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(-) Description

Title :  STX2 WITH ADENINE
 
Authors :  M. E. Fraser
Date :  07 Mar 06  (Deposition) - 11 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Ab5-Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Fraser, M. M. Cherney, P. Marcato, G. L. Mulvey, G. D. Armstrong, M. N. James
Binding Of Adenine To Stx2, The Protein Toxin From Escherichia Coli O157:H7.
Acta Crystallogr. , Sect. F V. 62 627 2006
PubMed-ID: 16820678  |  Reference-DOI: 10.1107/S1744309106021968
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SHIGA-LIKE TOXIN II SUBUNIT A
    Chains: A
    EC Number: 3.2.2.22
    Organism Scientific: ENTEROBACTERIA PHAGE 933W
    Organism Taxid: 10730
    Strain: C600 933W
    Synonym: VEROTOXIN 2 SUBUNIT A, RRNA N-GLYCOSIDASE, SLT- IIA
 
Molecule 2 - SHIGA-LIKE TOXIN II SUBUNIT B
    Chains: B, C, D, E, F
    Organism Scientific: ENTEROBACTERIA PHAGE 933W
    Organism Taxid: 10730
    Strain: C600 933W
    Synonym: VEROTOXIN 2 SUBUNIT B, SLT- IIB

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
11PS4Ligand/Ion3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
2ADE1Ligand/IonADENINE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4FMT5Ligand/IonFORMIC ACID
5NA5Ligand/IonSODIUM ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER F:53 , THR F:55 , SER F:60 , GLY F:61BINDING SITE FOR RESIDUE NA F 711
02AC2SOFTWARESER B:53 , THR B:55 , SER B:60 , GLY B:61BINDING SITE FOR RESIDUE NA B 712
03AC3SOFTWAREARG A:266 , SER A:278 , ASN A:279 , FMT A:709 , HOH A:838 , HOH C:729BINDING SITE FOR RESIDUE NA A 713
04AC4SOFTWARETHR A:22 , SER A:25 , HOH A:767 , HOH A:791 , HOH A:895 , HOH A:961BINDING SITE FOR RESIDUE NA A 714
05AC5SOFTWARESER A:15 , SER A:19 , HOH A:825 , HOH A:832 , HOH A:943BINDING SITE FOR RESIDUE NA A 715
06AC6SOFTWARELEU A:76 , TYR A:77 , VAL A:78 , SER A:112 , TYR A:114 , VAL A:162 , ALA A:166 , ARG A:170 , HOH A:830BINDING SITE FOR RESIDUE ADE A 701
07AC7SOFTWAREASN F:14 , ASP F:16 , THR F:18 , TRP F:29 , HOH F:722 , HOH F:762BINDING SITE FOR RESIDUE 1PS F 702
08AC8SOFTWAREASN B:14 , GLU B:15 , ASP B:16 , THR B:18 , TRP B:29 , HOH B:714 , HOH B:760BINDING SITE FOR RESIDUE 1PS B 703
09AC9SOFTWAREASN C:14 , ASP C:16 , THR C:18 , TRP C:29 , HOH C:742 , HOH C:750 , HOH C:766 , SER D:58BINDING SITE FOR RESIDUE 1PS C 704
10BC1SOFTWARESER C:58 , ASN D:14 , GLU D:15 , ASP D:16 , THR D:18 , TRP D:29 , FMT D:708 , HOH D:728 , HOH D:745 , HOH D:773BINDING SITE FOR RESIDUE 1PS D 705
11BC2SOFTWARESER A:229 , PHE A:291 , TYR B:13 , SER F:31 , ARG F:32 , TRP F:33 , ASN F:34BINDING SITE FOR RESIDUE EDO F 716
12BC3SOFTWAREGLN A:175 , ARG A:176 , ARG A:179 , HOH A:751BINDING SITE FOR RESIDUE FMT A 706
13BC4SOFTWAREARG A:179 , THR A:294 , HOH A:723 , ARG E:32 , TRP E:33 , ASN E:34 , HOH E:721BINDING SITE FOR RESIDUE FMT E 707
14BC5SOFTWARETHR D:20 , GLY D:59 , 1PS D:705 , HOH D:746 , HOH D:748BINDING SITE FOR RESIDUE FMT D 708
15BC6SOFTWAREASN A:207 , GLN A:261 , THR A:263 , ASP A:265 , ARG A:266 , PRO A:267 , NA A:713 , HOH A:760 , HOH C:729BINDING SITE FOR RESIDUE FMT A 709
16BC7SOFTWAREARG C:32 , TRP C:33 , HOH C:730 , HOH C:734 , HOH D:744BINDING SITE FOR RESIDUE FMT C 710

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:241 -A:260
2B:3 -B:56
3C:3 -C:56
4D:3 -D:56
5E:3 -E:56
6F:3 -F:56

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GA4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_STXA_BP933_002 *T26MSTXA_BP933  ---  ---AT4M
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.STXA_BP933184-200  1A:162-178

(-) Exons   (0, 0)

(no "Exon" information available for 2GA4)

(-) 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:283
 aligned with STXA_BP933 | P09385 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:297
                                    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       
           STXA_BP933    23 REFTIDFSTQQSYVSSLNSIRTEISTPLEHISQGTTSVSVINHTPPGSYFAVDIRGLDVYQARFDHLRLIIEQNNLYVAGFVNTATNTFYRFSDFTHISVPGVTTVSMTTDSSYTTLQRVAALERSGMQISRHSLVSSYLALMEFSGNTMTRDASRAVLRFVTVTAEALRFRQIQREFRQALSETAPVYTMTPGDVDLTLNWGRISNVLPEYRGEDGVRVGRISFNNISAILGTVAVILNCHHQGARSVRAVNEESQPECQITGDRPVIKINNTLWESNTAAAFLNRKSQFLYTTGK 319
               SCOP domains d2ga4a_ A: Shiga toxin, A-chain                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2ga4A01 A:1-170 Ricin (A subunit), domain 1                                                                                                                               2ga4A02 A:171-297 Ricin (A Subunit), domain 2                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhheeeeeeeee..eeeeee.......eeeeeee...........eeeeee.....eeeeee....eeee.hhhh.......eeee.....hhhhhhhhhh......eehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhhh....eeee..eee.hhhhhhhhh.ee....--------------...........eeee..eeeehhhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---M----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ga4 A   1 REFTIDFSTQQSYVSSLNSIRTEISTPLEHISQGTTSVSVINHTPPGSYFAVDIRGLDVYQARFDHLRLIIEQNNLYVAGFVNTATNTFYRFSDFTHISVPGVTTVSMTTDSSYTTLQRVAALERSGMQISRHSLVSSYLALMEFSGNTMTRDASRAVLRFVTVTAEALRFRQIQREFRQALSETAPVYTMTPGDVDLTLNWGRISNVLPEYRGEDGVRVGRISFNNISAILGTVAVILNCH--------------QPECQITGDRPVIKINNTLWESNTAAAFLNRKSQFLYTTGK 297
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 |       -      |260       270       280       290       
                                                                                                                                                                                                                                                                           242            257                                        


Chain B from PDB  Type:PROTEIN  Length:70
 aligned with STXB_BP933 | P09386 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:70
                                    29        39        49        59        69        79        89
           STXB_BP933    20 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  89
               SCOP domains d2ga4b_ B: Verotoxin-1/shiga-toxin, B-pentamer                         SCOP domains
               CATH domains 2ga4B00 B:1-70  [code=2.40.50.70, no name defined]                     CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee.......ee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 2ga4 B   1 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  70
                                    10        20        30        40        50        60        70


Chain C from PDB  Type:PROTEIN  Length:70
 aligned with STXB_BP933 | P09386 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:70
                                    29        39        49        59        69        79        89
           STXB_BP933    20 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  89
               SCOP domains d2ga4c_ C: Verotoxin-1/shiga-toxin, B-pentamer                         SCOP domains
               CATH domains 2ga4C00 C:1-70  [code=2.40.50.70, no name defined]                     CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee.......ee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 2ga4 C   1 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  70
                                    10        20        30        40        50        60        70


Chain D from PDB  Type:PROTEIN  Length:70
 aligned with STXB_BP933 | P09386 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:70
                                    29        39        49        59        69        79        89
           STXB_BP933    20 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  89
               SCOP domains d2ga4d_ D: Verotoxin-1/shiga-toxin, B-pentamer                         SCOP domains
               CATH domains 2ga4D00 D:1-70  [code=2.40.50.70, no name defined]                     CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee.......ee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 2ga4 D   1 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  70
                                    10        20        30        40        50        60        70


Chain E from PDB  Type:PROTEIN  Length:70
 aligned with STXB_BP933 | P09386 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:70
                                    29        39        49        59        69        79        89
           STXB_BP933    20 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  89
               SCOP domains d2ga4e_ E: Verotoxin-1/shiga-toxin, B-pentamer                         SCOP domains
               CATH domains 2ga4E00 E:1-70  [code=2.40.50.70, no name defined]                     CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 2ga4 E   1 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  70
                                    10        20        30        40        50        60        70


Chain F from PDB  Type:PROTEIN  Length:70
 aligned with STXB_BP933 | P09386 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:70
                                    29        39        49        59        69        79        89
           STXB_BP933    20 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  89
               SCOP domains d2ga4f_ F: Verotoxin-1/shiga-toxin, B-pentamer                         SCOP domains
               CATH domains 2ga4F00 F:1-70  [code=2.40.50.70, no name defined]                     CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee.......ee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 2ga4 F   1 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  70
                                    10        20        30        40        50        60        70
   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  (3, 7)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GA4)

(-) Gene Ontology  (6, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (STXA_BP933 | P09385)
molecular function
    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:0030598    rRNA N-glycosylase activity    Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
biological process
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
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 B,C,D,E,F   (STXB_BP933 | P09386)
biological process
    GO:0019836    hemolysis by symbiont of host erythrocytes    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in the host organism by a symbiont. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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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  2ga4
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  STXA_BP933 | P09385
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  STXB_BP933 | P09386
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 Related Entries

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

UniProtKB/Swiss-Prot
        STXA_BP933 | P09385: 1r4p
        STXB_BP933 | P09386: 1r4p

(-) Related Entries Specified in the PDB File

1r4p SHIGA TOXIN TYPE 2
1r4q SHIGA TOXIN