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(-) Description

Title :  PIRATOXIN-II (PRTX-II) - A K49 PLA2 FROM BOTHROPS PIRAJAI
 
Authors :  W. -H. Lee, I. Polikarpov
Date :  01 Sep 99  (Deposition) - 07 Sep 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Neurotoxin, K49 Phospholipase A2 (Pla2) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. H. Lee, M. T. Da Silva Giotto, S. Marangoni, M. H. Toyama, I. Polikarpov, R. C. Garratt
Structural Basis For Low Catalytic Activity In Lys49 Phospholipases A2-A Hypothesis: The Crystal Structure Of Piratoxin Ii Complexed To Fatty Acid
Biochemistry V. 40 28 2001
PubMed-ID: 11141053  |  Reference-DOI: 10.1021/BI0010470

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    ChainsA, B
    EC Number3.1.1.4
    Organism ScientificBOTHROPS PIRAJAI
    Organism Taxid113192
    Other DetailsFATTY ACID TRAPPED AT THE HYDROPHOBIC CHANNEL
    SecretionTOTAL VENOM
    SynonymMYOTOXIN II, BOTHROPSTOXIN I, BTXTX1, BTHTX1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1TDA2Ligand/IonN-TRIDECANOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:2 , GLY A:6 , ILE A:9 , PRO A:17 , TYR A:21 , CYS A:28 , GLY A:29 , HIS A:47 , HOH A:2002 , HOH A:2149 , HOH A:2150BINDING SITE FOR RESIDUE TDA A 122
2AC2SOFTWARELEU B:2 , GLY B:6 , ILE B:9 , PRO B:17 , TYR B:21 , CYS B:28 , GLY B:29 , HIS B:47 , HOH B:2001 , HOH B:2152BINDING SITE FOR RESIDUE TDA B 122

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:115
2A:28 -A:44
3A:43 -A:95
4A:49 -A:121
5A:50 -A:88
6A:57 -A:81
7A:75 -A:86
8B:26 -B:115
9B:28 -B:44
10B:43 -B:95
11B:49 -B:121
12B:50 -B:88
13B:57 -B:81
14B:75 -B:86

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2H2_BOTPI43-50
 
  2A:43-50
B:43-50
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2H2_BOTPI85-95
 
  2A:85-95
B:85-95

(-) Exons   (0, 0)

(no "Exon" information available for 1QLL)

(-) 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 PA2H2_BOTPI | P82287 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H2_BOTPI     1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC 121
               SCOP domains d1qlla_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1qllA00 A:1-121 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eee....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qll A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADKC 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA2H2_BOTPI | P82287 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H2_BOTPI     1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC 121
               SCOP domains d1qllb_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1qllB00 B:1-121 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eee....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qll B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADKC 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 

   Legend:   → Mismatch (orange background)
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    → 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 1QLL)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PA2H2_BOTPI | P82287)
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: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
        PA2H2_BOTPI | P822872q2j 3cyl

(-) Related Entries Specified in the PDB File

1clp MYOTOXIN II (PHOSPHOLIPASE A2) (E.C.3.1.1.4) MUTANT WITH ASP 49 REPLACED BY LYS (D49K) FROM TERCIOPELO (BOTHROPS ASPER)