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Title :   CRYSTAL STRUCTURE OF THE COMPLEX OF GROUP II PHOSPHOLIPASEA2 DIMER WITH A FATTY ACID TRIDECANOIC ACID AT 2.4 A RESOLUTION

Authors :   N. Singh, T. Jabeen, S. Sharma, T. P. Singh

Date :   15 Jun 04 (Deposition) - 29 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Catalysis, Inhibition, Fatty Acid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Singh, T. Jabeen, S. Sharma, T. P. Singh
Crystal Structure Of The Complex Of Group Ii Phospholipasea2 Dimer With A Fatty Acid Tridecanoic Acid At 2. 4 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PHOSPHOLIPASE A2 VRV-PL-VIIIA
	Chains	:	A, B
	EC Number	:	3.1.1.4
	Organism Scientific	:	DABOIA RUSSELLII PULCHELLA
	Organism Taxid	:	97228
	Secretion	:	VENOM
	Strain	:	PULCHELLA
	Synonym	:	PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE, DPLA2

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	SO4	1	Ligand/Ion	SULFATE ION
3	TDA	2	Ligand/Ion	N-TRIDECANOIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:67 , PRO A:68 , LYS A:69 , SER A:70 , HOH A:442 , HOH B:259	BINDING SITE FOR RESIDUE SO4 A 301
2	AC2	SOFTWARE	PHE A:5 , TYR A:22 , SER A:23 , TYR A:28 , GLY A:30 , TRP A:31 , CYS A:45 , HIS A:48 , ASP A:49 , HOH A:433 , VAL B:47	BINDING SITE FOR RESIDUE TDA A 201
3	AC3	SOFTWARE	ASN A:54 , ARG A:94 , LEU B:2 , PHE B:5 , ALA B:18 , ILE B:19 , TYR B:22 , TYR B:28 , GLY B:30 , CYS B:45 , HIS B:48 , ASP B:49 , HOH B:205	BINDING SITE FOR RESIDUE TDA B 202
4	AC4	SOFTWARE	ALA A:40 , HOH A:429	BINDING SITE FOR RESIDUE ACY A 401

Asymmetric/Biological Unit

No.	Residues
1	A:27	-	A:126
2	A:29	-	A:45
3	A:44	-	A:105
4	A:50	-	A:133
5	A:51	-	A:98
6	A:61	-	A:91
7	A:84	-	A:96
8	B:27	-	B:126
9	B:29	-	B:45
10	B:44	-	B:105
11	B:50	-	B:133
12	B:51	-	B:98
13	B:61	-	B:91
14	B:84	-	B:96

(no "Cis Peptide Bond" information available for 1TP2)

(no "SAP(SNP)/Variant" information available for 1TP2)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2B8_DABRR	43-50	2	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B8_DABRR	85-95	2	A:95-105 B:95-105

(no "Exon" information available for 1TP2)

Asymmetric/Biological 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:121
 aligned with PA2B8_DABRR | P59071 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2B8_DABRR     1 SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC 121
               SCOP domains d1tp2a_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1tp2A00 A:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tp2 A   1 SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131|
                                        14|                                      56|||                 86|                               122|    131|
                                         16                                       59||                  88                                124     133
                                                                                   61|                                                               
                                                                                    67

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA2B8_DABRR | P59071 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2B8_DABRR     1 SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC 121
               SCOP domains d1tp2b_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1tp2B00 B:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tp2 B   1 SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131|
                                        14|                                      56|||                 86|                               122|    131|
                                         16                                       59||                  88                                124     133
                                                                                   61|                                                               
                                                                                    67

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/Biological 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: Snake phospholipase A2 (124)

Snake (Daboia russellii pulchella), different isoforms [TaxId: 97228] (29)

1a	d1tp2a_	A:
1b	d1tp2b_	B:

Asymmetric/Biological 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)

Daboia russellii pulchella. Organism_taxid: 97228. Strain: pulchella. (21)

1a	1tp2A00	A:1-133
1b	1tp2B00	B:1-133

(no "Pfam Domain" information available for 1TP2)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PA2B8_DABRR | P59071)

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.
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.
	GO:0072556	other organism presynaptic membrane	A presynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A presynaptic membrane is specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tp2)

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1fvo	FIRST STRUCTURAL EVIDENCE OF THE INHIBITION OF PHOSPHOLIPASE A2 BY ARISTOLOCHIC ACID: CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 AND ARISTOLOCHIC ACID
1kpm	FIRST STRUCTURAL EVIDENCE OF A SPECIFIC INHIBITION OF PHOSPHOLIPASE A2 BY VITAMIN E AND ITS IMPLICATIONS IN INFLAMMATION: CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 AND VITAMIN E AT 1.8 A RESOLUTION

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Ligands, Modified Residues, Ions (3, 4)

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SS Bonds (14, 14)

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