Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  C3 EXOENZYME FROM CLOSTRIDIUM BOTULINUM, TETRAGONAL FORM
 
Authors :  H. R. Evans, D. E. Holloway, J. M. Sutton, J. Ayriss, C. C. Shone, K. R. Acharya
Date :  12 Mar 04  (Deposition) - 29 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, C3, Adp-Ribosyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. R. Evans, D. E. Holloway, J. M. Sutton, J. Ayriss, C. C. Shone, K. R. Acharya
C3 Exoenzyme From Clostridium Botulinum: Structure Of A Tetragonal Crystal Form And A Reassessment Of Nad-Induced Flexure
Acta Crystallogr. , Sect. D V. 60 1502 2004
PubMed-ID: 15272191  |  Reference-DOI: 10.1107/S0907444904011680

(-) Compounds

Molecule 1 - MONO-ADP-RIBOSYLTRANSFERASE C3
    Chains: A, B
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector: PBCMALE
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491
    Strain: 468C
    Synonym: C3BOT1, EXOENZYME C3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2V4O1Ligand/IonCYCLO-TETRAMETAVANADATE
3VO43Ligand/IonVANADATE ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2V4O1Ligand/IonCYCLO-TETRAMETAVANADATE
3VO42Ligand/IonVANADATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2V4O-1Ligand/IonCYCLO-TETRAMETAVANADATE
3VO41Ligand/IonVANADATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:81 , PRO A:101 , SER A:102 , HOH A:2153 , HOH A:2154 , HOH A:2155BINDING SITE FOR RESIDUE VO4 A1002
2AC2SOFTWARESER A:69 , LYS A:70 , SER A:71 , GOL A:1004 , GOL A:1005 , SER B:69 , LYS B:70 , SER B:71BINDING SITE FOR RESIDUE VO4 A1003
3AC3SOFTWARELYS B:81 , PRO B:101 , SER B:102 , HOH B:2150 , HOH B:2151 , HOH B:2152BINDING SITE FOR RESIDUE VO4 B1002
4AC4SOFTWAREASN A:145 , ILE A:150 , ASN A:151 , LYS A:152 , THR A:153 , ASN B:145 , ILE B:150 , ASN B:151 , LYS B:152BINDING SITE FOR RESIDUE V4O A1001
5AC5SOFTWARESER A:69 , SER A:71 , VO4 A:1003 , LYS B:70BINDING SITE FOR RESIDUE GOL A1004
6AC6SOFTWARELYS A:70 , VO4 A:1003 , SER B:69 , SER B:71BINDING SITE FOR RESIDUE GOL A1005

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UZI)

(-) 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: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 d1uzia_ A: Exoenzyme c3                                                                                                                                                                                             SCOP domains
               CATH domains 1uziA00 A:41-251 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhh..........hhhhhhhhhhhhh..eeee...eeee...........eeeeeee......ee...........eeee...eeeeeeeeee......eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uzi A  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 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 d1uzib_ B: Exoenzyme c3                                                                                                                                                                                             SCOP domains
               CATH domains 1uziB00 B:41-251 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                                    CATH domains
           Pfam domains (1) --------------ADPrib_exo_Tox-1uziB01 B:55-246                                                                                                                                                                 ----- Pfam domains (1)
           Pfam domains (2) --------------ADPrib_exo_Tox-1uziB02 B:55-246                                                                                                                                                                 ----- Pfam domains (2)
         Sec.struct. author ..........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhh..........hhhhhhhhhhhhh..eeee...eeee...........eeeeeee......ee...........eeee...eeeeeeeeee......eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uzi 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
   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  (1, 2)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    V4O  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    VO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1uzi)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1uzi
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ARC3_CBDP | P15879
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.4.2.30
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ARC3_CBDP | P15879
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ARC3_CBDP | P15879: 1g24 1gze 1gzf 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)
1gzf STRUCTURE OF THE CLOSTRIDIUM BOTULINUM C3 EXOENZYME (WILD-TYPE) IN COMPLEX WITH NAD