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(-) Description

Title :  CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE E CATALYTIC DOMAIN IN COMPLEX WITH SNAP-25 SUBSTRATE PEPTIDE
 
Authors :  R. Agarwal, S. Swaminathan
Date :  13 May 08  (Deposition) - 08 Jul 08  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Bont E, Snap-25, Enzyme-Substrate Complex, Hydrolase, Hydrolase- Hydrolase Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, S. Swaminathan
Snap-25 Substrate Peptide (Residues 180-183) Binds To But Bypasses Cleavage By Catalytically Active Clostridium Botulinum Neurotoxin E.
J. Biol. Chem. V. 283 25944 2008
PubMed-ID: 18658150  |  Reference-DOI: 10.1074/JBC.M803756200

(-) Compounds

Molecule 1 - TYPE E BOTULINUM TOXIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET9C
    Expression System Strain: BL21(DE3) RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Gene: BONT/E
    Organism Scientific: CLOSTRIDIUM BUTYRICUM
    Organism Taxid: 1492
    Strain: NCTC 11219
 
Molecule 2 - SNAP-25 SUBSTRATE PEPTIDE
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
2SO48Ligand/IonSULFATE ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1NH2-1Mod. Amino AcidAMINO GROUP
2SO46Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
2SO42Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN B:242 , GLU D:183BINDING SITE FOR RESIDUE NH2 D 184
02AC2SOFTWAREHIS A:211 , HIS A:215 , GLU A:250 , ARG C:180BINDING SITE FOR RESIDUE ZN A 428
03AC3SOFTWAREPHE A:357 , PRO A:397 , ILE A:398 , ARG A:401BINDING SITE FOR RESIDUE SO4 A 891
04AC4SOFTWAREARG A:192 , LYS A:355 , HOH A:971BINDING SITE FOR RESIDUE SO4 A 892
05AC5SOFTWAREARG A:393 , HOH A:960 , HOH A:1001 , ASP B:311 , ALA B:312BINDING SITE FOR RESIDUE SO4 A 893
06AC6SOFTWAREHIS A:124 , GLY A:126 , ASP A:127 , ARG A:167 , HOH A:943 , HOH A:967 , HOH A:998BINDING SITE FOR RESIDUE SO4 A 894
07AC7SOFTWAREASN A:163 , MET A:171 , LYS A:224 , HOH A:921BINDING SITE FOR RESIDUE SO4 A 896
08AC8SOFTWAREASP A:195 , ASN A:196 , SER A:197 , HOH A:911 , ASN B:364BINDING SITE FOR RESIDUE SO4 A 897
09AC9SOFTWAREHIS B:211 , HIS B:215 , GLU B:250 , ARG D:180BINDING SITE FOR RESIDUE ZN B 822
10BC1SOFTWARESER A:59 , HIS B:124 , GLY B:126 , ASP B:127 , LEU B:166 , ARG B:167 , HOH B:927 , HOH B:981 , HOH B:992 , HOH B:994BINDING SITE FOR RESIDUE SO4 B 890
11BC2SOFTWARESER B:162 , ASN B:163 , MET B:171 , LYS B:224BINDING SITE FOR RESIDUE SO4 B 895
12BC3SOFTWARETHR A:159 , PHE A:191 , THR A:208 , HIS A:211 , GLU A:212 , GLU A:250 , GLU A:335 , ARG A:347 , TYR A:350 , TYR A:354 , TYR A:356 , ZN A:428BINDING SITE FOR CHAIN C OF SNAP-25 SUBSTRATE PEPTIDE
13BC4SOFTWAREGLU B:158 , THR B:159 , ASN B:160 , SER B:161 , PHE B:191 , THR B:208 , HIS B:211 , GLU B:212 , ILE B:240 , THR B:241 , ASN B:242 , THR B:246 , GLU B:250 , GLU B:335 , ARG B:347 , TYR B:350 , ILE B:351 , GLY B:352 , GLN B:353 , TYR B:354 , TYR B:356 , ZN B:822 , HOH B:901 , NH2 D:184 , HOH D:230BINDING SITE FOR CHAIN D OF SNAP-25 SUBSTRATE PEPTIDE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D3X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D3X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D3X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D3X)

(-) Exons   (0, 0)

(no "Exon" information available for 3D3X)

(-) Sequences/Alignments

Asymmetric 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:407
 aligned with Q9K395_CLOBU | Q9K395 from UniProtKB/TrEMBL  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 
         Q9K395_CLOBU     2 PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPPTSLKNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGSIAIVTFSPEYSFRFNDNSMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTITQKQNPLITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTYIGQYKYFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIRFC 412
               SCOP domains d3d3xa_ A: Botulinum neurotoxin                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3d3xA00 A:1-411 Metalloproteases ('zincins'), catalytic domain like                                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeee.......eeeeeee..eeee........hhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................eeee.....eeee...eeee.........eeee..hhhhhhhhhh.....eeee....eeeeee.....eee.hhhhhhhhhhhhhhhhhh.hhhhhh..ee..----.......eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh............eeee....................hhhhhhhh...hhh.ee.....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d3x A   1 PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPPTSLKNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGSIAIVTFSPEYSFRFNDNSMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTITQ----LITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTYIGQYKYFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIRFC 411
                                    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 
                                                                                                                                                                                                                                                                   234  239                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:407
 aligned with Q9K395_CLOBU | Q9K395 from UniProtKB/TrEMBL  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         
         Q9K395_CLOBU     2 PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPPTSLKNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGSIAIVTFSPEYSFRFNDNSMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTITQKQNPLITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTYIGQYKYFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIR 410
               SCOP domains d3d3xb_ B: Botulinum neurotoxin                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3d3xB00 B:1-409 Metalloproteases ('zincins'), catalytic do  main like                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeee.......eeeeeee..eeeeeee.....hhhhhh...--..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................eeee.....eeee...eeeee........eeee.......hhhhh.....eeee....eeeeee.....eee.hhhhhhhhhhhhhhhhhh.........ee.............eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.eee.....eeehhhhhhhhhhhhhhhhhhhhhhhh............eeee.................hhhhhhhhhhhh...hhhhh....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d3x B   1 PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPPT--KNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGSIAIVTFSPEYSFRFNDNSMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTITQKQNPLITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTYIGQYKYFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIR 409
                                    10        20        30        40        50       | -|       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         
                                                                                    58 61                                                                                                                                                                                                                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 3d3x C 180 RIM 182


Chain D from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 3d3x D 180 RIMEx 184
                                |
                              184-NH2
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D3X)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9K395_CLOBU | Q9K395)
molecular function
    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: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.

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  3d3x
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 Related Entries

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(-) Related Entries Specified in the PDB File

1t3a WILD TYPE PROTEIN STRUCTURE
1t3c E212Q MUTANT
1zkw R347A MUTANT
1zkx E158A/THR159A/N160A TRIPLE MUTANT
1zl6 Y350A