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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ENZYMATIC COMPONET OF IOTA-TOXIN FROM CLOSTRIDIUM PERFRINGENS WITH NADH
 
Authors :  H. Tsuge, M. Nagahama, H. Nishimura, J. Hisatsune, Y. Sakaguchi, Y. Ito N. Katunuma, J. Sakurai
Date :  12 Mar 01  (Deposition) - 14 Jan 03  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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 Enzymati 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

(-) Compounds

Molecule 1 - IOTA TOXIN COMPONENT IA
    Chains: A, B
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:259 , ARG A:295 , ARG A:296 , GLN A:300 , GLU A:301 , ASN A:335 , SER A:338 , PHE A:349 , ARG A:352 , GLU A:380 , HOH A:4135 , HOH A:4215 , HOH A:4246 , HOH A:4282 , ASP B:1012 , ASN B:1015BINDING SITE FOR RESIDUE NAI A 500
2AC2SOFTWAREASP A:12 , ASN A:15 , ILE B:1259 , ARG B:1295 , ARG B:1296 , GLN B:1300 , GLU B:1301 , ASN B:1335 , SER B:1338 , THR B:1339 , PHE B:1349 , ARG B:1352 , GLU B:1380 , HOH B:4074 , HOH B:4092BINDING SITE FOR RESIDUE NAI B 1500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GIQ)

(-) 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: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 d1giqa1 A:3-209 Enzymatic component (Ia) of iota-toxin                                                                                                                                                         d1giqa2 A:210-413 Enzymatic component (Ia) of iota-toxin                                                                                                                                                     SCOP domains
               CATH domains 1giqA01 A:3-211 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                                  1giqA02 A:212-413 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhhh.............hhhhhhhhhhhh...eeeeeeeeee..............eeeeeee......eeee....eeeeeeeeeeeeeeeeeeeee..eeeeeeeeeee.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.......eeeeeeehhhhhh....hhhhh..hhhhhhhhhhhhh..eeee...eeee.............eeeeeee......ee.hhh.......eeee...eeeeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1giq 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 


Chain B 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 d1giqb1 B:1003-1209 Enzymatic component (Ia) of iota-toxin                                                                                                                                                     d1giqb2 B:1210-1413 Enzymatic component (Ia) of iota-toxin                                                                                                                                                   SCOP domains
               CATH domains 1giqB01 B:1003-1211 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                              1giqB02 B:1212-1413 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhh.............hhhhhhhhhhhh...eeeeeeeeee..............eeeeeee......eeee....eeeeeeeeeeeeeeeeeeeee..eeeeeeeeeee.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.......eeeeeeehhhhhh....hhhhh..hhhhhhhhhhhhh..eeee...eeee.............eeeeeee......ee.hhh.......eeee...eeeeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1giq B 1003 IERPEDFLKDKENAIQWEKKEAERVEKNLDTLEKEALELYKKDSEQISNYSQTRQYFYDYQIESNPREKEYKNLRNAISKNKIDKPINVYYFESPEKFAFNKEIRTENQNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYINSNDVKTLIEQDYSIKIDKIVRIVIEGKQYIKAEASIVNSLDFKDDVSKGDLWGKENYSDWSNKLTPNELADVNDYMRGGYTAINNYLISNGPLNNPNPELDSKVNNIENALKLTPIPSNLIVYRRSGPQEFGLTLTSPEYDFNKIENIDAFKEKWEGKVITYPNFISTSIGSVNMSAFAKRKIILRINIPKDSPGAYLSAIPGYAGEYEVLLNHGSKFKINKVDSYKDGTVTKLILDATLIN 1413
                                  1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402      1412
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 | Q46220: 1gir 3buz 4gy2 4h03 4h0t 4h0v 4h0x 4h0y

(-) Related Entries Specified in the PDB File

1gir 1GIR CONTAINS THE SAME PROTEIN WITH NADPH