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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF BOTHROPSTOXIN-I CHEMICALLY MODIFIED BY P-BROMOPHENACYL BROMIDE (BPB)

Authors :   C. A. H. Fernandes, D. P. Marchi-Salvador, A. M. Soares, M. R. M. Fontes

Date :   24 Jun 09 (Deposition) - 12 May 10 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

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

Keywords :   Lys49-Pla2, Phospholipase Homologue, Myotoxicity, P-Bromophenacyl Bromide, Bothropstoxin-I, Antibiotic, Antimicrobial, Disulfide Bond, Myotoxin, Secreted, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. A. Fernandes, D. P. Marchi-Salvador, G. M. Salvador, M. C. Silva, T. R. Costa, A. M. Soares, M. R. Fontes
Comparison Between Apo And Complexed Structures Of Bothropstoxin-I Reveals The Role Of Lys122 And Ca(2+)-Binding Loop Region For The Catalytically Inactive Lys49-Pla(2)S.
J. Struct. Biol. V. 171 31 2010
PubMed-ID: 20371382 | Reference-DOI: 10.1016/J.JSB.2010.03.019

Molecule 1 - PHOSPHOLIPASE A2 HOMOLOG BOTHROPSTOXIN-1
	Chains	:	A, B
	Organism Common	:	SNAKE
	Organism Scientific	:	BOTHROPS JARARACUSSU
	Organism Taxid	:	8726
	Other Details	:	BOTHROPSTOXIN-I CHEMICALLY MODIFIED BY P-BROMOPHENACYL BROMIDE (BPB)
	Other Details - Source	:	THE BOTHROPSTOXIN-I WAS ISOLATED FROM BOTHROPS JARARACUSSU VENOM.
	Synonym	:	PHOSPHOLIPASE A2 HOMOLOG 1, BOTHROPSTOXIN I, BTHTX-I, BTXTXI, BOJU-I, MYOTOXIC PHOSPHOLIPASE A2-LIKE
	Tissue	:	VENOM

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
2	PBP	2	Ligand/Ion	1-(4-BROMO-PHENYL)-ETHANONE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:30 , CYS A:45 , HIS A:48	BINDING SITE FOR RESIDUE PBP A 201
2	AC2	SOFTWARE	TYR B:22 , GLY B:30 , CYS B:45 , HIS B:48 , VAL B:102	BINDING SITE FOR RESIDUE PBP B 201
3	AC3	SOFTWARE	GLY B:33 , ARG B:34	BINDING SITE FOR RESIDUE IPA B 202

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 3HZW)

Asymmetric/Biological Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PA2B1_BOTJR_001 *	F	19	L	PA2B1_BOTJR	---	---	A/B	F	3	L
2	UniProt	VAR_PA2B1_BOTJR_002 *	Y	37	H	PA2B1_BOTJR	---	---	A/B	Y	22	H
3	UniProt	VAR_PA2B1_BOTJR_003 *	P	136	A	PA2B1_BOTJR	---	---	A/B	P	132	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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.	PA2B1_BOTJR	59-66	2	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B1_BOTJR	101-111	2	A:95-105 B:95-105

(no "Exon" information available for 3HZW)

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
	(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:121
 aligned with PA2B1_BOTJR | Q90249 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:121
                                    26        36        46        56        66        76        86        96       106       116       126       136 
          PA2B1_BOTJR    17 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 137
               SCOP domains d3hzwa_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 3hzwA00 A:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhee...ee........hhhhhhhhhhhhhhhhh...........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --L-----------------H--------------------------------------------------------------------------------------------------A- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hzw A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA2B1_BOTJR | Q90249 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:121
                                    26        36        46        56        66        76        86        96       106       116       126       136 
          PA2B1_BOTJR    17 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 137
               SCOP domains d3hzwb_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 3hzwB00 B:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhee...ee........hhhhhhhhhhhhhhhhh............ee....ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --L-----------------H--------------------------------------------------------------------------------------------------A- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hzw B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129

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(

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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)

Jararacussu (Bothrops jararacussu) [TaxId: 8726] (8)

1a	d3hzwa_	A:
1b	d3hzwb_	B:

Asymmetric/Biological 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)

Snake (Bothrops jararacussu) (3)

1a	3hzwA00	A:1-133
1b	3hzwB00	B:1-133

(no "Pfam Domain" information available for 3HZW)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PA2B1_BOTJR | Q90249)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004623	phospholipase A2 activity	Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
biological process
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	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.
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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	3hzw
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	PA2B1_BOTJR \| Q90249
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	PA2B1_BOTJR \| Q90249
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UniProtKB/Swiss-Prot
	PA2B1_BOTJR \| Q90249	:	2h8i 3cxi 3hzd 3i03 3i3h 3i3i 3iq3 4k06 4k09 4wtb

1y4l	CRYSTAL STRUCTURE OF BOTHROPS ASPER MYOTOXIN II COMPLEXED WITH THE ANTI-TRYPANOSOMAL DRUG SURAMIN
2q2j	CRYSTAL STRUCTURE OF PRTX-I, A PLA2 HOMOLOG FROM BOTHROPS PIRAJAI
3cxi	STRUCTURE OF BOTHROPSTOXIN-I COMPLEXED WITH ALPHA-TOCOPHEROL
3cyl	CRYSTAL STRUCTURE OF PIRATOXIN I (A MYOTOXIC LYS49-PLA2) COMPLEXED WITH ALPHA-TOCOPHEROL
3hzd	CRYSTAL STRUCTURE OF BOTHROPSTOXIN-I
3i03	CRYSTAL STRUCTURE OF BOTHROPSTOXIN-I CHEMICALLY MODIFIED BY P-BROMOPHENACYL BROMIDE (BPB) - MONOMERIC FORM AT A HIGH RESOLUTION

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Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (14, 14)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (3, 6)

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Exons (0, 0)

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