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(-) Description

Title :  STRUCTURE OF CDTB, THE BIOLOGICALLY ACTIVE SUBUNIT OF CYTOLETHAL DISTENDING TOXIN
 
Authors :  J. S. Hontz, M. D. Yoder, L. A. Dreyfus
Date :  14 Nov 05  (Deposition) - 04 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytolethal Distending Toxin, Cdt, E. Coli, Toxin, Dnase I, Microbatch (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Hontz, M. T. Villar-Lecumberri, B. M. Potter, M. D. Yoder, L. A. Dreyfus, J. H. Laity
Differences In Crystal And Solution Structures Of The Cytolethal Distending Toxin B Subunit: Relevance To Nuclear Translocation And Functional Activation.
J. Biol. Chem. V. 281 25365 2006
PubMed-ID: 16809347  |  Reference-DOI: 10.1074/JBC.M603727200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOLETHAL DISTENDING TOXIN SUBUNIT B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-45B
    Expression System Strain: BL21 DE3 STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CDTB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CDT B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2F1N)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2F1N)

(-) 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:253
 aligned with CDTB_ECOLX | Q46669 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:253
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266   
           CDTB_ECOLX    17 QADLTDFRVATWNLQGASATTESKWNINVRQLISGENAVDILAVQEAGSPPSTAVDTGTLIPSPGIPVRELIWNLSTNSRPQQVYIYFSAVDALGGRVNLALVSNRRADEVFVLSPVRQGGRPLLGIRIGNDAFFTAHAIAMRNNDAPALVEEVYNFFRDSRDPVHQALNWMILGDFNREPADLEMNLTVPVRRASEIISPAAATQTSQRTLDYAVAGNSVAFRPSPLQAGIVYGARRTQISSDHFPVGVSRR 269
               SCOP domains --d2f1na1 A:1-250 Cytolethal distending toxin subunit B                                                                                                                                                                                                     - SCOP domains
               CATH domains 2f1nA00 A:-1-251  [code=3.60.10.10, no name defined]                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeeeeeee....hhhhhhhhhhhhhh......eeeeeee.......ee............eeeeee........eeeeeee..........eeeee.....eeeee.........eeeeee..eeeeeee.......hhhhhhhhhhhhhhh..hhhhhh.eeeeeee...hhhhhhh..hhhhhhheeee.............eeeeeee........eeeee...............eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f1n A  -1 GTDLTDFRVATWNLQGASATTESKWNINVRQLISGENAVDILAVQEAGSPPSTAVDTGRVIPSPGIPVRELIWNLSTNSRPQQVYIYFSAVDALGGRVNLALVSNRRADEVFVLSPVRQGGRPLLGIRIGNDAFFTAHAIAMRNNDAPALVEEVYNFFRDSRDPVHQALNWMILGDFNREPADLEMNLTVPVRRASEIISPAAATQTSQRTLDYAVAGNSVAFRPSPLQAGIVYGARRTQISSDHFPVGVSRR 251
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248
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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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F1N)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CDTB_ECOLX | Q46669)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    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.
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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