1LE7 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CARBOXYLIC ESTER HYDROLASE, C 2 2 21 SPACE GROUP

Authors :   Y. H. Pan, M. K. Jain, B. J. Bahnson

Date :   09 Apr 02 (Deposition) - 14 Aug 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

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

Keywords :   Human Phosphatidylcholine 2-Acylhydrolase Gx, Gx Spla2, Spla2-X (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. H. Pan, B. Z. Yu, A. G. Singer, F. Ghomashchi, G. Lambeau, M. H. Gelb, M. K. Jain, B. J. Bahnson
Crystal Structure Of Human Group X Secreted Phospholipase A2. Electrostatically Neutral Interfacial Surface Targets Zwitterionic Membranes.
J. Biol. Chem. V. 277 29086 2002
PubMed-ID: 12161451 | Reference-DOI: 10.1074/JBC.M202531200
(for further references see the PDB file header)

Molecule 1 - GROUP X SECRETORY PHOSPHOLIPASE A2
	Chains	:	A, B
	EC Number	:	3.1.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PLA2GX10
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE GX, GX SPLA2, SPLA2-X

		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 (2, 7)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	MPD	5	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:26 , GLY A:28 , GLY A:30 , ASP A:47 , HOH A:226 , HOH A:233	BINDING SITE FOR RESIDUE CA A 215
2	AC2	SOFTWARE	PHE B:26 , GLY B:28 , GLY B:30 , ASP B:47 , HOH B:226	BINDING SITE FOR RESIDUE CA B 216
3	AC3	SOFTWARE	MET A:21 , GLY A:28 , LEU A:29 , MPD A:218	BINDING SITE FOR RESIDUE MPD A 217
4	AC4	SOFTWARE	ILE A:2 , ALA A:6 , PRO A:17 , ILE A:18 , MET A:21 , MPD A:217 , HOH A:369 , PHE B:113	BINDING SITE FOR RESIDUE MPD A 218
5	AC5	SOFTWARE	MET B:21 , GLY B:28 , LEU B:29 , HOH B:226 , HOH B:249	BINDING SITE FOR RESIDUE MPD B 219
6	AC6	SOFTWARE	ILE B:2 , PRO B:17 , TYR B:20	BINDING SITE FOR RESIDUE MPD B 220
7	AC7	SOFTWARE	CYS A:58 , ASN A:81 , LYS A:82 , GLU A:85 , HOH A:307	BINDING SITE FOR RESIDUE MPD A 221

Asymmetric Unit

No.	Residues
1	A:11	-	A:69
2	A:25	-	A:115
3	A:27	-	A:43
4	A:42	-	A:97
5	A:48	-	A:122
6	A:49	-	A:90
7	A:58	-	A:83
8	A:76	-	A:88
9	B:11	-	B:69
10	B:25	-	B:115
11	B:27	-	B:43
12	B:42	-	B:97
13	B:48	-	B:122
14	B:49	-	B:90
15	B:58	-	B:83
16	B:76	-	B:88

Asymmetric Unit

No.	Residues
1	Gly A:13	-	Pro A:14
2	Gly A:77	-	Pro A:78
3	Gly B:77	-	Pro B:78

(no "SAP(SNP)/Variant" information available for 1LE7)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2GX_HUMAN	84-91	2	A:42-49 B:42-49
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2GX_HUMAN	129-139	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.	PA2GX_HUMAN	84-91	1	A:42-49 -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2GX_HUMAN	129-139	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.	PA2GX_HUMAN	84-91	1	- B:42-49
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2GX_HUMAN	129-139	1	- B:87-97

(no "Exon" information available for 1LE7)

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:123
 aligned with PA2GX_HUMAN | O15496 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:123
                                    52        62        72        82        92       102       112       122       132       142       152       162   
          PA2GX_HUMAN    43 GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKCD 165
               SCOP domains d1le7a_ A: Phospholipase A2                                                                                                 SCOP domains
               CATH domains 1le7A00 A:1-123 Phospholipase A2                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhhhh..........eeee..eeee....hhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PA2_HIS -------------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1le7 A   1 GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKCD 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with PA2GX_HUMAN | O15496 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:123
                                    52        62        72        82        92       102       112       122       132       142       152       162   
          PA2GX_HUMAN    43 GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKCD 165
               SCOP domains d1le7b_ B: Phospholipase A2                                                                                                 SCOP domains
               CATH domains 1le7B00 B:1-123 Phospholipase A2                                                                                            CATH domains
           Pfam domains (1) -Phospholip_A2_1-1le7B01 B:2-122                                                                                          - Pfam domains (1)
           Pfam domains (2) -Phospholip_A2_1-1le7B02 B:2-122                                                                                          - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhhhh..........eee....eee....hhhhhhhhhhhhhhhhhhh....hhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PA2_HIS -------------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1le7 B   1 GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKCD 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

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( (-)

)

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), SPLA2 [TaxId: 9606] (2)

1a	d1le7a_	A:
1b	d1le7b_	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)

Human (Homo sapiens) (15)

1a	1le7A00	A:1-123
1b	1le7B00	B:1-123

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Phospholip_A2_1 (33)

Homo sapiens (Human) (8)

1a	Phospholip_A2_1-1le7B01	B:2-122
1b	Phospholip_A2_1-1le7B02	B:2-122

Asymmetric Unit(hide GO term definitions)

Chain A,B (PA2GX_HUMAN | O15496)

molecular function
	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:0004620	phospholipase activity	Catalysis of the hydrolysis of a glycerophospholipid.
biological process
	GO:0019369	arachidonic acid metabolic process	The chemical reactions and pathways involving arachidonic acid, a straight chain fatty acid with 20 carbon atoms and four double bonds per molecule. Arachidonic acid is the all-Z-(5,8,11,14)-isomer.
	GO:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0042632	cholesterol homeostasis	Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
	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:0051977	lysophospholipid transport	The directed movement of phospholipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lysophospholipid is a phospholipid that lacks one of its fatty acyl chains; it is an intermediate formed during digestion of dietary and biliary phospholipids.
	GO:0090370	negative regulation of cholesterol efflux	Any process that decreases the frequency, rate or extent of cholesterol efflux. Cholesterol efflux is the directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle.
	GO:0043433	negative regulation of sequence-specific DNA binding transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	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: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:0090238	positive regulation of arachidonic acid secretion	Any process that increases the rate, frequency, or extent of arachidonic acid secretion, the controlled release of arachidonic acid from a cell or a tissue.
	GO:0032270	positive regulation of cellular protein metabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
	GO:0010884	positive regulation of lipid storage	Any process that increases the rate, frequency or extent of lipid storage. Lipid storage is the accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
	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.
	GO:0032308	positive regulation of prostaglandin secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of a prostaglandin from a cell.
	GO:0043030	regulation of macrophage activation	Any process that modulates the frequency or rate of macrophage activation.
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
		Gly A:13 - Pro A:14	[ RasMol ]
		Gly A:77 - Pro A:78	[ RasMol ]
		Gly B:77 - Pro B:78	[ RasMol ]

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	1le7
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	PA2GX_HUMAN \| O15496	:	1le6 4uy1 5g3m

1le6	THE SAME PROTEIN CRYSTALLIZED UNDER DIFFERENT CONDITIONS AND OF DIFFERENT CRYSTAL FORM (P 1 21 1).

Description

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Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (16, 16)

Cis Peptide Bonds (3, 3)

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