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(-) Description

Title :  CRYSTAL STRUCTURE OF RECOMBINANT BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN, SELF-INHIBITING ZN ENDOPEPTIDASE.
 
Authors :  M. Knapp, B. Rupp
Date :  08 May 00  (Deposition) - 19 Jun 03  (Release) - 01 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Neurotoxin, Zn-Endopeptidase, Complex, Substrate Bound, Botulinum, Inhibitor Bound, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. W. Segelke, M. Knapp, S. Kadhkodayan, R. Balhorn, B. Rupp
Crystal Structure Of Clostridium Botulinum Neurotoxin Protease In A Product-Bound State: Evidence For Noncanonical Zinc Protease Activity
Proc. Natl. Acad. Sci. Usa V. 101 6888 2004
PubMed-ID: 15107500  |  Reference-DOI: 10.1073/PNAS.0400584101

(-) Compounds

Molecule 1 - BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN
    ChainsA, C
    EC Number3.4.24.69
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cell LineBLR DE-3
    Expression System Taxid562
    Expression System VectorPET-30
    FragmentRESIDUES 10-250
    Organism ScientificCLOSTRIDIUM BOTULINUM
    Organism Taxid1491
    PlasmidPET-30
    StrainKYOTO-F
    SynonymBONT/A LC
 
Molecule 2 - BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN
    ChainsB, D
    EC Number3.4.24.69
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cell LineBLR DE-3
    Expression System Taxid562
    Expression System VectorPET-30
    FragmentRESIDUES 252-416
    MutationYES
    Organism ScientificCLOSTRIDIUM BOTULINUM
    Organism Taxid1491
    Other DetailsHOMODIMER, CONTAINING CLEAVED SUBSTRATE ANALOG (LOOP 245-255) IN ACTIVE SITE
    PlasmidPET-30
    StrainKYOTO-F
    SynonymBONT/A LC

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:222 , HIS A:226 , GLU B:261 , TYR C:249BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWARETYR A:249 , HIS C:222 , HIS C:226 , GLU D:261BINDING SITE FOR RESIDUE ZN C 502
3S1AAUTHORPHE A:193 , PHE A:195 , THR A:214 , PHE B:265 , GLU B:350 , ARG B:362 , ASN B:361 , TYR B:365S1 BINDING POCKET OF THE LC ACTIVE SITE. QUITE LARGE.
4S1BAUTHORPHE C:193 , PHE C:195 , THR C:214 , PHE D:265 , GLU D:350 , ARG D:362 , ASN D:361 , TYR D:365S1 BINDING POCKET OF THE LC ACTIVE SITE. QUITE LARGE.
5S2AAUTHORGLU A:163 , ASP A:170 , ARG A:176 , ARG A:230S1' BINDING POCKET OF THE LC ACTIVE SITE.
6S2BAUTHORGLU C:163 , ASP C:170 , ARG C:176 , ARG C:230S1' BINDING POCKET OF THE LC ACTIVE SITE.
7ZNAAUTHORHIS A:222 , GLU A:223 , HIS A:226 , GLU B:261ZN ENDOPEPTIDASE ACTIVE SITE. ZN (II) COORDINATED BY STANDARD HEXXH AND E OF THE THERMOLYSIN MOTIF. HIS A 222, HIS A 226 AND GLU B 261. GLU A 223 SHARES COORDINATION OF TYR C 249 O WITH ZN A 501.
8ZNCAUTHORHIS C:222 , GLU C:223 , HIS C:226 , GLU D:261ZN ENDOPEPTIDASE ACTIVE SITE. ZN (II) COORDINATED BY STANDARD HEXXH AND E OF THE THERMOLYSIN MOTIF. HIS C 222, HIS C 226 AND GLU D 261. GLU C 223 SHARES COORDINATION OF TYR A 249 O WITH ZN C 502.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E1H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E1H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E1H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1E1H)

(-) Exons   (0, 0)

(no "Exon" information available for 1E1H)

(-) 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:235
 aligned with BXA2_CLOBO | Q45894 from UniProtKB/Swiss-Prot  Length:1296

    Alignment length:243
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247   
           BXA2_CLOBO     8 FNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHDVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAEHRLYGIAINPNRVFKVNTNAY 250
               SCOP domains d1e1h.1 A:,B: Botulinum neurotoxin                                                                                                                                                                                                                  SCOP domains
               CATH domains 1e1hA00 A:7-249 Metalloproteases ('zincins'), catalytic domain like                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee........eeeeeee..eeeeeee...............................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................eeeee.....eeeee..eeeee........eee.................eeee.......eeee.--------...eeee.hhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e1h A   7 MAYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHDVLNLTRNGYGSTQYIRFSPDFTFGFEES--------LGAGKFATDPAVTLAHELIHAEHRLYGIAINPNRVFKVNTNAY 249
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196 |       -|      216       226       236       246   
                                                                                                                                                                                                                         198      207                                          

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with BXA2_CLOBO | Q45894 from UniProtKB/Swiss-Prot  Length:1296

    Alignment length:165
                                   261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411     
           BXA2_CLOBO   252 EMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDVASTLNKAKSIIGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVNFFKVINRKTYLNFDKAVFRINIVPDENYTIKDGFNLKGANLSTNFNGQNTEINSRNFTRL 416
               SCOP domains d1e1h.1 A:,B: Botulinum neurotoxin                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh.hhhhhhhhhh..................................-......hhhh....hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e1h B 251 EMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDVASTLNKAKSIIGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVNFFKVINRKTYLNFDKAVFRINIVPDENYTIKDGFNLK-ANLSTNFNGQNTEINSRNFTRL 415
                                   260       270       280       290       300       310       320       330       340       350       360       370       380       390 | |   400       410     
                                                                                                                                                                       392 |                     
                                                                                                                                                                         394                     

Chain C from PDB  Type:PROTEIN  Length:235
 aligned with BXA2_CLOBO | Q45894 from UniProtKB/Swiss-Prot  Length:1296

    Alignment length:243
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247   
           BXA2_CLOBO     8 FNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHDVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAEHRLYGIAINPNRVFKVNTNAY 250
               SCOP domains d1e1h.2 C:,D: Botulinum neurotoxin                                                                                                                                                                                                                  SCOP domains
               CATH domains 1e1hC00 C:7-249 Metalloproteases ('zincins'), catalytic domain like                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee........eeeeeee..eeeeeee...............................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................eeeee.....eeeee..eeeee........eee.................eeee.......eeee.--------...eeee.hhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e1h C   7 MAYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHDVLNLTRNGYGSTQYIRFSPDFTFGFEES--------LGAGKFATDPAVTLAHELIHAEHRLYGIAINPNRVFKVNTNAY 249
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196 |       -|      216       226       236       246   
                                                                                                                                                                                                                         198      207                                          

Chain D from PDB  Type:PROTEIN  Length:165
 aligned with BXA2_CLOBO | Q45894 from UniProtKB/Swiss-Prot  Length:1296

    Alignment length:166
                                   260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410      
           BXA2_CLOBO   251 YEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDVASTLNKAKSIIGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVNFFKVINRKTYLNFDKAVFRINIVPDENYTIKDGFNLKGANLSTNFNGQNTEINSRNFTRL 416
               SCOP domains d1e1h.2 C:,D: Botulinum neurotoxin                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhhhhhhh..................................-......hhhh....hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e1h D 250 YEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDVASTLNKAKSIIGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVNFFKVINRKTYLNFDKAVFRINIVPDENYTIKDGFNLK-ANLSTNFNGQNTEINSRNFTRL 415
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389  | |  399       409      
                                                                                                                                                                        392 |                     
                                                                                                                                                                          394                     

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E1H)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (BXA2_CLOBO | Q45894)
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: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.
    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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 Related Entries

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        BXA2_CLOBO | Q458942g7k 2g7n 2g7p 2g7q 5moy

(-) Related Entries Specified in the PDB File

3bta CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE A