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(-) Description

Title :  CATALYTIC FRAGMENT OF CHOLIX TOXIN FROM VIBRIO CHOLERAE IN COMPLEX WITH THE 1,8-NAPHTHALIMIDE INHIBITOR
 
Authors :  A. R. Merrill, R. Jorgensen
Date :  06 Oct 08  (Deposition) - 15 Sep 09  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.19
Chains :  Asym./Biol. Unit :  A
Keywords :  Adp-Ribosyl Transferase, Domain Iii (C-Terminal Catalytic Domain), Alpha-Beta Complex, Toxin, Transferase, Transferase, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Turgeon, D. White, R. Jorgensen, D. Visschedyk, R. J. Fieldhouse, D. Mangroo, A. R. Merrill
Yeast As A Tool For Characterizing Mono-Adp-Ribosyltransferase Toxins
Fems Microbiol. Lett. V. 300 97 2009
PubMed-ID: 19793133  |  Reference-DOI: 10.1111/J.1574-6968.2009.01777.X

(-) Compounds

Molecule 1 - CHOLIX TOXIN
    Chains: A
    EC Number: 2.4.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A+
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL CATALYTIC DOMAIN (UNP RESIDUES 459 TO 665)
    Gene: CHXA, TOXA
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: TP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
118N1Ligand/Ion1H-BENZO[DE]ISOQUINOLINE-1,3(2H)-DIONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:138 , HOH A:316 , HIS A:460 , GLY A:461 , TYR A:493 , ALA A:501 , TYR A:504 , GLU A:581BINDING SITE FOR RESIDUE 18N A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ESS)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:563 -Pro A:564

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ESS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ESS)

(-) Exons   (0, 0)

(no "Exon" information available for 3ESS)

(-) 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:199
 aligned with CHXA_VIBCL | Q5EK40 from UniProtKB/Swiss-Prot  Length:666

    Alignment length:208
                                   467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657        
           CHXA_VIBCL   458 RAVITPQGVTNWTYQELEATHQALTREGYVFVGYHGTNHVAAQTIVNRIAPVPRGNNTENEEKWGGLYVATHAEVAHGYARIKEGTGEYGLPTRAERDARGVMLRVYIPRASLERFYRTNTPLENAEEHITQVIGHSLPLRNEAFTGPESAGGEDETVIGWDMAIHAVAIPSTIPGNAYEELAIDEEAVAKEQSISTKPPYKERKDEL 665
               SCOP domains d3essa_ A: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 3essA00 A:426-633 Diphtheria Toxin, domain 1                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee..hhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhhhhh....---------.....eee..hhhhhhh........hhhhh.hhhhhhh..eeeeeeee.hhhh.eee...hhhhhhhhhhhhhh........eeeee......eeeeehhhhhh..eeeeeeee.........hhhhhhhhhhhh.......hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ess A 426 MAVITPQGVTNWTYQELEATHQALTREGYVFVGYHGTNHVAAQTIVNRIAPV---------EKWGGLYVATHAEVAHGYARIKEGTGEYGLPTRAERDARGVMLRVYIPRASLERFYRTNTPLENAEEHITQVIGHSLPLRNEAFTGPESAGGEDETVIGWDMAIHAVAIPSTIPGNAYEELAIDEEAVAKEQSISTKPPYKERKDEL 633
                                   435       445       455       465       475 |       - |     495       505       515       525       535       545       555       565       575       585       595       605       615       625        
                                                                             477       487
   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, 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 3ESS)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CHXA_VIBCL | Q5EK40)
molecular function
    GO:0047286    NAD+-diphthamide ADP-ribosyltransferase activity    Catalysis of the reaction: peptide diphthamide + NAD+ = peptide N-(ADP-D-ribosyl)diphthamide + niacinamide.
    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).

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 Related Entries

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

UniProtKB/Swiss-Prot
        CHXA_VIBCL | Q5EK40: 2q5t 2q6m 3ki0 3ki1 3ki2 3ki3 3ki4 3ki5 3ki6 3ki7 3ny6 3q9o

(-) Related Entries Specified in the PDB File

2q5t FULL-LENGTH CHOLIX TOXIN FROM VIBRIO CHOLERAE
2q6m CATALYTIC FRAGMENT OF CHOLIX TOXIN FROM VIBRIO CHOLERAE IN COMPLEX WITH THE PJ34 INHIBITOR