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(-) Description

Title :  CHOLERA HOLOTOXIN WITH AN A-SUBUNIT Y30S MUTATION, CRYSTAL FORM 2
 
Authors :  C. J. O'Neal, E. I. Amaya, M. G. Jobling, R. K. Holmes, W. G. Hol
Date :  20 Jan 04  (Deposition) - 06 Apr 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,D,E,F,G,H
Keywords :  Cholera Toxin, Heat-Labile Enterotoxin, Adp Ribose Transferases, Ab5 Toxins, Transferase, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. O'Neal, E. I. Amaya, M. G. Jobling, R. K. Holmes, W. G. Hol
Crystal Structures Of An Intrinsically Active Cholera Toxin Mutant Yield Insight Into The Toxin Activation Mechanism
Biochemistry V. 43 3772 2004
PubMed-ID: 15049684  |  Reference-DOI: 10.1021/BI0360152

(-) Compounds

Molecule 1 - CHOLERA ENTEROTOXIN, A CHAIN
    Chains: A
    EC Number: 2.4.2.36
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PEIA154
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CTXA, TOXA, VC1457
    Mutation: YES
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Synonym: NAD(+)--DIPHTHAMIDE ADP- RIBOSYLTRANSFERASE, CHOLERA ENTEROTOXIN A SUBUNIT
 
Molecule 2 - CHOLERA TOXIN B PROTEIN (CTB)
    Chains: D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PEIA154
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CTXB, TOXB, VC1456
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ADEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1GAL5Ligand/IonBETA-D-GALACTOSE
2GOL5Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN D:14 , GLU D:51 , GLN D:56 , GLN D:61 , TRP D:88 , ASN D:90 , LYS D:91 , HOH D:779 , HOH E:734BINDING SITE FOR RESIDUE GAL D 704
02AC2SOFTWAREGLU E:51 , GLN E:56 , HIS E:57 , GLN E:61 , TRP E:88 , ASN E:90 , LYS E:91 , HOH E:787 , HOH E:798 , HOH F:798BINDING SITE FOR RESIDUE GAL E 705
03AC3SOFTWAREGLU F:51 , GLN F:56 , GLN F:61 , TRP F:88 , ASN F:90 , LYS F:91 , HOH F:724 , HOH F:753BINDING SITE FOR RESIDUE GAL F 706
04AC4SOFTWAREGLU G:51 , GLN G:56 , HIS G:57 , GLN G:61 , TRP G:88 , ASN G:90 , LYS G:91 , HOH G:721BINDING SITE FOR RESIDUE GAL G 707
05AC5SOFTWAREGLU H:51 , GLN H:56 , GLN H:61 , TRP H:88 , ASN H:90 , LYS H:91 , HOH H:712 , HOH H:716 , HOH H:797BINDING SITE FOR RESIDUE GAL H 708
06AC6SOFTWAREASN A:1 , THR A:90 , TYR A:150 , LEU A:153 , HOH A:289BINDING SITE FOR RESIDUE NA A 241
07AC7SOFTWARELYS A:219 , ASN D:103 , TYR E:76 , LEU E:77 , GLU E:79 , HOH E:723 , HOH E:759BINDING SITE FOR RESIDUE GOL E 706
08AC8SOFTWAREALA D:46 , THR D:47 , PRO D:93 , HIS D:94 , HOH D:746 , HOH H:764BINDING SITE FOR RESIDUE GOL D 705
09AC9SOFTWAREALA F:46 , THR F:47 , PRO F:93 , HIS F:94BINDING SITE FOR RESIDUE GOL F 707
10BC1SOFTWAREHIS G:18 , ALA G:46 , THR G:47 , PRO G:93 , HIS G:94BINDING SITE FOR RESIDUE GOL G 708
11BC2SOFTWAREARG A:146 , ARG A:148 , TYR A:149 , GLN A:221 , HOH A:283 , HOH A:346 , THR F:78 , ALA F:80 , LEU G:77 , GLU G:79BINDING SITE FOR RESIDUE GOL A 242

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:187 -A:199
2E:9 -E:86
3G:9 -G:86
4H:9 -H:86

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Glu A:177 -Pro A:178
2Thr D:92 -Pro D:93
3Thr E:92 -Pro E:93
4Ala E:102 -Asn E:103
5Thr F:92 -Pro F:93
6Thr G:92 -Pro G:93
7Thr H:92 -Pro H:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S5D)

(-) Exons   (0, 0)

(no "Exon" information available for 1S5D)

(-) 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:218
 aligned with CHTA_VIBCH | P01555 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:235
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248     
           CHTA_VIBCH    19 NDDKLYRADSRPPDEIKQSGGLMPRGQSEYFDRGTQMNINLYDHARGTQTGFVRHDDGYVSTSISLRSAHLVGQTILSGHSTYYIYVIATAPNMFNVNDVLGAYSPHPDEQEVSALGGIPYSQIYGWYRVHFGVLDEQLHRNRGYRDRYYSNLDIAPAADGYGLAGFPPEHRAWREEPWIHHAPPGCGNAPRSSMSNTCDEKTQSLGVKFLDEYQSKVKRQIFSGYQSDIDTHNR 253
               SCOP domains d1s5da_ A: Cholera toxin                                                                                                                                                                                                                    SCOP domains
               CATH domains 1s5dA00 A:1-235 Heat-Labile        Enterotoxin,  subunit A                                                                                                                                                                                  CATH domains
               Pfam domains Enterotoxin_a-1s5dA01 A:1-23       5                                                                                                                                                                                                        Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhee.hhhhh-------....hhhhhhhh.-.........eeee..hhhhhhhhhhhhh....eeeeeeee....eeehhhhhhhhh.hhhhh.eeee..ee...eeeeeeee..ee....ee....hhhhhhh....hhhhhhhhh.....hhhhhh.hhhhhh.....---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s5d A   1 NDDKLYRADSRPPDEIKQSGGLMPRGQS-------QMNINLYDHARGT-TGFVRHDDGYVSTSISLRSAHLVGQTILSGHSTYYIYVIATAPNMFNVNDVLGAYSPHPDEQEVSALGGIPYSQIYGWYRVHFGVLDEQLHRNRGYRDRYYSNLDIAPAADGYGLAGFPPEHRAWREEPWIHHAPPGCG---------TCDEKTQSLGVKFLDEYQSKVKRQIFSGYQSDIDTHNR 235
                                    10        20       | -     |  40       |50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -       200       210       220       230     
                                                      28      36          48 |                                                                                                                                       188       198                                     
                                                                            50                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:103
 aligned with CHTB_VIBCH | P01556 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
           CHTB_VIBCH    22 TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1s5dd_ D: Cholera toxin                                                                                SCOP domains
               CATH domains 1s5dD00 D:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh....eeeeeeee...eeeee.......eeee.....eeee.........hhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1s5d D   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100   


Chain E from PDB  Type:PROTEIN  Length:103
 aligned with CHTB_VIBCH | P01556 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
           CHTB_VIBCH    22 TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1s5de_ E: Cholera toxin                                                                                SCOP domains
               CATH domains 1s5dE00 E:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh....eeeeeeee...eeeee.......eeee.....eeee.......hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1s5d E   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100   


Chain F from PDB  Type:PROTEIN  Length:103
 aligned with CHTB_VIBCH | P01556 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
           CHTB_VIBCH    22 TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1s5df_ F: Cholera toxin                                                                                SCOP domains
               CATH domains 1s5dF00 F:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh....eeeeeeee...eeeee.......eeee.....eeee.......hhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1s5d F   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100   


Chain G from PDB  Type:PROTEIN  Length:103
 aligned with CHTB_VIBCH | P01556 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
           CHTB_VIBCH    22 TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1s5dg_ G: Cholera toxin                                                                                SCOP domains
               CATH domains 1s5dG00 G:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh....eeeeeeee...eeeee......eeeee.....eeee.........hhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1s5d G   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100   


Chain H from PDB  Type:PROTEIN  Length:103
 aligned with CHTB_VIBCH | P01556 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
           CHTB_VIBCH    22 TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1s5dh_ H: Cholera toxin                                                                                SCOP domains
               CATH domains 1s5dH00 H:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
           Pfam domains (1) Enterotoxin_b-1s5dH01 H:1-102                                                                         - Pfam domains (1)
           Pfam domains (2) Enterotoxin_b-1s5dH02 H:1-102                                                                         - Pfam domains (2)
           Pfam domains (3) Enterotoxin_b-1s5dH03 H:1-102                                                                         - Pfam domains (3)
           Pfam domains (4) Enterotoxin_b-1s5dH04 H:1-102                                                                         - Pfam domains (4)
           Pfam domains (5) Enterotoxin_b-1s5dH05 H:1-102                                                                         - Pfam domains (5)
         Sec.struct. author ...hhhhhhh....eeeeeeee...eeeee.......eeee.....eeee.......hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1s5d H   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100
   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  (2, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: ADP-ribosyl (56)
(-)
Clan: no clan defined [family: Enterotoxin_b] (23)

(-) Gene Ontology  (14, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CHTA_VIBCH | P01555)
molecular function
    GO:0003950    NAD+ ADP-ribosyltransferase activity    Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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).
biological process
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
    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:0030819    positive regulation of cAMP biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0006471    protein ADP-ribosylation    The transfer, from NAD, of ADP-ribose to protein amino acids.
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.

Chain D,E,F,G,H   (CHTB_VIBCH | P01556)
molecular function
    GO:0046812    host cell surface binding    Interacting selectively and non-covalently with the surface of a host cell.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
    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.
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.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  1s5d
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  CHTA_VIBCH | P01555
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  CHTB_VIBCH | P01556
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 Related Entries

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

UniProtKB/Swiss-Prot
        CHTA_VIBCH | P01555: 1s5b 1s5c 1s5e 1s5f 1xtc 2a5d 2a5f 2a5g
        CHTB_VIBCH | P01556: 1chp 1chq 1ct1 1fgb 1g8z 1jr0 1md2 1rcv 1rd9 1rdp 1rf2 1s5b 1s5c 1s5e 1s5f 1xtc 2chb 3chb 3efx 5elc 5ele 5elf 5lzg 5lzj

(-) Related Entries Specified in the PDB File

1lta HEAT-LABILE ENTEROTOXIN COMPLEXED WITH GALACTOSE
1ltg HEAT-LABILE ENTEROTOXIN WITH AN A-SUBUNIT R7K MUTATION
1lts HEAT-LABILE ENTEROTOXIN
1xtc CHOLERA HOLOTOXIN