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(-) Description

Title :  CRYSTAL STRUCTURE OF TYR350ALA MUTANT OF CLOSTRIDIUM BOTULINUM NEUROTOXIN E CATALYTIC DOMAIN
 
Authors :  R. Agarwal, T. Binz, S. Swaminathan
Date :  05 May 05  (Deposition) - 28 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Botulinum Neurotoxin E, Catalytic Domain, Light Chain, Tyr350Ala Mutant, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Agarwal, T. Binz, S. Swaminathan
Analysis Of Active Site Residues Of Botulinum Neurotoxin E By Mutational, Functional, And Structural Studies: Glu335Gln Is An Apoenzyme.
Biochemistry V. 44 8291 2005
PubMed-ID: 15938619  |  Reference-DOI: 10.1021/BI050253A
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BOTULINUM NEUROTOXIN TYPE E
    ChainsA, B
    EC Number3.4.24.69
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-9C
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypeT7
    FragmentCATALYTIC DOMAIN (RESIDUES 2-421)
    MutationYES
    Organism ScientificCLOSTRIDIUM BOTULINUM
    Organism Taxid1491
    StrainNCTC-11219

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:211 , HIS A:215 , GLU A:250 , SO4 A:500BINDING SITE FOR RESIDUE ZN A 422
2AC2SOFTWAREHIS B:211 , HIS B:215 , GLU B:250BINDING SITE FOR RESIDUE ZN B 822
3AC3SOFTWAREHIS A:211 , GLU A:212 , HIS A:215 , GLU A:250 , ZN A:422BINDING SITE FOR RESIDUE SO4 A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZL6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZL6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZL6)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.BXE_CLOBO209-218
 
  2A:208-217
B:208-217

(-) Exons   (0, 0)

(no "Exon" information available for 1ZL6)

(-) 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:400
 aligned with BXE_CLOBO | Q00496 from UniProtKB/Swiss-Prot  Length:1251

    Alignment length:411
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411 
            BXE_CLOBO     2 PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPPTSLKNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHRFGSIAIVTFSPEYSFRFNDNCMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTITQKQNPLITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLRTKFQVKCRQTYIGQYKYFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIRFC 412
               SCOP domains d1zl6a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1zl6A00 A:1-411 Metalloproteases ('zincins'), catalytic domain like                                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeee.......eeeeeee..eeeeeee.....hhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................eeee.....eeee...eeeee........eeee..hhhhhhhhhh.....eeee....eeeeee.....eee.hhhhhhhhhhhhhhhhhh............-----------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.eee.....eeehhhhhhhhhhhhh..hhhhhhhhhh............eeee................hhhhhhhhhhhh...hhh.ee.....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zl6 A   1 PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPPTSLKNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGSIAIVTFSPEYSFRFNDNSMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTIT-----------GTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTAIGQYKYFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIRFC 411
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  |      -    |  250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410 
                                                                                                                                                                                                                                                                  233         245                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:387
 aligned with BXE_CLOBO | Q00496 from UniProtKB/Swiss-Prot  Length:1251

    Alignment length:409
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401         
            BXE_CLOBO     2 PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPPTSLKNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHRFGSIAIVTFSPEYSFRFNDNCMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTITQKQNPLITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLRTKFQVKCRQTYIGQYKYFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIR 410
               SCOP domains d1zl6b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1zl6B00 B:1-409 Metalloproteases ('zincins'), catalyti           c domain like                                                                                                                                                                                                                                                                                                                                            CATH domains
           Pfam domains (1) Peptidase_M27-1zl6B01 B:1-392                                                                                                                                                                                                                                                                                                                                                                           ----------------- Pfam domains (1)
           Pfam domains (2) Peptidase_M27-1zl6B02 B:1-392                                                                                                                                                                                                                                                                                                                                                                           ----------------- Pfam domains (2)
         Sec.struct. author ................eeeee.......eeeeeee..eeeeeee.....hhhhh-----------.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................eeee.....eeee...eeeee........eeee..hhhhhhhhhh.....eeee....eeeeee.....eee.hhhhhhhhhhhhhhhhhh............-----------..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.eee.....eeehhhhhhhhhhhhh..hhhhhhhhhh...........eeee.................hhhhhhhhhhhh...hhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zl6 B   1 PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDF-----------SYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGSIAIVTFSPEYSFRFNDNSMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTIT-----------GTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTAIGQYKYFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIR 409
                                    10        20        30        40        50   |     -     |  70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  |      -    |  250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400         
                                                                                54          66                                                                                                                                                                    233         245                                                                                                                                                                    

   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  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BXE_CLOBO | Q00496)
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: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
        BXE_CLOBO | Q004961t3a 1t3c 1zkw 1zkx 1zl5 1zn3 3ffz

(-) Related Entries Specified in the PDB File

1t3a CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN E CATALYTIC DOMAIN
1t3c CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN E GLU212GLN MUTANT OF CATALYTIC DOMAIN
1zkw CRYSTAL STRUCTURE OF ARG347ALA MUTANT OF CLOSTRIDIUM BOTULINUM NEUROTOXIN E CATALYTIC DOMAIN
1zkx CRYSTAL STRUCTURE OF GLU158ALA/THR159ALA/ASN160ALA-TRIPLE MUTANT OF MUTANT OF CLOSTRIDIUM BOTULINUM NEUROTOXIN E CATALYTIC DOMAIN
1zl5 CRYSTAL STRUCTURE OF GLU335GLN MUTANT OF CLOSTRIDIUM BOTULINUM NEUROTOXIN E CATALYTIC DOMAIN