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(-) Description

Title :  STRUCTURE OF A FUNCTIONAL DERIVATIVE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN TYPE B
 
Authors :  G. Masuyer, M. Beard, V. A. Cadd, J. A. Chaddock, K. R. Acharya
Date :  18 Jun 10  (Deposition) - 01 Dec 10  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Metalloprotease, Membrane Domain, Endopeptidase, Zinc Protease, Botulism, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Masuyer, M. Beard, V. A. Cadd, J. A. Chaddock, K. R. Acharya
Structure And Activity Of A Functional Derivative Of Clostridium Botulinum Neurotoxin B.
J. Struct. Biol. V. 174 52 2011
PubMed-ID: 21078393  |  Reference-DOI: 10.1016/J.JSB.2010.11.010

(-) Compounds

Molecule 1 - BOTULINUM NEUROTOXIN B LIGHT CHAIN
    ChainsA
    EC Number3.4.24.69
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMODIFIED PET
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-437
    Organism ScientificCLOSTRIDIUM BOTULINUM
    Organism Taxid1491
    SynonymBONT/B, BONTOXILYSIN-B
 
Molecule 2 - BOTULINUM NEUROTOXIN B HEAVY CHAIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMODIFIED PET
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 446-858
    Organism ScientificCLOSTRIDIUM BOTULINUM
    Organism Taxid1491
    SynonymBONT/B, BONTOXILYSIN-B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:230 , HIS A:234 , GLU A:268 , HOH A:2022BINDING SITE FOR RESIDUE ZN A1442

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:437 -B:461

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XHL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XHL)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.BXB_CLOBO227-236  1A:227-236

(-) Exons   (0, 0)

(no "Exon" information available for 2XHL)

(-) 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:430
 aligned with BXB_CLOBO | P10844 from UniProtKB/Swiss-Prot  Length:1291

    Alignment length:445
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440     
            BXB_CLOBO     1 MPVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKITDRIWIIPERYTFGYKPEDFNKSSGIFNRDVCEYYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMIINGIPYLGDRRVPLEEFNTNIASVTVNKLISNPGEVERKKGIFANLIIFGPGPVLNENETIDIGIQNHFASREGFGGIMQMKFCPEYVSVFNNVQENKGASIFNRRGYFSDPALILMHELIHVLHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYDKVLQNFRGIVDRLNKVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESFDKLYKSLMFGFTETNIAENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNISDKDMEKEYRGQNKAINKQAYEEISKEHLAVYKIQMCKSVKAPGI 445
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Peptidase_M27-2xhlA01 A:3-418                                                                                                                                                                                                                                                                                                                                                                                                   -------------------    ---- Pfam domains
         Sec.struct. author ..................eeeeehhhhh.....eeeeeee..eeee........hhhhhh...ee......ee.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh............ee.......eeeee.........eeeee..eeee.........eee........hhhh.....eeee....eeeee....-----------.ee.hhhhhhhhhhhhhhhhhh........................hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhhh..ee.....ee.hhhhhhhhhhhhhhh.hhhhhhhhh............eeeeee................hhhhh.hhhhhhh........ee..hhh.ee..eeeee----.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xhl A   1 MPVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKITDRIWIIPERYTFGYKPEDFNKSSGIFNRDVCEYYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMIINGIPYLGDRRVPLEEFNTNIASVTVNKLISNPGEVERKKGIFANLIIFGPGPVLNENETIDIGIQNHFASREGFGGIMQMKFCPEYVSVFNNVQ-----------GYFSDPALILMHELIHVLHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYDKVLQNFRGIVDRLNKVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESFDKLYKSLMFGFTETNIAENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNISDKDMEKEYRGQNKAINKQAYEEISKEHLAVYKIQMC----VDGI 441
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      |  -       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430      |  - |   
                                                                                                                                                                                                                                        207         219                                                                                                                                                                                                                       437  438   

Chain B from PDB  Type:PROTEIN  Length:410
 aligned with BXB_CLOBO | P10844 from UniProtKB/Swiss-Prot  Length:1291

    Alignment length:441
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856 
            BXB_CLOBO   417 NKQAYEEISKEHLAVYKIQMCKSVKAPGICIDVDNEDLFFIADKNSFSDDLSKNERIEYNTQSNYIENDFPINELILDTDLISKIELPSENTESLTDFNVDVPVYEKQPAIKKIFTDENTIFQYLYSQTFPLDIRDISLTSSFDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAGWVKQIVNDFVIEANKSNTMDKIADISLIVPYIGLALNVGNETAKGNFENAFEIAGASILLEFIPELLIPVVGAFLLESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIVAQWLSTVNTQFYTIKEGMYKALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDNINNFINGCSVSYLMKKMIPLAVEKLLDFDNTLKKNLLNYIDENKLYLIGSAEYEKSKVNKYLKTIMPFDLSIYTNDTILIEMFNKYN 857
               SCOP domains d2x                          hlb1 B:458-549 automated matches                                                         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---                          ------------------------------------------------------------------------------------------Toxin_trans-2xhlB01 B:551-868                                                                                                                                                                                                                                                                                                 ---- Pfam domains
         Sec.struct. author ...--------------------------eeeee.hhh....hhhhh.hhhhh.eee.............hhhhhhhhhhhh........ee...............ee.eeeee....hhhhhhhh..........eee.hhhhhhhh..eee...hhhhhhhh.......hhhhhhhhhhhhhhhhhh....-----.......hhhhhhh........hhhhhhhhhhhhhh..............eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh......hhhhh....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xhl B 458 NLQ--------------------------CIDVDNEDLFFIADKNSFSDDLSKNERIEYNTQSNYIENDFPINELILDTDLISKIELPSENTESLTDFNVDVPVYEKQPAIKKIFTDENTIFQYLYSQTFPLDIRDISLTSSFDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAGWVKQIVNDFVIEANKSNT-----DISLIVPYIGLALNVGNETAKGNFENAFEIAGASILLEFIPELLIPVVGAFLLESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIVAQWLSTVNTQFYTIKEGMYKALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDNINNFINGCSVSYLMKKMIPLAVEKLLDFDNTLKKNLLNYIDENKLYLIGSAEYEKSKVNKYLKTIMPFDLSIYTNDTILIEMFNKYN 872
                              |      -         -       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621   |   631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871 
                            460                        461                                                                                                                                                                 625   631                                                                                                                                                                                                                                                 

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XHL)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BXB_CLOBO | P10844)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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: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: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
        BXB_CLOBO | P108441epw 1f31 1f82 1g9a 1g9b 1g9c 1g9d 1i1e 1s0b 1s0c 1s0d 1s0e 1s0f 1s0g 1z0h 2etf 2nm1 2np0 3zuq 4kbb

(-) Related Entries Specified in the PDB File

1epw CRYSTAL STRUCTURE OF CLOSTRIDIUM NEUROTOXIN TYPE B
1f31 CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH A TRISACCHARIDE
1f82 BOTULINUM NEUROTOXIN TYPE B CATALYTIC DOMAIN
1g9a CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN BCOMPLEXED WITH AN INHIBITOR (EXPERIMENT 3)
1g9b CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN BCOMPLEXED WITH AN INHIBITOR (EXPERIMENT 1)
1g9c CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN BCOMPLEXED WITH AN INHIBITOR (EXPERIMENT 4)
1g9d CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN BCOMPLEXED WITH AN INHIBITOR (EXPERIMENT 2)
1i1e CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN BCOMPLEXED WITH DOXORUBICIN
1s0b CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN TYPE B AT PH 4.0
1s0c CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN TYPE B AT PH 5.0
1s0d CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN TYPE B AT PH 5.5
1s0e CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN TYPE B AT PH 6.0
1s0f CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN TYPE B AT PH 7.0
1s0g CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN TYPE B APO FORM
1z0h N-TERMINAL HELIX REORIENTS IN RECOMBINANT C -FRAGMENT OFCLOSTRIDIUM BOTULINUM TYPE B
2etf CRYSTAL STRUCTURE OF FULL LENGTH BOTULINUM NEUROTOXIN (TYPEB) LIGHT CHAIN