1GMZ - JenaLib

Title :   CRYSTAL STRUCTURE OF THE D49 PHOSPHOLIPASE A2 PIRATOXIN III FROM BOTHROPS PIRAJAI.

Authors :   D. J. Rigden, W. H. Lee, I. Polikarpov

Date :   27 Sep 01 (Deposition) - 01 Nov 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Hydrolase, Phospholipase A2, X-Ray Structure, Neurotoxic, Bothrops Pirajai (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Rigden, L. Hwa, S. Marangoni, M. Toyama, I. Polikarpov
The Structure Of The D49 Phospholipase A2 Piratoxin Iii From Bothrops Pirajai Reveals Unprecedented Structural Displacement Of The Calcium-Binding Loop: Possible Relationship To Cooperative Substrate Binding
Acta Crystallogr. , Sect. D V. 59 255 2003
PubMed-ID: 12554936 | Reference-DOI: 10.1107/S0907444902021467

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (14, 14)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2B3_BOTPI	43-50	2	A:43-50 B:43-50
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B3_BOTPI	84-94	2	A:86-95 B:86-95

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2B3_BOTPI	43-50	2	A:43-50 -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B3_BOTPI	84-94	2	A:86-95 -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2B3_BOTPI	43-50	2	- B:43-50
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B3_BOTPI	84-94	2	- B:86-95

Exons (0, 0)

Sequences/Alignments

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:119
 aligned with PA2B3_BOTPI | P58464 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:122
                                                                                                             82                             113       
                                                                                                           81 |                           112 |       
                                    10        20        30        40        50        60        70        80| |     89        99       109  | |  118  
          PA2B3_BOTPI     1 DLWQFGQMILKETGKLPFPYYTYGGCYCGVGGRRGLGTKDDRCCYVHDCCYKKLTGCPKTDDRYSYSWLDLTIVCGEDDPC-KELCECDKAIAVCFRENLGTYNKKYRYHLKP-CKKADKPC 120
               SCOP domains d1gmza_ A: Snake phospholipase A2                                                                                          SCOP domains
               CATH domains 1gmzA00 A:1-122 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh.....hhhhh......hhhhhhhhhhhhhhhh............ee......ee..-hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..--... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gmz A   1 DLWQFGKMILKETGKLPFPYYVTYGCYCGVGGRGGPKDATDRCCFVHDCCYGKLTSCKPKTDRYSYSRKDGTIVCGE-DPCRKEICECDKAAAVCFRENLDTYNKKYMSYLKSLCKK--DDC 122
                                    10        20        30        40        50        60        70      | 80        90       100       110      |120  
                                                                                                       77 |                                   117  |  
                                                                                                         79                                      120

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with PA2B3_BOTPI | P58464 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:122
                                                                                                             82                             113       
                                                                                                           81 |                           112 |       
                                    10        20        30        40        50        60        70        80| |     89        99       109  | |  118  
          PA2B3_BOTPI     1 DLWQFGQMILKETGKLPFPYYTYGGCYCGVGGRRGLGTKDDRCCYVHDCCYKKLTGCPKTDDRYSYSWLDLTIVCGEDDPC-KELCECDKAIAVCFRENLGTYNKKYRYHLKP-CKKADKPC 120
               SCOP domains d1gmzb_ B: Snake phospholipase A2                                                                                          SCOP domains
               CATH domains 1gmzB00 B:1-122 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhh............ee......ee..-hhhhhhhhhhhhhhhhhhhhhhhhh..............-.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gmz B   1 DLWQFGKMILKETGKLPFPYYVTYGCYCGVGGRGGPKDATDRCCFVHDCCYGKLTSCKPKTDRYSYSRKDGTIVCGE-DPCRKEICECDKAAAVCFRENLDTYNKKYMSYLKSLCKK-ADDC 122
                                    10        20        30        40        50        60        70      | 80        90       100       110      |120  
                                                                                                       77 |                                   117 |   
                                                                                                         79                                     119

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PA2B3_BOTPI | P58464)

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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