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(-) Description

Title :  CRYSTAL STRUCTURE OF APO FORM (ZINC REMOVED) OF THE BOTULINUM NEUROTOXIN TYPE C LIGHT CHAIN
 
Authors :  R. Rawat, D. Kumaran, S. Swaminathan
Date :  09 Jun 08  (Deposition) - 07 Apr 09  (Release) - 07 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Botulism, Botulinum Neurotoxin, Apo Form, Light Chain, Snare Proteins, Protease, Hydrolase, Membrane, Metal- Binding, Metalloprotease, Neurotoxin, Secreted, Toxin, Transmembrane, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Rawat, D. Kumaran, S. Swaminathan
Crystal Structure Of Apo Form (Zinc Removed) Of The Botulinum Neurotoxin Type C Light Chain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BOTULINUM NEUROTOXIN C1 LIGHT CHAIN
    Chains: A
    EC Number: 3.4.24.69
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BONT/C
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491
    Synonym: BONT/C1, BONTOXILYSIN-C1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA1Ligand/IonCALCIUM ION
3FMT7Ligand/IonFORMIC ACID
4NA1Ligand/IonSODIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:168 , GLU A:269 , HOH A:531 , HOH A:554 , HOH A:949 , HOH A:971 , HOH A:972BINDING SITE FOR RESIDUE NA A 499
02AC2SOFTWARESER A:135 , ACT A:501 , HOH A:557 , HOH A:640 , HOH A:874 , HOH A:875BINDING SITE FOR RESIDUE CA A 500
03AC3SOFTWAREASP A:132 , PHE A:133 , SER A:135 , CA A:500 , HOH A:640 , HOH A:648 , HOH A:874 , HOH A:875 , HOH A:908BINDING SITE FOR RESIDUE ACT A 501
04AC4SOFTWAREASN A:119 , ASN A:121 , THR A:122 , ASP A:128 , HOH A:691 , HOH A:960BINDING SITE FOR RESIDUE FMT A 502
05AC5SOFTWARETHR A:277 , ILE A:374 , TYR A:375 , LEU A:376 , HOH A:783BINDING SITE FOR RESIDUE FMT A 503
06AC6SOFTWARESER A:171 , THR A:172 , PHE A:180BINDING SITE FOR RESIDUE FMT A 504
07AC7SOFTWARELEU A:29 , ASP A:48 , ARG A:49BINDING SITE FOR RESIDUE FMT A 505
08AC8SOFTWAREGLU A:89 , ASN A:386 , ILE A:387 , LEU A:388BINDING SITE FOR RESIDUE FMT A 506
09AC9SOFTWARETYR A:71 , ARG A:197 , THR A:384 , VAL A:424 , ASN A:425 , HOH A:736BINDING SITE FOR RESIDUE FMT A 507
10BC1SOFTWAREASP A:208 , SER A:314 , PHE A:315 , HOH A:544BINDING SITE FOR RESIDUE FMT A 508

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:66 -Pro A:67
2Asn A:311 -Pro A:312

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.BXC1_CLOBO226-235  1A:226-235

(-) Exons   (0, 0)

(no "Exon" information available for 3DEB)

(-) 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:432
 aligned with BXC1_CLOBO | P18640 from UniProtKB/Swiss-Prot  Length:1291

    Alignment length:432
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428  
           BXC1_CLOBO     - --MPITINNFNYSDPVDNKNILYLDTHLNTLANEPEKAFRITGNIWVIPDRFSRNSNPNLNKPPRVTSPKSGYYDPNYLSTDSDKDPFLKEIIKLFKRINSREIGEELIYRLSTDIPFPGNNNTPINTFDFDVDFNSVDVKTRQGNNWVKTGSINPSVIITGPRENIIDPETSTFKLTNNTFAAQEGFGALSIISISPRFMLTYSNATNDVGEGRFSKSEFCMDPILILMHELNHAMHNLYGIAIPNDQTISSVTSNIFYSQYNVKLEYAEIYAFGGPTIDLIPKSARKYFEEKALDYYRSIAKRLNSITTANPSSFNKYIGEYKQKLIRKYRFVVESSGEVTVNRNKFVELYNELTQIFTEFNYAKIYNVQNRKIYLSNVYTPVTANILDDNVYDIQNGFNIPKSNLNVLFMGQNLSRNPALRKVNPENML 430
               SCOP domains d3deba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3debA00 A:-2-430 Metalloproteases ('zincins'), catalytic domain like                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................eeeee..........eeeeeee..eeee................................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh............eee.......eeeeeee..eeeeeeee...eeee.........eee........hhhhh.....eeee.......ee................ee.hhhhhhhhhhhhhhhhhh........eeeeee.......eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhh.ee.....ee.hhhhhhhhhhhhhhh.hhhhhhhhh...............ee................hhhhh....hhhhh.......ee.hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3deb A  -2 SHMPITINNFNYSDPVDNKNILYLDTHLNTLANEPEKAFRITGNIWVIPDRFSRNSNPNLNKPPRVTSPKSGYYDPNYLSTDSDKDTFLKEIIKLFKRINSREIGEELIYRLSTDIPFPGNNNTPINTFDFDVDFNSVDVKTRQGNNWVKTGSINPSVIITGPRENIIDPETSTFKLTNNTFAAQEGFGALSIISISPRFMLTYSNATNDVGEGRFSKSEFCMDPILILMHELNHAMHNLYGIAIPNDQTISSVTSNIFYSQYNVKLEYAEIYAFGGPTIDLIPKSARKYFEEKALDYYRSIAKRLNSITTANPSSFNKYIGEYKQKLIRKYRFVVESSGEVTVNRNKFVELYNELTQIFTEFNYAKIYNVQNRKIYLSNVYTPVTANILDDNVYDIQNGFNIPKSNLNVLFMGQNLSRNPALRKVNPENML 430
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428  
                             ||                                                                                                                                                                                                                                                                                                                                                                                                                                             
                            -1|                                                                                                                                                                                                                                                                                                                                                                                                                                             
                              1
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BXC1_CLOBO | P18640)
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:0033619    membrane protein proteolysis    The proteolytic cleavage of a transmembrane protein leading to the release of its intracellular or ecto-domains.
    GO:0045955    negative regulation of calcium ion-dependent exocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of calcium ion-dependent exocytosis.
    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

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

UniProtKB/Swiss-Prot
        BXC1_CLOBO | P18640: 2qn0 3n7k 3r4s 3r4u

(-) Related Entries Specified in the PDB File

2qn0 STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE C1 LIGHT CHAIN PROTEASE