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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEUROTOXIN BONT/A C134S MUTANT WITH COVALENT INHIBITOR THAT MODIFIES CYS-165 CAUSING DISORDER IN 166-174 STRETCH
 
Authors :  E. A. Stura, L. Vera, K. Guitot, V. Dive
Date :  17 May 13  (Deposition) - 25 Jun 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Clostridial Neurotoxin Zinc Protease, Peptidase_m27, Snap 25, Covalent Inhibition, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Guitot, L. Vera, L. Le Roux, S. Bregant, D. Ptchelkine, F. Beau, E. A. Stura, V. Dive
Covalent Modification Of The Active Site Cysteine Stresses Clostridium Botulinum Neurotoxin A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BOTULINUM NEUROTOXIN A LIGHT CHAIN
    Chains: A
    EC Number: 3.4.24.69
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A+
    Expression System Strain: ROSETTA DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN RESIDUES 1-425
    Gene: BOTA, CBO0806, CLC_0862
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM BOTULINUM A
    Organism Taxid: 441771
    Strain: STRAIN HALL / ATCC 3502 / NCTC 13319 / TYPE A
    Synonym: BOTULINUM NEUROTOXIN TYPE A, BONT/A, BONTOXILYSIN-A, BOTOX
 
Molecule 2 - PEPTIDE INHIBITOR MPT-DPP-DAR-G-DPN-NH2
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (11, 16)

Asymmetric/Biological Unit (11, 16)
No.NameCountTypeFull Name
1DAR1Mod. Amino AcidD-ARGININE
2DPN1Mod. Amino AcidD-PHENYLALANINE
3DPP1Mod. Amino AcidDIAMINOPROPANOIC ACID
4EDO3Ligand/Ion1,2-ETHANEDIOL
5GOL3Ligand/IonGLYCEROL
6MPT1Mod. Amino AcidBETA-MERCAPTOPROPIONIC ACID
7NH21Mod. Amino AcidAMINO GROUP
8PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
9PGO2Ligand/IonS-1,2-PROPANEDIOL
10SO41Ligand/IonSULFATE ION
11ZN1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:223 , HIS A:227 , GLU A:262 , DPP B:2BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWARELYS A:375 , ILE A:376 , THR A:414BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWAREASP A:339 , ASN A:400 , ASN A:402 , PGO A:506 , HOH A:764BINDING SITE FOR RESIDUE GOL A 503
04AC4SOFTWAREPRO A:140 , ASP A:141 , LYS A:415 , LEU A:416 , ASN A:418BINDING SITE FOR RESIDUE GOL A 504
05AC5SOFTWARELYS A:6 , GLN A:7 , PHE A:8 , THR A:92BINDING SITE FOR RESIDUE PEG A 505
06AC6SOFTWAREARG A:283 , LEU A:284 , TYR A:287 , PHE A:338 , ASP A:339 , GOL A:503 , HOH A:943BINDING SITE FOR RESIDUE PGO A 506
07AC7SOFTWAREASN A:383 , MET A:411 , ASN A:412 , HOH A:774BINDING SITE FOR RESIDUE GOL A 507
08AC8SOFTWAREASN A:238 , PHE A:282 , TYR A:285 , TYR A:286 , HOH A:941BINDING SITE FOR RESIDUE PGO A 508
09AC9SOFTWAREGLN A:139 , HOH A:660BINDING SITE FOR RESIDUE EDO A 509
10BC1SOFTWAREILE A:160 , PHE A:188 , SER A:189 , HOH A:904BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWARELYS A:212 , ARG A:283 , ASP A:339 , ASN A:405 , GLU A:407 , HOH A:872BINDING SITE FOR RESIDUE EDO A 511
12BC3SOFTWAREPHE A:163 , GLU A:164 , CYS A:165 , PHE A:194 , THR A:215 , HIS A:223 , GLU A:224 , HIS A:227 , TYR A:251 , LEU A:256 , GLU A:262 , ARG A:363 , TYR A:366 , ASN A:368 , PHE A:369 , ASP A:370 , ZN A:501 , HOH A:782 , HOH A:804 , HOH A:811 , HOH A:824 , HOH A:825 , HOH B:101 , HOH B:102BINDING SITE FOR CHAIN B OF PEPTIDE INHIBITOR MPT-DPP-DAR-G-DPN-NH2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KS6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4KS6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KS6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KS6)

(-) Exons   (0, 0)

(no "Exon" information available for 4KS6)

(-) 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:428
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeee.........eeeeeee..eeee.................hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee..hhh.eeeee.....eeeee..eeee.................hhhhhh......eeee....eeeee..hhhhhh........ee.hhhhhhhhhhhhhhhhhh........eee...hhhhhh...eeehhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhh..ee.....ee.hhhhhhhhhhhhhh..hhhhhhhhhh............eeee.........................hhhhh...hhhhheeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ks6 A  -2 GSHMPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNSINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTGLFEF 425
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417        


Chain B from PDB  Type:PROTEIN  Length:6
                                      
               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
                 4ks6 B   1 xaxGxx   6
                            ||| ||
                            1-MPT|
                             2-DPP
                              3-DAR
                                5-DPN
                                 6-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  (0, 0)

(no "SCOP Domain" information available for 4KS6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KS6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KS6)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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  BXA1_CLOBH | A5HZZ9
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 Related Entries

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UniProtKB/Swiss-Prot
        BXA1_CLOBH | A5HZZ9: 1xtf 1xtg 2w2d 3bwi 3c8a 3c8b 3dda 3ddb 3ds9 3dse 3k3q 3qix 3qiy 3qiz 3qj0 3qw5 3qw6 3qw7 3qw8 4ktx 4kuf

(-) Related Entries Specified in the PDB File

4ej5 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEUROTOXIN BONT/A WILD-TYPE
4el4 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEUROTOXIN BONT/A C134S/C165S DOUBLE MUTANT
4elc CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEUROTOXIN BONT/A C134 MUTANT WITH MTSEA MODIFIED CYS-165
4ktx