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(-) Description

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

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2 HOMOLOG BOTHROPSTOXIN-1
    ChainsA, B
    Organism CommonSNAKE
    Organism ScientificBOTHROPS JARARACUSSU
    Organism Taxid8726
    Other DetailsBOTHROPSTOXIN-I CHEMICALLY MODIFIED BY P-BROMOPHENACYL BROMIDE (BPB)
    Other Details - SourceTHE BOTHROPSTOXIN-I WAS ISOLATED FROM BOTHROPS JARARACUSSU VENOM.
    SynonymPHOSPHOLIPASE A2 HOMOLOG 1, BOTHROPSTOXIN I, BTHTX-I, BTXTXI, BOJU-I, MYOTOXIC PHOSPHOLIPASE A2-LIKE
    TissueVENOM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
2PBP2Ligand/Ion1-(4-BROMO-PHENYL)-ETHANONE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:30 , CYS A:45 , HIS A:48BINDING SITE FOR RESIDUE PBP A 201
2AC2SOFTWARETYR B:22 , GLY B:30 , CYS B:45 , HIS B:48 , VAL B:102BINDING SITE FOR RESIDUE PBP B 201
3AC3SOFTWAREGLY B:33 , ARG B:34BINDING SITE FOR RESIDUE IPA B 202

(-) SS Bonds  (14, 14)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HZW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PA2B1_BOTJR_001 *F19LPA2B1_BOTJR  ---  ---A/BF3L
2UniProtVAR_PA2B1_BOTJR_002 *Y37HPA2B1_BOTJR  ---  ---A/BY22H
3UniProtVAR_PA2B1_BOTJR_003 *P136APA2B1_BOTJR  ---  ---A/BP132A
   * ID not provided by source

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2B1_BOTJR59-66
 
  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2B1_BOTJR101-111
 
  2A:95-105
B:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 3HZW)

(-) Sequences/Alignments

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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PA2B1_BOTJR | Q902492h8i 3cxi 3hzd 3i03 3i3h 3i3i 3iq3 4k06 4k09 4wtb

(-) Related Entries Specified in the PDB File

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