2BD1 - JenaLib

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Title :   A POSSIBLE ROLE OF THE SECOND CALCIUM ION IN INTERFACIAL BINDING: ATOMIC AND MEDIUM RESOLUTION CRYSTAL STRUCTURES OF THE QUADRUPLE MUTANT OF PHOSPHOLIPASE A2

Authors :   K. Sekar, D. Velmurugan, M. D. Tsai

Date :   19 Oct 05 (Deposition) - 04 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Alpha Helix, Beta Sheet, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Sekar, M. Yogavel, S. P. Kanaujia, A. Sharma, D. Velmurugan, M. J. Poi, Z. Dauter, M. D. Tsai
Suggestive Evidence For The Involvement Of The Second Calcium And Surface Loop In Interfacial Binding: Monoclinic And Trigonal Crystal Structures Of A Quadruple Mutant Of Phospholipase A(2).
Acta Crystallogr. , Sect. D V. 62 717 2006
PubMed-ID: 16790927 | Reference-DOI: 10.1107/S0907444906014855
(for further references see the PDB file header)

Molecule 1 - PHOSPHOLIPASE A2
	Chains	:	A, B
	EC Number	:	3.1.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTO-A2MBL21
	Expression System Strain	:	BL21 (DE3) PLYSS
	Expression System Taxid	:	562
	Gene	:	PLA2G1B
	Mutation	:	YES
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE, GROUP IB PHOSPHOLIPASE A2

		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, 6)

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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:28 , GLY A:30 , GLY A:32 , ASP A:49 , HOH A:202 , HOH A:208	BINDING SITE FOR RESIDUE CA A 847
2	AC2	SOFTWARE	ASN A:71 , ASN A:72 , GLU A:92 , HOH A:226 , HOH A:238 , HOH A:239	BINDING SITE FOR RESIDUE CA A 848
3	AC3	SOFTWARE	TYR B:28 , GLY B:30 , GLY B:32 , ASP B:49 , HOH B:203 , HOH B:206	BINDING SITE FOR RESIDUE CA B 849
4	AC4	SOFTWARE	ASN B:71 , ASN B:72 , GLU B:92 , HOH B:245 , HOH B:254 , HOH B:261	BINDING SITE FOR RESIDUE CA B 850
5	AC5	SOFTWARE	PHE A:22 , GLY A:30 , LEU A:31 , HIS A:48 , HOH A:202	BINDING SITE FOR RESIDUE MPD A 723
6	AC6	SOFTWARE	PHE B:22 , GLY B:30 , HOH B:203	BINDING SITE FOR RESIDUE MPD B 724

Asymmetric Unit

No.	Residues
1	A:11	-	A:77
2	A:27	-	A:123
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
8	B:11	-	B:77
9	B:27	-	B:123
10	B:29	-	B:45
11	B:44	-	B:105
12	B:51	-	B:98
13	B:61	-	B:91
14	B:84	-	B:96

(no "Cis Peptide Bond" information available for 2BD1)

(no "SAP(SNP)/Variant" information available for 2BD1)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA21B_BOVIN	66-73	2	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA21B_BOVIN	117-127	2	A:95-105 B: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_BOVIN	66-73	1	A:44-51 -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA21B_BOVIN	117-127	1	A:95-105 -

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.	PA21B_BOVIN	66-73	1	- B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA21B_BOVIN	117-127	1	- B:95-105

(no "Exon" information available for 2BD1)

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:123
 aligned with PA21B_BOVIN | P00593 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:123
                                    32        42        52        62        72        82        92       102       112       122       132       142   
          PA21B_BOVIN    23 ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYKQAKKLDSCKVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSKVPYNKEHKNLDKKNC 145
               SCOP domains d2bd1a_ A: Phospholipase A2                                                                                                 SCOP domains
               CATH domains 2bd1A00 A:1-123 Phospholipase A2                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh................hhhhhhhhhhhhhhhhhhhh................eee....eee....hhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS -------------------------------------------PA2_ASP    ------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bd1 A   1 ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYMQAMKLDSCKVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSKVPYNKEHKNLDMMNC 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with PA21B_BOVIN | P00593 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:123
                                    32        42        52        62        72        82        92       102       112       122       132       142   
          PA21B_BOVIN    23 ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYKQAKKLDSCKVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSKVPYNKEHKNLDKKNC 145
               SCOP domains d2bd1b_ B: Phospholipase A2                                                                                                 SCOP domains
               CATH domains 2bd1B00 B:1-123 Phospholipase A2                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh................hhhhhhhhhhhhhhhhhhhh................eee....eee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS -------------------------------------------PA2_ASP    ------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bd1 B   1 ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYMQAMKLDSCKVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSKVPYNKEHKNLDMMNC 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

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	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( (-)

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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: Phospholipase A2 (72)

Cow (Bos taurus), pancreas [TaxId: 9913] (32)

1a	d2bd1a_	A:
1b	d2bd1b_	B:

Asymmetric Unit

Classes(

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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)

Cattle (Bos taurus) (29)

1a	2bd1A00	A:1-123
1b	2bd1B00	B:1-123

(no "Pfam Domain" information available for 2BD1)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PA21B_BOVIN | P00593)

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.

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