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(-) Description

Title :  CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE D/C VPI 5993 BINDING DOMAIN
 
Authors :  Z. Fu, A. Karalewitz, A. Kroken, M. R. Baldwin, J. T. Barbieri, J. -J. P. K
Date :  27 May 10  (Deposition) - 08 Sep 10  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Botulinum Neurotoxin, Hcr/D-Sa, Ganglioside Binding Loop, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Karalewitz, A. R. Kroken, Z. Fu, M. R. Baldwin, J. J. Kim, J. T. Barbieri
Identification Of A Unique Ganglioside Binding Loop Within Botulinum Neurotoxins C And D-Sa .
Biochemistry V. 49 8117 2010
PubMed-ID: 20731382  |  Reference-DOI: 10.1021/BI100865F

(-) Compounds

Molecule 1 - NEUROTOXIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28
    Expression System Strain: BL-21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RECEPTOR BINDING DOMAIN (UNP RESIDUES 862-1285)
    Gene: CLOSTRIDIUM BOTULINUM
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:1156 , TYR A:1251 , TRP A:1252 , PHE A:1253 , HIS A:1255 , HOH A:1488 , HOH A:1513BINDING SITE FOR RESIDUE SO4 A 1301
2AC2SOFTWAREASN A:1092 , ASN A:1152 , THR A:1153 , ARG A:1159 , HOH A:1430BINDING SITE FOR RESIDUE SO4 A 1302
3AC3SOFTWAREASN A:1185 , GLY A:1187 , THR A:1188 , ASP A:1189 , HOH A:1573BINDING SITE FOR RESIDUE SO4 A 1303
4AC4SOFTWAREARG A:1103 , LYS A:1106 , ARG A:1184 , ASN A:1254 , HOH A:1411BINDING SITE FOR RESIDUE GOL A 1401
5AC5SOFTWAREPHE A:901 , TYR A:1090 , ASP A:1101 , ARG A:1157 , ARG A:1159 , HOH A:1417 , HOH A:1540BINDING SITE FOR RESIDUE GOL A 1402
6AC6SOFTWARELYS A:1147 , ASN A:1167 , GLN A:1174 , SER A:1242 , GLU A:1256 , LEU A:1258 , GOL A:1404BINDING SITE FOR RESIDUE GOL A 1403
7AC7SOFTWAREARG A:1118 , ASN A:1130 , THR A:1131 , LYS A:1147 , TYR A:1165 , ASN A:1167 , GOL A:1403BINDING SITE FOR RESIDUE GOL A 1404
8AC8SOFTWAREHIS A:1266 , TYR A:1267 , ALA A:1268 , GOL A:1406BINDING SITE FOR RESIDUE GOL A 1405
9AC9SOFTWAREGLU A:1265 , TYR A:1267 , ALA A:1268 , GOL A:1405BINDING SITE FOR RESIDUE GOL A 1406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N7L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:901 -Pro A:902

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N7L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N7L)

(-) Exons   (0, 0)

(no "Exon" information available for 3N7L)

(-) 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:418
 aligned with Q9LBR1_CLOBO | Q9LBR1 from UniProtKB/TrEMBL  Length:1285

    Alignment length:422
                                   872       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  
        Q9LBR1_CLOBO    863 SINDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSSGDDRGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKELTGINFSKTITFQMNKIPNTGLITSDSDNINMWIRDFYIFAKELDDKDINILFNSLQYTNVVKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIRGNTNDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFIIQPCNTFDYYASQLFLSSNATTNRLGILSIGSYSFKLGDDYWFNHEYLIPVIKIEHYASLLESTSTHWVFVPAS 1284
               SCOP domains d3n7la1 A:863-1076 automated matches                                                                                                                                                                                  d3n7la2 A:1077-1284 automated matches                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------Toxin_R_bind_N-3n7lA01 A:876-1076                                                                                                                                                                        --------Toxin_R_bind_C-3n7lA02 A:1085-1284                                                                                                                                                                       Pfam domains
         Sec.struct. author .hhh.eeeeeeee..eeee......eeeee...ee.......eeee.......eeeee.hhhhhhh....eeeeeeeeeee........eeeeeee....eeeeeee..eeeeeeeee..eeeeeeee.hhhhh.......eeeeeeee...eeeeee..eeeeeee...........eeeeeeee........----..eeeeeeeeee....hhhhhhhhhhhh..................eeeeee.....eeeeee..eeeeee............eeeeeee............eeeeeee....eeeeee..........eeeeeee..hhhhhhhhh.eeeeeee....eeeeeeee......eeeeeeeeeeee.........eeeeeeeee.....hhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3n7l A  863 SINDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSSGDDRGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKELTGINFSKTITFQMNKIPNTGLIT----NINMWIRDFYIFAKELDDKDINILFNSLQYTNVVKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIRGNTNDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFIIQPCNTFDYYASQLFLSSNATTNRLGILSIGSYSFKLGDDYWFNHEYLIPVIKIEHYASLLESTSTHWVFVPAS 1284
                                   872       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  
                                                                                                                                                                                                                          1056 1061
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "CATH Domain" information available for 3N7L)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9LBR1_CLOBO | Q9LBR1)
molecular function
    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: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: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.

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 Related Entries

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        Q9LBR1_CLOBO | Q9LBR1: 3azv 3azw 3n7m 4fvv 4isq 4isr

(-) Related Entries Specified in the PDB File

3n7j 3n7k 3n7m