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(-) Description

Title :  CRYSTAL STRUCTURE OF HCR/T COMPLEXED WITH GT2
 
Authors :  C. Chen, Z. Fu, J. -J. P. Kim, J. T. Barbieri, M. R. Baldwin
Date :  29 May 09  (Deposition) - 14 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Tetanus Neurotoxin, Gt2, Ganglioside, Carbohydrate Binding Pocket, Disulfide Bond, Hydrolase, Metal-Binding, Metalloprotease, Neurotoxin, Protease, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chen, Z. Fu, J. J. Kim, J. T. Barbieri, M. R. Baldwin
Gangliosides As High Affinity Receptors For Tetanus Neurotoxin.
J. Biol. Chem. V. 284 26569 2009
PubMed-ID: 19602728  |  Reference-DOI: 10.1074/JBC.M109.027391

(-) Compounds

Molecule 1 - TETANUS TOXIN
    Chains: A
    EC Number: 3.4.24.68
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28
    Expression System Strain: BL-21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RECEPTOR BINDING DOMAIN (UNP RESIDUES 866-1315)
    Organism Scientific: CLOSTRIDIUM TETANI
    Organism Taxid: 1513
    Synonym: TENTOXYLYSIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SIA3Ligand/IonO-SIALIC ACID
3SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESIA A:5BINDING SITE FOR RESIDUE SIA A 4
2AC2SOFTWARESIA A:4 , SIA A:6 , ASP A:1147 , ASN A:1216 , ILE A:1275 , HOH A:1548BINDING SITE FOR RESIDUE SIA A 5
3AC3SOFTWARESIA A:5 , ASP A:1214 , GLY A:1215 , ASN A:1216 , ARG A:1226 , TYR A:1229 , ALA A:1231BINDING SITE FOR RESIDUE SIA A 6
4AC4SOFTWAREASP A:1222 , THR A:1270 , HIS A:1271 , ILE A:1285 , HOH A:1798 , HOH A:1831BINDING SITE FOR RESIDUE GOL A 1400
5AC5SOFTWARESER A:1007 , ALA A:1063 , ARG A:1065 , ARG A:1223 , ASN A:1288 , HOH A:1559 , HOH A:1676BINDING SITE FOR RESIDUE SO4 A 1401
6AC6SOFTWARELYS A:921 , LYS A:1138 , ASN A:1153 , HOH A:1709BINDING SITE FOR RESIDUE SO4 A 1402
7AC7SOFTWARETYR A:1180 , LEU A:1236 , TYR A:1237 , LYS A:1238 , LYS A:1239 , TYR A:1258 , ASP A:1259 , ASP A:1260 , HOH A:1670BINDING SITE FOR RESIDUE SO4 A 1403
8AC8SOFTWARELYS A:1143 , ASP A:1278 , ARG A:1281BINDING SITE FOR RESIDUE SO4 A 1404

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:869 -A:1093

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HMY)

(-) 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:442
 aligned with TETX_CLOTE | P04958 from UniProtKB/Swiss-Prot  Length:1315

    Alignment length:450
                                   875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305      1315
          TETX_CLOTE    866 NLDCWVDNEEDIDVILKKSTILNLDINNDIISDISGFNSSVITYPDAQLVPGINGKAIHLVNNESSEVIVHKAMDIEYNDMFNNFTVSFWLRVPKVSASHLEQYGTNEYSIISSMKKHSLSIGSGWSVSLKGNNLIWTLKDSAGEVRQITFRDLPDKFNAYLANKWVFITITNDRLSSANLYINGVLMGSAEITGLGAIREDNNITLKLDRCNNNNQYVSIDKFRIFCKALNPKEIEKLYTSYLSITFLRDFWGNPLRYDTEYYLIPVASSSKDVQLKNITDYMYLTNAPSYTNGKLNIYYRRLYNGLKFIIKRYTPNNEIDSFVKSGDFIKLYVSYNNNEHIVGYPKDGNAFNNLDRILRVGYNAPGIPLYKKMEAVKLRDLKTYSVQLKLYDDKNASLGLVGTHNGQIGNDPNRDILIASNWYFNHLKDKILGCDWYFVPTDEGWTND 1315
               SCOP domains d3hmy    a1 A:866-1110 automated matches                                                                                                                                                                                                             d3hmya2 A:1111-1315 automated matches                                                                                                                                                                         SCOP domains
               CATH domains 3hmyA    01 A:866-1109  [code=2.60.120.200, no name defined]                                                                                                                                                                                        3hmyA02 A:1110-1315  [code=2.80.10.50, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....----.hhhhhhhhheeeeeeee..eeee......eeee....eeee....eeeeee......eeee.............eeeeeeee....hhhhhhhhh..eeeeee...----....eeeeeee..eeeeeee.....eeeeeee..............eeeeeee....eeeeee..eeeeeee...........eeeeeee.......eeeeeeeeee....hhhhhhhhhhhh..................eeeeee.hhh.eeeee......eeeee..eeee....eeee......eeeeee..............eeeeeeeee..eeeeeeee....eehhheee.ee........ee..eeee..........eeeee.....eeeeeeeeee.......eeeeeeehhhhhh.........eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3hmy A  866 NLDCW----EDIDVILKKSTILNLDINNDIISDISGFNSSVITYPDAQLVPGINGKAIHLVNNESSEVIVHKAMDIEYNDMFNNFTVSFWLRVPKVSASHLEQYGTNEYSIISSMK----SIGSGWSVSLKGNNLIWTLKDSAGEVRQITFRDLPDKFNAYLANKWVFITITNDRLSSANLYINGVLMGSAEITGLGAIREDNNITLKLDRCNNNNQYVSIDKFRIFCKALNPKEIEKLYTSYLSITFLRDFWGNPLRYDTEYYLIPVASSSKDVQLKNITDYMYLTNAPSYTNGKLNIYYRRLYNGLKFIIKRYTPNNEIDSFVKSGDFIKLYVSYNNNEHIVGYPKDGNAFNNLDRILRVGYNAPGIPLYKKMEAVKLRDLKTYSVQLKLYDDKNASLGLVGTHNGQIGNDPNRDILIASNWYFNHLKDKILGCDWYFVPTDEGWTND 1315
                                |  875       885       895       905       915       925       935       945       955       965       975     |   -|      995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305      1315
                              870  875                                                                                                       981  986
   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  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TETX_CLOTE | P04958)
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: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:0046929    negative regulation of neurotransmitter secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a neurotransmitter.
    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:0030669    clathrin-coated endocytic vesicle membrane    The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030666    endocytic vesicle membrane    The lipid bilayer surrounding an endocytic vesicle.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  3hmy
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 Related Entries

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

UniProtKB/Swiss-Prot
        TETX_CLOTE | P04958: 1a8d 1af9 1d0h 1dfq 1diw 1dll 1fv2 1fv3 1yvg 1yxw 1yyn 1z7h 3hn1 4j1l 5n0b 5n0c

(-) Related Entries Specified in the PDB File

1fv2 HCR/T COMPLEXED WITH GT1B
3hn1