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(-) Description

Title :  A COMMON BINDING SITE FOR DISIALYLLACTOSE AND A TRI-PEPTIDE IN THE C-FRAGMENT OF TETANUS NEUROTOXIN
 
Authors :  J. Seetharaman, S. Eswaramoorthy, D. Kumaran, S. Swaminathan
Date :  25 Feb 05  (Deposition) - 15 Mar 05  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Tetanus Toxin, Gd3, Ganglioside, X-Ray Crystallography, Beta-Trefoil, Inhibitors, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Jayaraman, S. Eswaramoorthy, D. Kumaran, S. Swaminathan
Common Binding Site For Disialyllactose And Tri-Peptide In C-Fragment Of Tetanus Neurotoxin
Proteins V. 61 288 2005
PubMed-ID: 16104015  |  Reference-DOI: 10.1002/PROT.20595
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TETANUS TOXIN
    Chains: A
    EC Number: 3.4.24.68
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 875-1315
    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, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GLA1Ligand/IonALPHA D-GALACTOSE
3SIA2Ligand/IonO-SIALIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:1214 , ASN A:1216 , ARG A:1226 , TYR A:1229 , SIA A:2001BINDING SITE FOR RESIDUE SIA A 2000
2AC2SOFTWAREASP A:1147 , ASN A:1216 , ARG A:1226 , ILE A:1275 , SIA A:2000 , GLA A:2002BINDING SITE FOR RESIDUE SIA A 2001
3AC3SOFTWARESIA A:2001 , BGC A:2003BINDING SITE FOR RESIDUE GLA A 2002
4AC4SOFTWAREHOH A:79 , GLA A:2002BINDING SITE FOR RESIDUE BGC A 2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YYN)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YYN)

(-) Exons   (0, 0)

(no "Exon" information available for 1YYN)

(-) 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:441
 aligned with TETX_CLOTE | P04958 from UniProtKB/Swiss-Prot  Length:1315

    Alignment length:441
                                   884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314 
          TETX_CLOTE    875 EDIDVILKKSTILNLDINNDIISDISGFNSSVITYPDAQLVPGINGKAIHLVNNESSEVIVHKAMDIEYNDMFNNFTVSFWLRVPKVSASHLEQYGTNEYSIISSMKKHSLSIGSGWSVSLKGNNLIWTLKDSAGEVRQITFRDLPDKFNAYLANKWVFITITNDRLSSANLYINGVLMGSAEITGLGAIREDNNITLKLDRCNNNNQYVSIDKFRIFCKALNPKEIEKLYTSYLSITFLRDFWGNPLRYDTEYYLIPVASSSKDVQLKNITDYMYLTNAPSYTNGKLNIYYRRLYNGLKFIIKRYTPNNEIDSFVKSGDFIKLYVSYNNNEHIVGYPKDGNAFNNLDRILRVGYNAPGIPLYKKMEAVKLRDLKTYSVQLKLYDDKNASLGLVGTHNGQIGNDPNRDILIASNWYFNHLKDKILGCDWYFVPTDEGWTND 1315
               SCOP domains d1yyna1 A:875-1110 Tetanus neurotoxin                                                                                                                                                                                                       d1yyna2 A:1111-1315 Tetanus neurotoxin                                                                                                                                                                        SCOP domains
               CATH domains 1yynA01 A:875-1109  [code=2.60.120.200, no name defined]                                                                                                                                                                                   1yynA02 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...eeeee............eeeeee..eeeeeee.....eeeeeee..............eeeeeee....eeeeee..eeeeeee...........eeeeeee.......eeeeeeeeee....hhhhhhhhhhhh..................eeeeee.hhh.eeeee......eeeee..eeee....eeee......eeeeee...............eeeeeeee..eeeeeeee....eehhheee.ee........ee.eeeee..........eeeee.....eeeeeeeeee.......eeeeeeehhhhhh.........eeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yyn A  875 EDIDVILKKSTILNLDINNDIISDISGFNSSVITYPDAQLVPGINGKAIHLVNNESSEVIVHKAMDIEYNDMFNNFTVSFWLRVPKVSASHLEQYGTNEYSIISSMKKHSLSIGSGWSVSLKGNNLIWTLKDSAGEVRQITFRDLPDKFNAYLANKWVFITITNDRLSSANLYINGVLMGSAEITGLGAIREDNNITLKLDRCNNNNQYVSIDKFRIFCKALNPKEIEKLYTSYLSITFLRDFWGNPLRYDTEYYLIPVASSSKDVQLKNITDYMYLTNAPSYTNGKLNIYYRRLYNGLKFIIKRYTPNNEIDSFVKSGDFIKLYVSYNNNEHIVGYPKDGNAFNNLDRILRVGYNAPGIPLYKKMEAVKLRDLKTYSVQLKLYDDKNASLGLVGTHNGQIGNDPNRDILIASNWYFNHLKDKILGCDWYFVPTDEGWTND 1315
                                   884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314
   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 1YYN)

(-) 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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  1yyn
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  TETX_CLOTE | P04958
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  3.4.24.68
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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 1z7h 3hmy 3hn1 4j1l 5n0b 5n0c

(-) Related Entries Specified in the PDB File

1af9