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(-) Description

Title :  ADP-RIBOSYLTRANSFERASE C3BOT2 FROM CLOSTRIDIUM BOTULINUM, TRICLINIC FORM
 
Authors :  A. Teplyakov, G. Obmolova, G. L. Gilliland, S. Narumiya
Date :  03 Oct 03  (Deposition) - 16 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
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)
Biol. Unit 5:  A (1x),B (1x)
Keywords :  Adp-Ribosyltransferase, Binary Toxin, C3 Exoenzyme, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Teplyakov, G. Obmolova, G. L. Gilliland, S. Narumiya
Crystal Structure Of Adp-Ribosyltransferase C3Bot2 From Clostridium Botulinum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MONO-ADP-RIBOSYLTRANSFERASE C3
    Chains: A, B, C, D
    EC Number: 2.4.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MATURE PROTEIN
    Organism Scientific: CLOSTRIDIUM PHAGE C-ST
    Organism Taxid: 12336
    Strain: C003-9
    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
Biological Unit 5 (1x): A (1x)B (1x)  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 5 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:91 , ARG A:167 , GOL A:1001 , HOH A:1039 , HOH A:1053 , HOH A:1181 , GLN B:94 , TYR B:170 , HOH B:1069 , HOH B:1142 , HOH B:1153BINDING SITE FOR RESIDUE SO4 A 1003
02AC2SOFTWAREGLN A:94 , TYR A:170 , ARG B:91 , ARG B:167 , GOL B:1002 , HOH B:1038 , HOH B:1050 , HOH B:1051 , HOH B:1142 , HOH B:1153 , HOH B:1154 , HOH B:1250BINDING SITE FOR RESIDUE SO4 B 1004
03AC3SOFTWAREALA A:83 , SER A:84 , ASN A:87 , ARG A:91 , HOH A:1127 , HOH A:1156 , HOH A:1186 , HOH B:1146BINDING SITE FOR RESIDUE SO4 A 1005
04AC4SOFTWAREALA B:83 , SER B:84 , ASN B:87 , ARG B:91 , HOH B:1119 , HOH B:1149 , HOH B:1173 , HOH B:1220BINDING SITE FOR RESIDUE SO4 B 1006
05AC5SOFTWAREALA C:83 , SER C:84 , ASN C:87 , ARG C:91 , HOH C:1086 , HOH C:1113 , HOH C:1176BINDING SITE FOR RESIDUE SO4 C 1007
06AC6SOFTWAREALA D:83 , SER D:84 , ASN D:87 , ARG D:91 , HOH D:1095 , HOH D:1118BINDING SITE FOR RESIDUE SO4 D 1008
07AC7SOFTWARELYS A:64 , GLN A:228 , HOH A:1061 , HOH A:1229BINDING SITE FOR RESIDUE SO4 A 1009
08AC8SOFTWARESER B:116 , LYS B:119 , LYS B:198 , HOH B:1249BINDING SITE FOR RESIDUE SO4 B 1010
09AC9SOFTWAREARG A:128 , ASP A:130 , TYR A:134 , GLU A:169 , SO4 A:1003 , HOH A:1013 , HOH A:1127 , GLN B:94 , HOH B:1146 , HOH B:1171BINDING SITE FOR RESIDUE GOL A 1001
10BC1SOFTWAREGLN A:94 , ASP B:130 , TYR B:134 , GLU B:169 , SO4 B:1004 , HOH B:1024 , HOH B:1114 , HOH B:1119 , HOH B:1149BINDING SITE FOR RESIDUE GOL B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R45)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R45)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R45)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R45)

(-) Exons   (0, 0)

(no "Exon" information available for 1R45)

(-) 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:201
 aligned with ARC3_CBCP | Q00901 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:201
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 
            ARC3_CBCP    44 DTFTEFTNVEEAKKWGNAQYKKYGLSKPEQEAIKFYTRDASKINGPLRANQGNENGLPADILQKVKLIDQSFSKMKMPQNIILFRGDDPAYLGPEFQDKILNKDGTINKTVFEQVKAKFLKKDRTEYGYISTSLMSAQFGGRPIVTKFKVTNGSKGGYIDPISYFPGQLEVLLPRNNSYYISDMQISPNNRQIMITAMIFK 244
               SCOP domains d1r45a_ A: Exoenzyme c3                                                                                                                                                                                   SCOP domains
               CATH domains 1r45A00 A:44-244 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhh.........hhhhhhhhhhhhh..ee.....eeee..hhhhh...eeeeeee......ee.hhhh......eeee.....eeeeeeee......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r45 A  44 DTFTEFTNVEEAKKWGNAQYKKYGLSKPEQEAIKFYTRDASKINGPLRANQGNENGLPADILQKVKLIDQSFSKMKMPQNIILFRGDDPAYLGPEFQDKILNKDGTINKTVFEQVKAKFLKKDRTEYGYISTSLMSAQFGGRPIVTKFKVTNGSKGGYIDPISYFPGQLEVLLPRNNSYYISDMQISPNNRQIMITAMIFK 244
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 


Chain B from PDB  Type:PROTEIN  Length:201
 aligned with ARC3_CBCP | Q00901 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:201
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 
            ARC3_CBCP    44 DTFTEFTNVEEAKKWGNAQYKKYGLSKPEQEAIKFYTRDASKINGPLRANQGNENGLPADILQKVKLIDQSFSKMKMPQNIILFRGDDPAYLGPEFQDKILNKDGTINKTVFEQVKAKFLKKDRTEYGYISTSLMSAQFGGRPIVTKFKVTNGSKGGYIDPISYFPGQLEVLLPRNNSYYISDMQISPNNRQIMITAMIFK 244
               SCOP domains d1r45b_ B: Exoenzyme c3                                                                                                                                                                                   SCOP domains
               CATH domains 1r45B00 B:44-244 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhh.........hhhhhhhhhhhhh..ee.....eeee..hhhhh...eeeeeee......ee.hhhh......eeee.....eeeeeeee......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r45 B  44 DTFTEFTNVEEAKKWGNAQYKKYGLSKPEQEAIKFYTRDASKINGPLRANQGNENGLPADILQKVKLIDQSFSKMKMPQNIILFRGDDPAYLGPEFQDKILNKDGTINKTVFEQVKAKFLKKDRTEYGYISTSLMSAQFGGRPIVTKFKVTNGSKGGYIDPISYFPGQLEVLLPRNNSYYISDMQISPNNRQIMITAMIFK 244
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 


Chain C from PDB  Type:PROTEIN  Length:200
 aligned with ARC3_CBCP | Q00901 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:200
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244
            ARC3_CBCP    45 TFTEFTNVEEAKKWGNAQYKKYGLSKPEQEAIKFYTRDASKINGPLRANQGNENGLPADILQKVKLIDQSFSKMKMPQNIILFRGDDPAYLGPEFQDKILNKDGTINKTVFEQVKAKFLKKDRTEYGYISTSLMSAQFGGRPIVTKFKVTNGSKGGYIDPISYFPGQLEVLLPRNNSYYISDMQISPNNRQIMITAMIFK 244
               SCOP domains d1r45c_ C: Exoenzyme c3                                                                                                                                                                                  SCOP domains
               CATH domains 1r45C00 C:45-244 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhhh..............hhhhhhhhhhhhh..eeee...eeee..hhhhh...eeeeeee......ee.hhhh......eeee...eeeeeeeeee......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r45 C  45 TFTEFTNVEEAKKWGNAQYKKYGLSKPEQEAIKFYTRDASKINGPLRANQGNENGLPADILQKVKLIDQSFSKMKMPQNIILFRGDDPAYLGPEFQDKILNKDGTINKTVFEQVKAKFLKKDRTEYGYISTSLMSAQFGGRPIVTKFKVTNGSKGGYIDPISYFPGQLEVLLPRNNSYYISDMQISPNNRQIMITAMIFK 244
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244


Chain D from PDB  Type:PROTEIN  Length:200
 aligned with ARC3_CBCP | Q00901 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:200
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244
            ARC3_CBCP    45 TFTEFTNVEEAKKWGNAQYKKYGLSKPEQEAIKFYTRDASKINGPLRANQGNENGLPADILQKVKLIDQSFSKMKMPQNIILFRGDDPAYLGPEFQDKILNKDGTINKTVFEQVKAKFLKKDRTEYGYISTSLMSAQFGGRPIVTKFKVTNGSKGGYIDPISYFPGQLEVLLPRNNSYYISDMQISPNNRQIMITAMIFK 244
               SCOP domains d1r45d_ D: Exoenzyme c3                                                                                                                                                                                  SCOP domains
               CATH domains 1r45D00 D:45-244 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                         CATH domains
           Pfam domains (1) ----------ADPrib_exo_Tox-1r45D01 D:55-244                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) ----------ADPrib_exo_Tox-1r45D02 D:55-244                                                                                                                                                                Pfam domains (2)
           Pfam domains (3) ----------ADPrib_exo_Tox-1r45D03 D:55-244                                                                                                                                                                Pfam domains (3)
           Pfam domains (4) ----------ADPrib_exo_Tox-1r45D04 D:55-244                                                                                                                                                                Pfam domains (4)
         Sec.struct. author ......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhh.........hhhhhhhhhhhhh..eeee...eeee..hhhhh...eeeeeee......ee.hhhh......eeee...eeeeeeeeee......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r45 D  45 TFTEFTNVEEAKKWGNAQYKKYGLSKPEQEAIKFYTRDASKINGPLRANQGNENGLPADILQKVKLIDQSFSKMKMPQNIILFRGDDPAYLGPEFQDKILNKDGTINKTVFEQVKAKFLKKDRTEYGYISTSLMSAQFGGRPIVTKFKVTNGSKGGYIDPISYFPGQLEVLLPRNNSYYISDMQISPNNRQIMITAMIFK 244
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: ADP-ribosyl (56)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (ARC3_CBCP | Q00901)
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.
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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  1r45
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 Related Entries

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

UniProtKB/Swiss-Prot
        ARC3_CBCP | Q00901: 1r4b

(-) Related Entries Specified in the PDB File

1g24 ADP-RIBOSYLTRANSFERASE C3BOT1
1gze ADP-RIBOSYLTRANSFERASE C3BOT1
1gzf ADP-RIBOSYLTRANSFERASE C3BOT1 WITH NAD