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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HAEMOPHILUS DUCREYI CYTOLETHAL DISTENDING TOXIN
 
Authors :  D. Nesic, Y. Hsu, C. E. Stebbins
Date :  22 Mar 04  (Deposition) - 15 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Toxin, Bacterial, Haemophilus Ducreyi, Virulence, Dna Damage, Genotoxin, Cytotoxins, Cell Cycle, Apoptosis, Lectin, Deoxyribonuclease I (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Nesic, Y. Hsu, C. E. Stebbins
Assembly And Function Of A Bacterial Genotoxin
Nature V. 429 429 2004
PubMed-ID: 15164065  |  Reference-DOI: 10.1038/NATURE02532
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOLETHAL DISTENDING TOXIN SUBUNIT A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Gene: CDTA, HD0902
    Organism Scientific: HAEMOPHILUS DUCREYI
    Organism Taxid: 730
    Synonym: CDT A
 
Molecule 2 - CYTOLETHAL DISTENDING TOXIN PROTEIN B
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PAC28
    Expression System Vector Type: PLASMID
    Organism Scientific: HAEMOPHILUS DUCREYI
    Organism Taxid: 730
    Synonym: CDT B
 
Molecule 3 - CYTOLETHAL DISTENDING TOXIN PROTEIN C
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET21A
    Expression System Vector Type: PLASMID
    Organism Scientific: HAEMOPHILUS DUCREYI
    Organism Taxid: 730
    Synonym: CDT C

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 26)

Asymmetric/Biological Unit (1, 26)
No.NameCountTypeFull Name
1BR26Ligand/IonBROMIDE ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:135 , SER B:136 , SER B:143 , ARG B:144 , PRO B:145BINDING SITE FOR RESIDUE BR B 501
02AC2SOFTWARESER B:139 , VAL B:140BINDING SITE FOR RESIDUE BR B 502
03AC3SOFTWAREASN A:112 , HOH A:613BINDING SITE FOR RESIDUE BR A 503
04AC4SOFTWAREGLN B:127BINDING SITE FOR RESIDUE BR B 504
05AC5SOFTWARETRP A:100 , HOH A:541 , HOH A:585BINDING SITE FOR RESIDUE BR A 505
06AC6SOFTWARELYS C:89 , GLY C:92 , ALA C:93BINDING SITE FOR RESIDUE BR C 506
07AC7SOFTWAREPRO A:74 , GLN A:132 , HOH A:620BINDING SITE FOR RESIDUE BR A 507
08AC8SOFTWARESER A:72 , ASN A:76 , GLU B:56BINDING SITE FOR RESIDUE BR A 508
09AC9SOFTWARELEU A:93 , HOH A:611BINDING SITE FOR RESIDUE BR A 510
10BC1SOFTWARELYS A:95BINDING SITE FOR RESIDUE BR A 511
11BC2SOFTWARETHR B:92 , MET B:103BINDING SITE FOR RESIDUE BR B 512
12BC3SOFTWAREBR B:522BINDING SITE FOR RESIDUE BR B 513
13BC4SOFTWARESER A:63 , HOH A:662 , HOH C:639BINDING SITE FOR RESIDUE BR C 514
14BC5SOFTWARETYR A:141BINDING SITE FOR RESIDUE BR A 515
15BC6SOFTWAREALA C:94BINDING SITE FOR RESIDUE BR C 516
16BC7SOFTWAREARG A:67 , LEU A:70BINDING SITE FOR RESIDUE BR A 517
17BC8SOFTWAREASN A:58BINDING SITE FOR RESIDUE BR A 518
18BC9SOFTWAREARG B:250BINDING SITE FOR RESIDUE BR B 519
19CC1SOFTWAREPHE A:189 , HOH A:557 , SER B:99BINDING SITE FOR RESIDUE BR B 520
20CC2SOFTWAREPRO B:204 , ALA B:205 , HOH B:621BINDING SITE FOR RESIDUE BR B 521
21CC3SOFTWAREVAL B:280 , ARG B:281 , BR B:513BINDING SITE FOR RESIDUE BR B 522
22CC4SOFTWAREHIS B:160 , ASN B:201BINDING SITE FOR RESIDUE BR B 523
23CC5SOFTWAREGLY C:150BINDING SITE FOR RESIDUE BR C 524
24CC6SOFTWAREARG A:124BINDING SITE FOR RESIDUE BR A 525
25CC7SOFTWAREASP A:199 , LYS C:174 , ILE C:175BINDING SITE FOR RESIDUE BR C 526

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:137 -A:150
2A:179 -A:198
3C:96 -C:107
4C:135 -C:149

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SR4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SR4)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.CDTA_HAEDU123-212  1A:123-212

(-) Exons   (0, 0)

(no "Exon" information available for 1SR4)

(-) 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:167
 aligned with CDTA_HAEDU | O06522 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:167
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       
           CDTA_HAEDU    57 LNLLSSSGPNRQVLPSEPSNFMTLMGQNGALLTVWALAKRNWLWAYPNIYSQDFGNIRNWKMEPGKHREYFRFVNQSLGTCVEAYGNGLIHDICSLDKLAQEFELLPTDSGAVVIKSVSQGRCVTYNPVSTTFYSTVTLSVCDGATEPSRDQTWYLAPPVLEATAVN 223
               SCOP domains d1sr4a_ A: Cytolethal distending toxin subunit A                                                                                                                        SCOP domains
               CATH domains 1sr4A00 A:57-223  [code=2.80.10.50, no name defined]                                                                                                                    CATH domains
               Pfam domains --------------------CDtoxinA-1sr4A01 A:77-221                                                                                                                        -- Pfam domains
         Sec.struct. author ...ee..ee......hhhhhh.eeee...eeeee........eeeee.hhhhhhhhhh.eeeee......eeeee.....eeeee..eeeee.....hhhh.eeeee.....eeeee.....eeee..........eeee.....ee..ee..eeee.....ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------RICIN_B_LECTIN  PDB: A:123-212 UniProt: 123-212                                           ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sr4 A  57 LNLLSSSGPNRQVLPSEPSNFMTLMGQNGALLTVWALAKRNWLWAYPNIYSQDFGNIRNWKMEPGKHREYFRFVNQSLGTCVEAYGNGLIHDICSLDKLAQEFELLPTDSGAVVIKSVSQGRCVTYNPVSTTFYSTVTLSVCDGATEPSRDQTWYLAPPVLEATAVN 223
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with O06523_HAEDC | O06523 from UniProtKB/TrEMBL  Length:283

    Alignment length:261
                                    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 
         O06523_HAEDC    23 NLSDFKVATWNLQGSSAVNESKWNINVRQLLSGEQGADILMVQEAGSLPSSAVRTSRVIQHGGTPIEEYTWNLGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAFIVHSDSSVLQSRPAVGIRIGTDVFFTVHALATGGSDAVSLIRNIFTTFNSSSSPPERRVYSWMVVGDFNRAPANLEVALRQEPAVSENTIIIAPTEPTHRSGNILDYAILHDAHLPRREQARERIGASLMLNQLRSQITSDHFPVSFVRDR 283
               SCOP domains d1sr4b_ B: Cytolethal distending toxin subunit B                                                                                                                                                                                                                      SCOP domains
               CATH domains 1sr4B00 B:23-283  [code=3.60.10.10, no name defined]                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeee.......hhhhhhhhhhhhhh......eeeee.........ee............eeeeee........eeeeeee..........eeeee.....eeeee...........eeeeee..eeeeeee.......hhhhhhhhhhhhhhh---hhhhhhheeeeeee...hhhhhhhhhh.hhhhhhh.eee.............eeeeee.......hhhhh.eeeee.hhhh..........eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sr4 B  23 NLSDFKVATWNLQGSSAVNESKWNINVRQLLSGEQGADILMVQEAGSLPSSAVRTSRVIQHGGTPIEEYTWNLGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAFIVHSDSSVLQSRPAVGIRIGTDVFFTVHALATGGSDAVSLIRNIFTTFNS---PPERRVYSWMVVGDFNRAPANLEVALRQEPAVSENTIIIAPTEPTHRSGNILDYAILHDAHLPRREQARERIGASLMLNQLRSQITSDHFPVSFVRDR 283
                                    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 
                                                                                                                                                                                         182 186                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:154
 aligned with O06524_HAEDC | O06524 from UniProtKB/TrEMBL  Length:186

    Alignment length:154
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174    
         O06524_HAEDC    25 DPTTYPDVELSPPPRISLRSLLTAQPVKNDHYDSHNYLSTHWELIDYKGKEYEKLRDGGTLVQFKVVGAAKCFAFLGKGTTDCKDTDHTVFNLIPTNTGAFLIKDALLGFCITSHDFDDLKLEPCGGSVSGRTFSLAYQWGILPPFGPSKILIP 178
               SCOP domains d1sr4c_ C: Cytolethal distending toxin subunit C                                                                                                           SCOP domains
               CATH domains 1sr4C00 C:25-178  [code=2.80.10.50, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee...............hhhhhheeeee.............eeeeee.....eee......eee..hhhhhheeeee.....eeeee.....eee.......eee.........eehhhh.eeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sr4 C  25 DPTTYPDVELSPPPRISLRSLLTAQPVKNDHYDSHNYLSTHWELIDYKGKEYEKLRDGGTLVQFKVVGAAKCFAFLGKGTTDCKDTDHTVFNLIPTNTGAFLIKDALLGFCITSHDFDDLKLEPCGGSVSGRTFSLAYQWGILPPFGPSKILIP 178
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
   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  (3, 3)

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

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Trefoil (131)

(-) Gene Ontology  (4, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CDTA_HAEDU | O06522)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
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:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B   (O06523_HAEDC | O06523)
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.

Chain C   (O06524_HAEDC | O06524)
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.

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  Cis Peptide Bonds
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  1sr4
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  CDTA_HAEDU | O06522
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 Related Entries

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