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(-) Description

Title :  STRUCTURE OF BETA2-BUNGAROTOXIN: POTASSIUM CHANNEL BINDING BY KUNITZ MODULES AND TARGETED PHOSPHOLIPASE ACTION
 
Authors :  P. D. Kwong, N. Q. Mcdonald, P. B. Sigler, W. A. Hendrickson
Date :  15 Oct 95  (Deposition) - 03 Apr 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Presynaptic Neurotoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. D. Kwong, N. Q. Mcdonald, P. B. Sigler, W. A. Hendrickson
Structure Of Beta 2-Bungarotoxin: Potassium Channel Binding By Kunitz Modules And Targeted Phospholipase Action.
Structure V. 3 1109 1995
PubMed-ID: 8590005  |  Reference-DOI: 10.1016/S0969-2126(01)00246-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA2-BUNGAROTOXIN
    ChainsA
    EC Number3.1.1.4
    Organism CommonMANY-BANDED KRAIT
    Organism ScientificBUNGARUS MULTICINCTUS
    Organism Taxid8616
    Other DetailsNUMEROUS NATURAL ISOFORMS, THIS IS THE BETA2 ISOFORM
    SynonymPHOSPHATIDE ACYL-HYDROLASE, PHOSPHATIDYLCHOLINE 2- ACYLHYDROLASE
    TissueVENOM
 
Molecule 2 - BETA2-BUNGAROTOXIN
    ChainsB
    EC Number3.1.1.4
    Organism CommonMANY-BANDED KRAIT
    Organism ScientificBUNGARUS MULTICINCTUS
    Organism Taxid8616
    Other DetailsNUMEROUS NATURAL ISOFORMS, THIS IS THE BETA2 ISOFORM
    SynonymPHOSPHATIDE ACYL-HYDROLASE, PHOSPHATIDYLCHOLINE 2- ACYLHYDROLASE
    TissueVENOM

 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
1NA2Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:28 , GLY A:30 , GLY A:32 , ASP A:49BINDING SITE FOR RESIDUE NA A 121
2AC2SOFTWAREASP A:39 , ALA A:40 , LEU A:41 , GLU A:105BINDING SITE FOR RESIDUE NA A 122

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:15 -B:55
2A:27 -A:119
3A:29 -A:45
4A:44 -A:100
5A:51 -A:93
6A:61 -A:86
7A:79 -A:91
8B:7 -B:57
9B:16 -B:40
10B:32 -B:53

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PA2B1_BUNMU_001 *I116VPA2B1_BUNMU  ---  ---AI89V
   * ID not provided by source

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

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPTI_KUNITZ_2PS50279 Pancreatic trypsin inhibitor (Kunitz) family profile.VKTH2_BUNMU31-81  1B:7-57
2BPTI_KUNITZ_1PS00280 Pancreatic trypsin inhibitor (Kunitz) family signature.VKTH2_BUNMU59-77  1B:35-53
3PA2_HISPS00118 Phospholipase A2 histidine active site.PA2B1_BUNMU71-78  1A:44-51
4PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2B1_BUNMU117-127  1A:90-100

(-) Exons   (0, 0)

(no "Exon" information available for 1BUN)

(-) 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:120
 aligned with PA2B1_BUNMU | P00617 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:120
                                    37        47        57        67        77        87        97       107       117       127       137       147
          PA2B1_BUNMU    28 NLINFMEMIRYTIPCEKTWGEYADYGCYCGAGGSGRPIDALDRCCYVHDNCYGDAEKKHKCNPKTQSYSYKLTKRTIICYGAAGTCGRIVCDCDRTAALCFGNSEYIEGHKNIDTARFCQ 147
               SCOP domains d1buna_ A: Snake phospholipase A2                                                                                        SCOP domains
               CATH domains 1bunA00 A:1-120 Phospholipase A2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhh........hhhhh................hhhhhhhhhhhhhhhhh.............eeee..eeee......hhhhhhhhhhhhhhhhhh....hhh....hhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------V------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) -------------------------------------------PA2_HIS --------------------------------------------------------------------- PROSITE (3)
                PROSITE (1) -----------------------------------------------------------------------------------------PA2_ASP    -------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bun A   1 NLINFMEMIRYTIPCEKTWGEYADYGCYCGAGGSGRPIDALDRCCYVHDNCYGDAEKKHKCNPKTQSYSYKLTKRTIICYGAAGTCARIVCDCDRTAALCFGNSEYIEGHKNIDTARFCQ 120
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:61
 aligned with VKTH2_BUNMU | P00989 from UniProtKB/Swiss-Prot  Length:85

    Alignment length:61
                                    34        44        54        64        74        84 
          VKTH2_BUNMU    25 RKRHPDCDKPPDTKICQTVVRAFYYKPSAKRCVQFRYGGCNGNGNHFKSDHLCRCECLEYR  85
               SCOP domains d1bunb_ B: beta2-bungarotoxin, neurotoxin chain               SCOP domains
               CATH domains 1bunB00 B:1-61 Factor Xa Inhibitor                            CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeeeehhh.eeeeeee............hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------BPTI_KUNITZ_2  PDB: B:7-57 UniProt: 31-81          ---- PROSITE (1)
                PROSITE (2) ----------------------------------BPTI_KUNITZ_1      -------- PROSITE (2)
                 Transcript ------------------------------------------------------------- Transcript
                 1bun B   1 RKRHPDCDKPPDTKICQTVVRAFYYKPSAKRCVQFRYGGCNGNGNHFKSDHLCRCECLEYR  61
                                    10        20        30        40        50        60 

   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BUN)

(-) Gene Ontology  (10, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PA2B1_BUNMU | P00617)
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.
    GO:0072556    other organism presynaptic membrane    A presynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A presynaptic membrane is specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

Chain B   (VKTH2_BUNMU | P00989)
molecular function
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
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.
    GO:0072556    other organism presynaptic membrane    A presynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A presynaptic membrane is specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

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