains
               CATH domains 3eloA00 A:-6-126 Phospholipase A2                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh....hhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) A------------------------------------------------------------------------K----------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------T----------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------------------------------------------------PA2_HIS -------------------------------------------PA2_ASP    --------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:-6-43 UniProt: 12-65 [INCOMPLETE]------------------------------------------Exon 1.4  PDB: A:86-126 UniProt: 108-148  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.3  PDB: A:43-86 UniProt: 65-108      ---------------------------------------- Transcript 1 (2)
                 3elo A  -6 DSGISPRAVWQFRKMIKCVIPGSDPFLEYNNYGCYCGLGGSGTPVDELDKCCQTHDNCYDQAKKLDSCKFLLDNPYTHTYSYSCSGSAITCSSKNKECEAFICNCDRNAAICFSKAPYNKAHKNLDTKKYCQS 126
                                     3        13        23        33        43        53        63        73        83        93       103       113       123

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( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

Human (Homo sapiens) [TaxId: 9606] (1)

d3eloa_

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)

Human (Homo sapiens) (15)

3eloA00

A:-6-126

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

Asymmetric Unit(hide GO term definitions)

Chain A (PA21B_HUMAN | P04054)

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:0047498	calcium-dependent phospholipase A2 activity	Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate. This reaction requires 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:0007015	actin filament organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
	GO:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	GO:0032431	activation of phospholipase A2 activity	Any process that initiates the activity of the inactive enzyme phospholipase A2.
	GO:0019731	antibacterial humoral response	An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
	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:0050830	defense response to Gram-positive bacterium	Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
	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:0002227	innate immune response in mucosa	Any process of the innate immune response that takes place in the mucosal tissues.
	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:0044240	multicellular organismal lipid catabolic process	The chemical reactions and pathways resulting in the breakdown of lipids, occurring at the tissue, organ, or organismal level of a multicellular organism.
	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:0006654	phosphatidic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
	GO:0036151	phosphatidylcholine acyl-chain remodeling	Remodeling the acyl chains of phosphatidylcholine, through sequential deacylation and re-acylation reactions, to generate phosphatidylcholine containing different types of fatty acid acyl chains.
	GO:0046470	phosphatidylcholine metabolic process	The chemical reactions and pathways involving phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline. They are important constituents of cell membranes.
	GO:0036152	phosphatidylethanolamine acyl-chain remodeling	Remodeling the acyl chains of phosphatidylethanolamine, through sequential deacylation and re-acylation reactions, to generate phosphatidylethanolamine containing different types of fatty acid acyl chains.
	GO:0036148	phosphatidylglycerol acyl-chain remodeling	Remodeling the acyl chains of phosphatidylglycerol, through sequential deacylation and re-acylation reactions, to generate phosphatidylglycerol containing different types of fatty acid acyl chains.
	GO:0036149	phosphatidylinositol acyl-chain remodeling	Remodeling the acyl chains of phosphatidylinositol, through sequential deacylation and re-acylation reactions, to generate phosphatidylinositol containing different types of fatty acid acyl chains.
	GO:0036150	phosphatidylserine acyl-chain remodeling	Remodeling the acyl chains of phosphatidylserine, through sequential deacylation and re-acylation reactions, to generate phosphatidylserine containing different types of fatty acid acyl chains.
	GO:0006644	phospholipid metabolic process	The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester.
	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:0050714	positive regulation of protein secretion	Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
	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.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0030141	secretory granule	A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

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