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(-) Description

Title :  CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE A BINDING DOMAIN IN COMPLEX WITH GT1B
 
Authors :  P. Stenmark, J. Dupuy, R. C. Stevens
Date :  22 May 08  (Deposition) - 26 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Metalloprotease, Neurotoxin, Ganglioside, Metal-Binding, Toxin, Protease, Membrane, Receptor, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Stenmark, J. Dupuy, A. Imamura, M. Kiso, R. C. Stevens
Crystal Structure Of Botulinum Neurotoxin Type A In Complex With The Cell Surface Co-Receptor Gt1B- Insight Into The Toxin-Neuron Interaction.
Plos Pathog. V. 4 E129 2008
PubMed-ID: 18704164  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1000129

(-) Compounds

Molecule 1 - BOTULINUM NEUROTOXIN A HEAVY CHAIN
    Chains: A
    EC Number: 3.4.24.69
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: BINDING DOMAIN, RESIDUES 876-1296
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 36826
    Strain: A
    Synonym: BOTULINUM NEUROTOXIN SEROTYPE A BINDING DOMAIN, BONT/A, BONTOXILYSIN-A, BOTOX

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3MG1Ligand/IonMAGNESIUM ION
4NGA1Ligand/IonN-ACETYL-D-GALACTOSAMINE
5SIA2Ligand/IonO-SIALIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:1089 , ASN A:1093 , HOH A:3177 , HOH A:3318 , HOH A:3319 , HOH A:3321BINDING SITE FOR RESIDUE MG A2298
2AC2SOFTWAREGAL A:2300 , SIA A:2302BINDING SITE FOR RESIDUE BGC A2299
3AC3SOFTWAREBGC A:2299 , SIA A:2302 , NGA A:2304 , HOH A:3397BINDING SITE FOR RESIDUE GAL A2300
4AC4SOFTWAREGLU A:1203 , PHE A:1252 , HIS A:1253 , SER A:1264 , TRP A:1266 , TYR A:1267 , SIA A:2303 , NGA A:2304 , HOH A:3350 , HOH A:3394BINDING SITE FOR RESIDUE GAL A2301
5AC5SOFTWAREGLU A:969 , ASN A:970 , TRP A:1266 , ARG A:1276 , BGC A:2299 , GAL A:2300 , NGA A:2304 , HOH A:3396 , HOH A:3397BINDING SITE FOR RESIDUE SIA A2302
6AC6SOFTWAREILE A:927 , LEU A:928 , ASN A:1051 , ASN A:1052 , TYR A:1117 , PHE A:1252 , TYR A:1267 , SER A:1275 , ARG A:1276 , GAL A:2301 , HOH A:3373 , HOH A:3376BINDING SITE FOR RESIDUE SIA A2303
7AC7SOFTWAREVAL A:1202 , GLU A:1203 , HIS A:1253 , TRP A:1266 , GAL A:2300 , GAL A:2301 , SIA A:2302 , HOH A:3394 , HOH A:3395BINDING SITE FOR RESIDUE NGA A2304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VU9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:1138 -Pro A:1139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VU9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VU9)

(-) Exons   (0, 0)

(no "Exon" information available for 2VU9)

(-) 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:425
 aligned with BXA1_CLOBO | P10845 from UniProtKB/Swiss-Prot  Length:1296

    Alignment length:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                1296 
                                   882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292   | 
          BXA1_CLOBO    873 IINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGTKFIIKKYASGNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVDDGWGERPL-    -
               SCOP domains d2vu9a1 A:873-1079 automated matches                                                                                                                                                                           d2vu9a2 A:1080-1297 automated matches                                                                                                                                                                                      SCOP domains
               CATH domains 2vu9A01 A:873-1099  [code=2.60.120.200, no name defined]                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------Toxin_R_bind_N-2vu9A01 A:885-1079                                                                                                                                                                  --------Toxin_R_bind_C-2vu9A02 A:1088-1293                                                                                                                                                                            ---- Pfam domains
         Sec.struct. author ....eeeeeeee..eeee......eeee...eee.......eeee......eeee.hhhhh.ee....eeeeeeee.....hhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeee..............eeeeeee....eeeeee..eeeeeee......ee...eeeeeee.......eeeeeeeeee....hhhhhhhhhhhhhh..................eeee......eeeee......eeeee....eeee...eeee..........................eeeeeee..................ee....hhhhh.....eeeeee.........eeeeee.....eeeeeeeeee..eeeeeee.hhhhh...hhhhh...eeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2vu9 A  873 HMDTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGTKFIIKKYASGNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVDDGWGERPLQ 1297
                                   882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Concanavalin (293)
(-)
Clan: Trefoil (131)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BXA1_CLOBO | P10845)
molecular function
    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:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008320    protein transmembrane transporter activity    Enables the transfer of a protein from one side of a membrane to the other.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0051609    inhibition of neurotransmitter uptake    Any process that prevents the activation of the directed movement of a neurotransmitter into a cell.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0071806    protein transmembrane transport    The directed movement of a protein across a membrane by means of some agent such as a transporter or pore.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044164    host cell cytosol    The part of the host cell cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0044156    host cell junction    A plasma membrane part that forms a specialized region of connection between two host cells or between a host cell and the host extracellular matrix. At a host cell junction, anchoring proteins extend through the host plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0044231    host cell presynaptic membrane    A specialized area of membrane of the host axon terminal that faces the plasma membrane of the host neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many host synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.
    GO:0044221    host cell synapse    The junction between a nerve fiber of one host neuron and another host neuron or muscle fiber or glial cell; the site of interneuronal communication.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  3.4.24.69
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 Related Entries

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

UniProtKB/Swiss-Prot
        BXA1_CLOBO | P10845: 1uee 1xtf 1xtg 2ilp 2ima 2imb 2imc 2ise 2isg 2ish 2nyy 2nz9 2vua 2w2d 3bok 3bon 3boo 3bta 3bwi 3c88 3c89 3c8a 3c8b 3dda 3ddb 3ds9 3fuo 3v0a 3v0b 3v0c 3zur 3zus 4ej5 4el4 4elc 4hev 4iqp 4jra 4zjx 5jlv 5jmc 5tpb 5tpc 5vgv 5vgx

(-) Related Entries Specified in the PDB File

1uee THE STRUCTURE OF SUBSTRATE-BOUND BOTOX LIGHT CHAIN
2vua CRYSTAL STRUCTURE OF A TOXIN
3bta CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE A