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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ENZYMATIC COMPONET OF IOTA-TOXIN FROM CLOSTRIDIUM PERFRINGENS WITH NADPH
 
Authors :  H. Tsuge, M. Nagahama, H. Nishimura, J. Hisatsune, Y. Sakaguchi, Y. Itogawa, N. Katunuma, J. Sakurai
Date :  12 Mar 01  (Deposition) - 14 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Enzymatic Component, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Tsuge, M. Nagahama, H. Nishimura, J. Hisatsune, Y. Sakaguchi, Y. Itogawa, N. Katunuma, J. Sakurai
Crystal Structure And Site-Directed Mutagenesis Of Enzymatic Components From Clostridium Perfringens Iota-Toxin
J. Mol. Biol. V. 325 471 2003
PubMed-ID: 12498797  |  Reference-DOI: 10.1016/S0022-2836(02)01247-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IOTA TOXIN COMPONENT IA
    ChainsA
    Organism ScientificCLOSTRIDIUM PERFRINGENS
    Organism Taxid1502

 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
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:11 , ARG A:295 , ARG A:296 , GLY A:298 , PRO A:299 , GLN A:300 , GLU A:301 , TYR A:333 , ASN A:335 , THR A:339 , PHE A:349 , ARG A:352 , GLU A:378 , GLU A:380 , HOH A:515 , HOH A:523 , HOH A:605BINDING SITE FOR RESIDUE NDP A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GIR)

(-) 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:411
 aligned with Q46220_CLOPF | Q46220 from UniProtKB/TrEMBL  Length:454

    Alignment length:411
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453 
         Q46220_CLOPF    44 IERPEDFLKDKENAIQWEKKEAERVEKNLDTLEKEALELYKKDSEQISNYSQTRQYFYDYQIESNPREKEYKNLRNAISKNKIDKPINVYYFESPEKFAFNKEIRTENQNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYINSNDVKTLIEQDYSIKIDKIVRIVIEGKQYIKAEASIVNSLDFKDDVSKGDLWGKENYSDWSNKLTPNELADVNDYMRGGYTAINNYLISNGPLNNPNPELDSKVNNIENALKLTPIPSNLIVYRRSGPQEFGLTLTSPEYDFNKIENIDAFKEKWEGKVITYPNFISTSIGSVNMSAFAKRKIILRINIPKDSPGAYLSAIPGYAGEYEVLLNHGSKFKINKVDSYKDGTVTKLILDATLIN 454
               SCOP domains d1gira1 A:3-209 Enzymatic component (Ia) of iota-toxin                                                                                                                                                         d1gira2 A:210-413 Enzymatic component (Ia) of iota-toxin                                                                                                                                                     SCOP domains
               CATH domains 1girA01 A:3-211 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                                  1girA02 A:212-413 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhh.............hhhhhhhhhhhh...eeeeeeeeee..............eeeeeee......eeee....eeeeeeeeeeeeeeeeeeeee..eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh........eeeeeeehhhhhh....hhhhh..hhhhhhhhhhhhh..eee....eeee.............eeeeeee......ee.hhh.......eeee....eeeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gir A   3 IERPEDFLKDKENAIQWEKKEAERVEKNLDTLEKEALELYKKDSEQISNYSQTRQYFYDYQIESNPREKEYKNLRNAISKNKIDKPINVYYFESPEKFAFNKEIRTENQNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYINSNDVKTLIEQDYSIKIDKIVRIVIEGKQYIKAEASIVNSLDFKDDVSKGDLWGKENYSDWSNKLTPNELADVNDYMRGGYTAINNYLISNGPLNNPNPELDSKVNNIENALKLTPIPSNLIVYRRSGPQEFGLTLTSPEYDFNKIENIDAFKEKWEGKVITYPNFISTSIGSVNMSAFAKRKIILRINIPKDSPGAYLSAIPGYAGEYEVLLNHGSKFKINKVDSYKDGTVTKLILDATLIN 413
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412 

   Legend:   → Mismatch (orange background)
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  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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q46220_CLOPF | Q46220)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
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.
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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 Related Entries

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

UniProtKB/TrEMBL
        Q46220_CLOPF | Q462201giq 3buz 4gy2 4h03 4h0t 4h0v 4h0x 4h0y

(-) Related Entries Specified in the PDB File

1giq 1GIQ CONTAINS THE SAME PROTEIN WITH NADH