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(-) Description

Title :  COMPLEX OF [E160A-E189A] TRICHOSANTHIN AND ADENINE
 
Authors :  P. C. Shaw, K. B. Wong, D. S. B. Chan, R. L. Williams
Date :  07 Jan 03  (Deposition) - 21 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Dna Complex, Ribosome-Inactivating Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. C. Shaw, K. B. Wong, D. S. Chan, R. L. Williams
Structural Basis For The Interaction Of [E160A-E189A]-Trichosanthin With Adenine.
Toxicon V. 41 575 2003
PubMed-ID: 12676436  |  Reference-DOI: 10.1016/S0041-0101(02)00387-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOME-INACTIVATING PROTEIN ALPHA- TRICHOSANTHIN
    Chains: A
    EC Number: 3.2.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET8C
    Expression System Strain: BL21 [DE3, PLYSS]
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRICHOSANTHIN
    Mutation: YES
    Organism Scientific: TRICHOSANTHES KIRILOWII
    Organism Taxid: 3677
    Synonym: TRICHOSANTHIN, RRNA N-GLYCOSIDASE, ALPHA-TCS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:69 , TYR A:70 , ILE A:71 , GLY A:109 , TYR A:111 , ILE A:155 , SER A:159 , ARG A:163 , HOH A:360BINDING SITE FOR RESIDUE ADE A 248

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIPT_TRIKI178-194  1A:155-171

(-) Exons   (0, 0)

(no "Exon" information available for 1NLI)

(-) 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:248
 aligned with RIPT_TRIKI | P09989 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:248
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262        
           RIPT_TRIKI    23 GDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA 270
               SCOP domains d1nlia_ A: alpha-Trichosanthin                                                                                                                                                                                                                           SCOP domains
               CATH domains -1nliA01 A:1-162 Ricin (A subunit), domain 1                                                                                                                       1nliA02 A:163-247 Ricin (A Subunit), domain 2                                         CATH domains
               Pfam domains ---RIP-1nliA01 A:3-202                                                                                                                                                                                     --------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhhh..eeeee..eeee....hhhhheeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhh........eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee..hhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ---------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nli A   0 MDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSAAARYKFIEQQIGKRVDKTFLPSLAIISLANSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA 247
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239
   Legend:   → Mismatch (orange background)
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  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, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RIP] (62)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RIPT_TRIKI | P09989)
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:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    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.
    GO:0050688    regulation of defense response to virus    Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIPT_TRIKI | P09989: 1gis 1giu 1j4g 1mrj 1mrk 1qd2 1tcs 2jdl 2jjr 2vs6

(-) Related Entries Specified in the PDB File

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