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Title :   X-RAY CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN TWO HOMOLOGOUS ISOFORMS OF PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA: PRINCIPLE OF MOLECULAR ASSOCIATION AND INACTIVATION

Authors :   T. Jabeen, S. Sharma, R. K. Singh, P. Kaur, T. P. Singh

Date :   23 Jan 04 (Deposition) - 10 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Phospholipase A2, Molecular Conformation, Enzyme Activity, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Jabeen, S. Sharma, N. Singh, R. K. Singh, P. Kaur, M. Perbandt, C. H. Betzel, A. Srinivasan, T. P. Singh
Crystal Structure Of A Calcium-Induced Dimer Of Two Isoforms Of Cobra Phospholipase A2 At 1. 6 A Resolution.
Proteins V. 59 856 2005
PubMed-ID: 15828003 | Reference-DOI: 10.1002/PROT.20464
(for further references see the PDB file header)

Molecule 1 - PHOSPHOLIPASE A2 ISOFORM 1
	Chains	:	A
	EC Number	:	3.1.1.4
	Organism Scientific	:	NAJA SAGITTIFERA
	Organism Taxid	:	195058
	Secretion	:	VENOM
	Synonym	:	PHOSPHOLIPASE A2, PHOSPHATIDYLCHOLINE 2- ACYLHYDROLASE

Molecule 2 - PHOSPHOLIPASE A2 ISOFORM 2
	Chains	:	B
	EC Number	:	3.1.1.4
	Organism Scientific	:	NAJA SAGITTIFERA
	Organism Taxid	:	195058
	Secretion	:	VENOM
	Synonym	:	PHOSPHOLIPASE A2, PHOSPHATIDYLCHOLINE 2- ACYLHYDROLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	CA	2	Ligand/Ion	CALCIUM ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:24 , ASN A:112 , HOH A:537 , ASP B:24 , ASN B:112 , HOH B:715	BINDING SITE FOR RESIDUE CA A 401
2	AC2	SOFTWARE	TYR B:28 , GLY B:30 , GLY B:32 , ASP B:49 , PO4 B:501 , HOH B:627	BINDING SITE FOR RESIDUE CA B 402
3	AC3	SOFTWARE	TYR B:28 , CYS B:29 , GLY B:30 , CYS B:45 , HIS B:48 , ASP B:49 , CA B:402 , HOH B:673 , HOH B:697 , HOH B:799	BINDING SITE FOR RESIDUE PO4 B 501
4	AC4	SOFTWARE	ASN A:1 , TYR A:3 , GLN A:65 , HOH A:606 , ASN B:109 , HOH B:731	BINDING SITE FOR RESIDUE PO4 A 502
5	AC5	SOFTWARE	GLY B:32 , HOH B:674 , HOH B:745	BINDING SITE FOR RESIDUE ACY B 601
6	AC6	SOFTWARE	HOH B:634 , HOH B:702 , HOH B:718 , HOH B:775 , HOH B:784	BINDING SITE FOR RESIDUE ACY B 602

Asymmetric/Biological Unit

No.	Residues
1	A:11	-	A:72
2	A:27	-	A:119
3	A:29	-	A:45
4	A:44	-	A:100
5	A:51	-	A:93
6	A:61	-	A:86
7	A:79	-	A:91
8	B:11	-	B:72
9	B:27	-	B:119
10	B:29	-	B:45
11	B:44	-	B:100
12	B:51	-	B:93
13	B:61	-	B:86
14	B:79	-	B:91

(no "Cis Peptide Bond" information available for 1S6B)

(no "SAP(SNP)/Variant" information available for 1S6B)

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.	PA2A2_NAJSG	50-57	1	B:44-51
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2B1_NAJSG	50-57	1	A:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A2_NAJSG	96-106	1	B:90-100
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B1_NAJSG	96-106	1	A:90-100

(no "Exon" information available for 1S6B)

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:119
 aligned with PA2B1_NAJSG | P60043 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    17        27        37        47        57        67        77        87        97       107       117         
          PA2B1_NAJSG     8 NTYQFKNMIQCTVPKRSWWDFADYGCYCGRGGSGTPIDDLDRCCQVHDNCYNSAREQGGCRPKQKTYSYECKAGTLSCSGSNNSCAATVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 126
               SCOP domains d1s6ba_ A: Snake phospholipase A2                                                                                       SCOP domains
               CATH domains 1s6bA00 A:1-120 Phospholipase A2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhhh..............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------PA2_HIS --------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------PA2_ASP    -------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1s6b A   1 NTYQFKNMIQCTVPKRSWWDFADYGCYCGRGGSGTPIDDLDRCCQVHDNCYNSAREQGGCRPKQKTYSYECKAGTLSCSGSNNSCAATVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 120
                                    10    ||  21        31        41        51        61        71        81        91       101       111         
                                         15|                                                                                                       
                                          17

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with PA2A2_NAJSG | P60044 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    17        27        37        47        57        67        77        87        97       107       117         
          PA2A2_NAJSG     8 NRWQFKNMISCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCNPRFRTYSYECTAGTLTCTGRNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLQARCN 126
               SCOP domains d1s6bb_ B: Snake phospholipase A2                                                                                       SCOP domains
               CATH domains 1s6bB00 B:1-120 Phospholipase A2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh...............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------PA2_HIS --------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ----------------------------------------------------------------------------------------PA2_ASP    -------------------- PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1s6b B   1 NRWQFKNMISCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCNPRFRTYSYECTAGTLTCTGRNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLQARCN 120
                                    10    ||  21        31        41        51        61        71        81        91       101       111         
                                         15|                                                                                                       
                                          17

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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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: Snake phospholipase A2 (124)

Andaman cobra (Naja sagittifera), isoform 2 [TaxId: 195058] (4)

d1s6ba_

Andaman cobra (Naja sagittifera), isoform 3 [TaxId: 195058] (4)

d1s6bb_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Phospholipase A2 (241)

Homologous Superfamily: Phospholipase A2 (241)

Naja sagittifera. Organism_taxid: 195058. (12)

1a	1s6bA00	A:1-120
1b	1s6bB00	B:1-120

(no "Pfam Domain" information available for 1S6B)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PA2B1_NAJSG | P60043)

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.

Chain B (PA2A2_NAJSG | P60044)

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.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 1s6b)

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Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (14, 14)

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