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(-) Description

Title :  CRYSTAL STRUCTURE OF LYCHNIN A TYPE 1 RIBOSOME INACTIVATING PROTEIN (RIP)
 
Authors :  S. Fermani, G. Falini, G. Tosi, A. Ripamonti, L. Polito, A. Bolognesi, F. Stirpe
Date :  23 Feb 06  (Deposition) - 06 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Fermani, G. Falini, G. Tosi, A. Ripamonti, L. Polito, A. Bolognesi, F. Stirpe
Crystal Structure Of Lychnin A Type 1 Ribosome Inactivating Protein (Rip)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOME-INACTIVATING PROTEIN
    Chains: A
    EC Number: 3.2.2.22
    Organism Common: SCARLET LYCHNIS
    Organism Scientific: LYCHNIS CHALCEDONICA
    Organism Taxid: 39855
    Synonym: LYCHNIN
    Tissue: SEEDS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2G5X)

(-) Sites  (0, 0)

(no "Site" information available for 2G5X)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:32 -A:214

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G5X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G5X)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIPLY_SILCH165-181  1A:165-181

(-) Exons   (0, 0)

(no "Exon" information available for 2G5X)

(-) 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:234
 aligned with RIPLY_SILCH | P85101 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:234
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    
          RIPLY_SILCH     1 RPSWTVDSDSAKYSSFLDSLREEFGRGTPKVCNIPVTKKANNDKFVLVNLVLPFNRNTITLAFRASDAYLVGFQDRDSKTNKLRANFFSDEYRALSGKYKSIFTDAEVLAPALPCASTYTDLQNKAGVSREKLSLGVSSLQTAFTAVYGKVFTGKNVAKFALISIQMVAEAARFKYIEDQVINRGMYSSFEAGARITLLENNWSKISEQYHKSCKLGGGQFTEEEMKLGLLLYN 234
               SCOP domains d2g5xa_ A: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee...hhhhhhhhhhhhhhhhhh.............hhhh.eeeeeee......eeeeeee....eeeeeeee......eeeee...hhhhhh.hhhhhh....ee........hhhhhhhhhh........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ----------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2g5x A   1 RPSWTVDSDSAKYSSFLDSLREEFGRGTPKVCNIPVTKKANNDKFVLVNLVLPFNRNTITLAFRASDAYLVGFQDRDSKTNKLRANFFSDEYRALSGKYKSIFTDAEVLAPALPCASTYTDLQNKAGVSREKLSLGVSSLQTAFTAVYGKVFTGKNVAKFALISIQMVAEAARFKYIEDQVINRGMYSSFEAGARITLLENNWSKISEQYHKSCKLGGGQFTEEEMKLGLLLYN 234
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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  (0, 0)

(no "CATH Domain" information available for 2G5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G5X)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RIPLY_SILCH | P85101)
molecular function
    GO:0030597    RNA glycosylase activity    Catalysis of the hydrolysis of N-glycosidic bonds in an RNA molecule.
    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.

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(-) Related Entries Specified in the PDB File

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