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(-) Description

Title :  CRYSTAL STRUCTURE OF DIPHTHERIA TOXIN MUTANT CRM197 IN COMPLEX WITH NICOTINAMIDE
 
Authors :  E. Malito, G. Spraggon
Date :  04 Jan 12  (Deposition) - 28 Mar 12  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Malito, B. Bursulaya, C. Chen, P. L. Surdo, M. Picchianti, E. Balducci, M. Biancucci, A. Brock, F. Berti, M. J. Bottomley, M. Nissum, P. Costantino, R. Rappuoli, G. Spraggon
Structural Basis For Lack Of Toxicity Of The Diphtheria Toxin Mutant Crm197.
Proc. Natl. Acad. Sci. Usa V. 109 5229 2012
PubMed-ID: 22431623  |  Reference-DOI: 10.1073/PNAS.1201964109

(-) Compounds

Molecule 1 - DIPHTHERIA TOXIN
    Chains: A, B
    EC Number: 2.4.2.36
    Mutation: YES
    Organism Scientific: CORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid: 1717
    Synonym: DT, NAD(+)--DIPHTHAMIDE ADP-RIBOSYLTRANSFERASE, DIPHTHERIA TOXIN FRAGMENT A, DIPHTHERIA TOXIN FRAGMENT B, CRM197

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NCA2Ligand/IonNICOTINAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:21 , GLY B:22 , TYR B:54 , TYR B:65 , GLU B:148BINDING SITE FOR RESIDUE NCA B1536
2AC2SOFTWAREHIS A:21 , GLY A:22 , TYR A:65 , GLU A:148BINDING SITE FOR RESIDUE NCA A1536

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:186 -A:201
2A:461 -A:471
3B:186 -B:201
4B:461 -B:471

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AE1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AE1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AE1)

(-) Exons   (0, 0)

(no "Exon" information available for 4AE1)

(-) 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:501
 aligned with DTX_CORBE | P00588 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:535
                                    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       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562     
            DTX_CORBE    33 GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACAGNRVRRSVGSSLSCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS 567
               SCOP domains d4ae1a1 A:1-187 automated matches                                                                                                                                                                      d4ae1a2 A:200-380 automated matches                                                                                                                                                  d4ae1a3 A:381-535 automated matches                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.hhhhheeee..eeeeee......hhhhh...-------------..eeee.hhhhhhh..............eeeeee...eeeeee....hhhhhhhhh......hhhhhhhhhhhhhhhh....eeeeeee.......eeeeehhhhhh..eeeeeee........hhhhhhhhhhhhh------------.....hhhhhhhhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhh.----hhhhhhhhhhhhhhhhhhhhhhhh...........eee..eeeee..hhh.eee....eeeeeeeeeee....ee..eeeee......ee.....eeee..eeeeeeeeee...eeeeee....ee.....eeeeeeeee........--....eeeeeeeee---...eeeeeeee.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ae1 A   1 GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQK-------------KEFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACA------------SCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGE----GFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHS--ISSDSIGVLGYQK---HTKVNSKLSLFFEIKS 535
                                    10        20        30      |  -         -|       60        70        80        90       100       110       120       130       140       150       160       170       180      |  -       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340        |-   |   360       370       380       390       400       410       420       430       440       450       460       470       480       490       500|  |   510     | 520       530     
                                                               37            51                                                                                                                                     187          200                                                                                                                                                  349  354                                                                                                                                                501  |         516 520               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 504                               


Chain B from PDB  Type:PROTEIN  Length:501
 aligned with DTX_CORBE | P00588 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:533
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564   
            DTX_CORBE    35 DDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACAGNRVRRSVGSSLSCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS 567
               SCOP domains d4ae1b1 B:3-187 automated matches                                                                                                                                                                     d4ae1b2 B:201-380 automated matches                                                                                                                                                 d4ae1b3 B:381-535 automated matches                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhheeeeeeeeeeee...hhhhhh.....-------------..eeee.hhhhhhh..............eeeeeeeeeeeeeee....hhhhhhhhh.......hhhhhhhhhhhhhhh....eeeeeee.......eeeeehhhhhh.................hhhhhhhhhhhhh-------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhh...--....hhhhhhhhhhhhhhhhhhhh...........eee..eeeee.hhhh.eee....eeeeeeeeeee....ee..eeeee......ee.....eeee..eeeeeeeee....eeeeee....ee.....eeeeeeeee..............eeeeeeeee----..eeeeeeee.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ae1 B   3 DDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQK-------------KEFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACA-------------CINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELV--GFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQK----TKVNSKLSLFFEIKS 535
                                    12        22        32    |    -        52        62        72        82        92       102       112       122       132       142       152       162       172       182    |    -       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342        |- |     362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512   |   522       532   
                                                             37            51                                                                                                                                     187           201                                                                                                                                                   351  |                                                                                                                                                               516  521              
                                                                                                                                                                                                                                                                                                                                                                                         354
   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, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AE1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AE1)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DTX_CORBE | P00588)
molecular function
    GO:0047286    NAD+-diphthamide ADP-ribosyltransferase activity    Catalysis of the reaction: peptide diphthamide + NAD+ = peptide N-(ADP-D-ribosyl)diphthamide + niacinamide.
    GO:0008320    protein transmembrane transporter activity    Enables the transfer of a protein from one side of a membrane to the other.
    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: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:0071806    protein transmembrane transport    The directed movement of a protein across a membrane by means of some agent such as a transporter or pore.
cellular component
    GO:0030669    clathrin-coated endocytic vesicle membrane    The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030666    endocytic vesicle membrane    The lipid bilayer surrounding an endocytic vesicle.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  2.4.2.36
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 Related Entries

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

UniProtKB/Swiss-Prot
        DTX_CORBE | P00588: 1ddt 1dtp 1f0l 1mdt 1sgk 1tox 1xdt 4ae0

(-) Related Entries Specified in the PDB File

1ddt DIPHTHERIA TOXIN (DIMERIC)
1dtp DIPHTHERIA TOXIN CATALYTIC DOMAIN (RESIDUES 1 - 190) COMPLEXED WITH ADENYLYL(3'->5')URIDINE 3'-MONOPHOSPHATE (APUP)
1f0l 1.55 ANGSTROM CRYSTAL STRUCTURE OF WILD TYPE DIPHTHERIA TOXIN
1mdt MONOMERIC DIPHTHERIA TOXIN
1sgk NUCLEOTIDE-FREE DIPHTHERIA TOXIN
1tox DIPHTHERIA TOXIN DIMER COMPLEXED WITH NAD
1xdt COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR
4ae0 CRYSTAL STRUCTURE OF DIPHTHERIA TOXIN MUTANT CRM197