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(-) Description

Title :  STRUCTURE OF THE CLOSTRIDIUM BOTULINUM C3 EXOENZYME (WILD-TYPE) IN COMPLEX WITH NAD
 
Authors :  J. Menetrey, G. Flatau, E. A. Stura, J. B. Charbonnier, F. Gas, J. M. Teulon, M. H. Le Du, P. Boquet, A. Menez
Date :  21 May 02  (Deposition) - 29 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Transferase, Adp-Ribosyltransferase, Bacterial Toxin, C3 Exoenzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Menetrey, G. Flatau, E. A. Stura, J. B. Charbonnier, F. Gas, J. M. Teulon, M. H. Le Du, P. Boquet, A. Menez
Nad Binding Induces Conformational Changes In Rho Adp-Ribosylating Clostridium Botulinum C3 Exoenzyme
J. Biol. Chem. V. 277 30950 2002
PubMed-ID: 12029083  |  Reference-DOI: 10.1074/JBC.M201844200

(-) Compounds

Molecule 1 - MONO-ADP-RIBOSYLTRANSFERASE C3
    Chains: A, B, C, D
    EC Number: 2.4.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN, RESIDUES 41-251
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491
    Synonym: EXOENZYME C3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3NIR1Ligand/Ion3-(AMINOCARBONYL)-1-[(3R,4S,5R)-3,4-DIHYDROXY-5-METHYLTETRAHYDRO-2-FURANYL]PYRIDINIUM
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ADP-1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3NIR-1Ligand/Ion3-(AMINOCARBONYL)-1-[(3R,4S,5R)-3,4-DIHYDROXY-5-METHYLTETRAHYDRO-2-FURANYL]PYRIDINIUM
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADP-1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3NIR-1Ligand/Ion3-(AMINOCARBONYL)-1-[(3R,4S,5R)-3,4-DIHYDROXY-5-METHYLTETRAHYDRO-2-FURANYL]PYRIDINIUM
4SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2NAD-1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3NIR1Ligand/Ion3-(AMINOCARBONYL)-1-[(3R,4S,5R)-3,4-DIHYDROXY-5-METHYLTETRAHYDRO-2-FURANYL]PYRIDINIUM
4SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2NAD-1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3NIR-1Ligand/Ion3-(AMINOCARBONYL)-1-[(3R,4S,5R)-3,4-DIHYDROXY-5-METHYLTETRAHYDRO-2-FURANYL]PYRIDINIUM
4SO4-1Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:56 , ASP A:204 , ALA A:210 , GLY A:211 , HOH A:2133 , HOH A:2166 , HOH A:2167 , HOH A:2168 , LYS C:251BINDING SITE FOR RESIDUE SO4 A1249
2AC2SOFTWAREALA B:41 , SER B:43 , GLU B:48 , THR B:50 , LYS B:191 , HOH B:2005BINDING SITE FOR RESIDUE SO4 B1253
3AC3SOFTWARETHR A:80 , ASN A:87 , ARG A:91 , ARG A:128 , GLY A:129 , ASP A:130 , ASP A:131 , ALA A:133 , ARG A:167 , GLU A:169 , THR A:175 , SER A:176 , PHE A:183 , ARG A:186 , GLN A:212 , GLU A:214 , HOH A:2160 , HOH A:2161 , HOH A:2164 , HOH A:2165BINDING SITE FOR RESIDUE NAD A1248
4AC4SOFTWAREASN B:87 , ARG B:91 , ARG B:128 , GLY B:129 , ASP B:130 , ASP B:131 , ALA B:133 , ARG B:167 , GLU B:169 , SER B:174 , PHE B:183 , ARG B:186 , PHE B:209 , GLY B:211 , HOH B:2098 , HOH B:2124 , HOH B:2125BINDING SITE FOR RESIDUE NAD B1252
5AC5SOFTWAREALA C:83 , ARG C:128 , GLY C:129 , SER C:174 , THR C:175 , SER C:176 , PHE C:183 , GLY C:211 , GLU C:214 , ADP C:1253 , HOH C:2033 , HOH C:2087 , HOH C:2113BINDING SITE FOR RESIDUE NIR C1252
6AC6SOFTWARESER C:84 , ASN C:87 , ARG C:91 , ARG C:128 , ASP C:130 , ASP C:131 , ALA C:133 , ARG C:167 , GLU C:169 , ARG C:186 , NIR C:1252 , HOH C:2138 , HOH C:2139BINDING SITE FOR RESIDUE ADP C1253
7AC7SOFTWAREARG D:128 , ASP D:130 , ASP D:131 , ALA D:133 , ARG D:167 , GLU D:169 , ARG D:186BINDING SITE FOR RESIDUE ADP D1247

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GZF)

(-) Exons   (0, 0)

(no "Exon" information available for 1GZF)

(-) 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:203
 aligned with ARC3_CBDP | P15879 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:203
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244   
            ARC3_CBDP    45 TYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSQFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGTA 247
               SCOP domains d1gzfa_ A: Exoenzyme c3                                                                                                                                                                                     SCOP domains
               CATH domains 1gzfA00 A:45-247 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhh..........hhhhhhhhhhhhh..eeee...eeee...hhhhhh..eeeeeee......ee.hhhh......eeee...eeeeeeeeee......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gzf A  45 TYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSQFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGTA 247
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244   


Chain B from PDB  Type:PROTEIN  Length:211
 aligned with ARC3_CBDP | P15879 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:211
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 
            ARC3_CBDP    41 AYSNTYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSQFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGTAINPK 251
               SCOP domains d1gzfb_ B: Exoenzyme c3                                                                                                                                                                                             SCOP domains
               CATH domains 1gzfB00 B:41-251 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhh.........hhhhhhhhhhhhh..eeee...eeee...hhhhhh..eeeeeee......ee...........eeee...eeeeeeeeee......eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gzf B  41 AYSNTYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSQFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGTAINPK 251
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 


Chain C from PDB  Type:PROTEIN  Length:208
 aligned with ARC3_CBDP | P15879 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:208
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243        
            ARC3_CBDP    44 NTYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSQFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGTAINPK 251
               SCOP domains d1gzfc_ C: Exoenzyme c3                                                                                                                                                                                          SCOP domains
               CATH domains 1gzfC00 C:44-251 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh........eeeeeeehhhhhh..............hhhhhhhhhhhhh..eeee...eeee...hhhhhh..eeeeeee......ee...........eeee...eeeeeeeeee......eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gzf C  44 NTYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSQFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGTAINPK 251
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243        


Chain D from PDB  Type:PROTEIN  Length:203
 aligned with ARC3_CBDP | P15879 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:203
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            ARC3_CBDP    44 NTYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSQFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGT 246
               SCOP domains d1gzfd_ D: Exoenzyme c3                                                                                                                                                                                     SCOP domains
               CATH domains 1gzfD00 D:44-246 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhh.........hhhhhhhhhhhhh..eeee...eeee...hhhhhh..eeeeeee......ee...........eeee...eeeeeeeeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gzf D  44 NTYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSQFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGT 246
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GZF)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (ARC3_CBDP | P15879)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
    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:0006471    protein ADP-ribosylation    The transfer, from NAD, of ADP-ribose to protein amino acids.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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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  1gzf
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  ARC3_CBDP | P15879
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 Related Entries

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

UniProtKB/Swiss-Prot
        ARC3_CBDP | P15879: 1g24 1gze 1uzi 2a78 2a9k 2bov 2c89 2c8a 2c8b 2c8c 2c8d 2c8e 2c8f 2c8g 2c8h

(-) Related Entries Specified in the PDB File

1g24 THE CRYSTAL STRUCTURE OF EXOENZYME C3 FROM CLOSTRIDIUMBOTULINUM
1gze STRUCTURE OF THE CLOSTRIDIUM BOTULINUM C3 EXOENZYME (L177C MUTANT)