3U8I - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   FUNCTIONALLY SELECTIVE INHIBITION OF GROUP IIA PHOSPHOLIPASE A2 REVEALS A ROLE FOR VIMENTIN IN REGULATING ARACHIDONIC ACID METABOLISM

Authors :   L. K. Lee, K. J. Bryant, R. Bouveret, P. -W. Lei, A. P. Duff, S. J. Harrop, E R. P. Harvey, M. H. Gelb, P. P. Gray, P. M. Curmi, A. M. Cunningham, W. B. C K. F. Scott

Date :   17 Oct 11 (Deposition) - 17 Oct 12 (Release) - 12 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.10

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

Keywords :   Secreted Phospholipase A2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. K. Lee, K. J. Bryant, R. Bouveret, P. W. Lei, A. P. Duff, S. J. Harrop, E. P. Huang, R. P. Harvey, M. H. Gelb, P. P. Gray, P. M. Curmi, A. M. Cunningham, W. B. Church, K. F. Scott
Selective Inhibition Of Human Group Iia-Secreted Phospholipase A2 (Hgiia) Signaling Reveals Arachidonic Acid Metabolism Is Associated With Colocalization Of Hgiia To Vimentin In Rheumatoid Synoviocytes.
J. Biol. Chem. V. 288 15269 2013
PubMed-ID: 23482564 | Reference-DOI: 10.1074/JBC.M112.397893

Molecule 1 - PHOSPHOLIPASE A2, MEMBRANE ASSOCIATED
	Chains	:	A, B
	EC Number	:	3.1.1.4
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Taxid	:	10029
	Gene	:	PLA2G2A, PLA2B, PLA2L, RASF-A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GIIC SPLA2, GROUP IIA PHOSPHOLIPASE A2, NON-PANCREATIC SECRETORY PHOSPHOLIPASE A2, NPS-PLA2, PHOSPHATIDYLCHOLINE 2- ACYLHYDROLASE 2A

		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 (4, 14)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	CL	4	Ligand/Ion	CHLORIDE ION
3	NA	4	Ligand/Ion	SODIUM ION
4	OLD	2	Mod. Amino Acid	3-[2-(4-BROMOPHENYL)-2-OXOETHYL]-L-HISTIDINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	OLD	1	Mod. Amino Acid	3-[2-(4-BROMOPHENYL)-2-OXOETHYL]-L-HISTIDINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	OLD	1	Mod. Amino Acid	3-[2-(4-BROMOPHENYL)-2-OXOETHYL]-L-HISTIDINE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:23 , GLY A:25 , TYR A:112 , ASN A:114 , HOH A:401 , HOH A:403	BINDING SITE FOR RESIDUE CA A 201
02	AC2	SOFTWARE	HIS A:27 , GLY A:29 , GLY A:31 , ASP A:48 , HOH A:425 , HOH A:443	BINDING SITE FOR RESIDUE CA A 202
03	AC3	SOFTWARE	ASN A:4 , ARG A:7 , ARG B:118	BINDING SITE FOR RESIDUE CL A 203
04	AC4	SOFTWARE	HOH A:294	BINDING SITE FOR RESIDUE NA A 204
05	AC5	SOFTWARE	SER A:65	BINDING SITE FOR RESIDUE NA A 125
06	AC6	SOFTWARE	LYS A:108 , SER B:65 , ARG B:84	BINDING SITE FOR RESIDUE CL A 126
07	AC7	SOFTWARE	PHE B:23 , GLY B:25 , TYR B:112 , ASN B:114 , HOH B:402 , HOH B:404	BINDING SITE FOR RESIDUE CA B 201
08	AC8	SOFTWARE	HIS B:27 , GLY B:29 , GLY B:31 , ASP B:48 , HOH B:428 , HOH B:442	BINDING SITE FOR RESIDUE CA B 202
09	AC9	SOFTWARE	ARG A:118 , ASN B:4 , ARG B:7	BINDING SITE FOR RESIDUE CL B 203
10	BC1	SOFTWARE	SER A:65 , ARG A:84 , HOH A:344 , LYS B:108	BINDING SITE FOR RESIDUE CL B 125
11	BC2	SOFTWARE	SER B:65	BINDING SITE FOR RESIDUE NA B 126

Asymmetric Unit

No.	Residues
1	A:26	-	A:117
2	A:28	-	A:44
3	A:43	-	A:97
4	A:49	-	A:124
5	A:50	-	A:90
6	A:59	-	A:83
7	A:77	-	A:88
8	B:26	-	B:117
9	B:28	-	B:44
10	B:43	-	B:97
11	B:49	-	B:124
12	B:50	-	B:90
13	B:59	-	B:83
14	B:77	-	B:88

(no "Cis Peptide Bond" information available for 3U8I)

(no "SAP(SNP)/Variant" information available for 3U8I)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2GA_HUMAN	63-70	2	A:43-50 B:43-50
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2GA_HUMAN	107-117	2	A:87-97 B:87-97

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.	PA2GA_HUMAN	63-70	1	A:43-50 -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2GA_HUMAN	107-117	1	A:87-97 -

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.	PA2GA_HUMAN	63-70	1	- B:43-50
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2GA_HUMAN	107-117	1	- B:87-97

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2c	ENST00000400520	2c	ENSE00001543334	chr1:20306111-20306073	39	PA2GA_HUMAN	-	0	0	-	-
1.3c	ENST00000400520	3c	ENSE00002182826	chr1:20305372-20305227	146	PA2GA_HUMAN	1-14	14	0	-	-
1.3e	ENST00000400520	3e	ENSE00001326822	chr1:20305017-20304873	145	PA2GA_HUMAN	14-62	49	2	A:1-42 B:1-42	42 42
1.3g	ENST00000400520	3g	ENSE00000873019	chr1:20304614-20304508	107	PA2GA_HUMAN	62-98	37	2	A:42-78 B:42-78	37 37
1.4d	ENST00000400520	4d	ENSE00001543318	chr1:20302336-20301929	408	PA2GA_HUMAN	98-144	47	2	A:78-124 B:78-124	47 47

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
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Chain A from PDB  Type:PROTEIN  Length:124
 aligned with PA2GA_HUMAN | P14555 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:124
                                    30        40        50        60        70        80        90       100       110       120       130       140    
          PA2GA_HUMAN    21 NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC 144
               SCOP domains d3u8ia_ A: Phospholipase A2                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhh..........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ------------------------------------PA2_ASP    --------------------------- PROSITE
           Transcript 1 (1) Exon 1.3e  PDB: A:1-42 UniProt: 14-62     -----------------------------------Exon 1.4d  PDB: A:78-124 UniProt: 98-144        Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3g  PDB: A:42-78              ---------------------------------------------- Transcript 1 (2)
                 3u8i A   1 NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVThDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC 124
                                    10        20        30        40      | 50        60        70        80        90       100       110       120    
                                                                         47-OLD

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with PA2GA_HUMAN | P14555 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:124
                                    30        40        50        60        70        80        90       100       110       120       130       140    
          PA2GA_HUMAN    21 NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC 144
               SCOP domains d3u8ib_ B: Phospholipase A2                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhh..........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ------------------------------------PA2_ASP    --------------------------- PROSITE
           Transcript 1 (1) Exon 1.3e  PDB: B:1-42 UniProt: 14-62     -----------------------------------Exon 1.4d  PDB: B:78-124 UniProt: 98-144        Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3g  PDB: B:42-78              ---------------------------------------------- Transcript 1 (2)
                 3u8i B   1 NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVThDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC 124
                                    10        20        30        40      | 50        60        70        80        90       100       110       120    
                                                                         47-OLD

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: 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), synovial fluid [TaxId: 9606] (16)

1a	d3u8ia_	A:
1b	d3u8ib_	B:

(no "CATH Domain" information available for 3U8I)

(no "Pfam Domain" information available for 3U8I)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PA2GA_HUMAN | P14555)

molecular function
	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:0005543	phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
biological process
	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: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:0034374	low-density lipoprotein particle remodeling	The acquisition, loss or modification of a protein or lipid within a low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL.
	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:0046473	phosphatidic acid metabolic process	The chemical reactions and pathways involving 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: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:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0050729	positive regulation of inflammatory response	Any process that activates or increases the frequency, rate or extent of the inflammatory response.
	GO:0010744	positive regulation of macrophage derived foam cell differentiation	Any process that increases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	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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Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (11, 11)

SS Bonds (14, 14)

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