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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF RECOMBINANT DIANTHIN ANTIVIRAL PROTEIN-POTENT ANTI-HIV AGENT
 
Authors :  I. V. Kurinov, F. Rajamohan, F. M. Uckun
Date :  07 May 02  (Deposition) - 11 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Dianthin Antiviral Protein, Ribosome Inactivating Protein, Anti-Hiv Agent, Hiv-1 Integrase Inhibitor, Polynucleotide:Adenosine Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. V. Kurinov, F. Rajamohan, F. M. Uckun
High Resolution X-Ray Structure And Potent Anti-Hiv Activity Of Recombinant Dianthin Antiviral Protein.
Arzneimittelforschung V. 54 692 2004
PubMed-ID: 15553110
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIANTHIN 30
    Chains: A
    EC Number: 3.2.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: CLOVE PINK
    Organism Scientific: DIANTHUS CARYOPHYLLUS
    Organism Taxid: 3570
    Synonym: ANTIVIRAL PROTEIN DAP-30, RRNA N-GLYCOSYLASE, RRNA N-GLYCOSIDASE, RIBOSOME-INACTIVATING PROTEIN

 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 1LP8)

(-) Sites  (0, 0)

(no "Site" information available for 1LP8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LP8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:192 -Pro A:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LP8)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIP0_DIACA195-211  1A:172-188

(-) Exons   (0, 0)

(no "Exon" information available for 1LP8)

(-) 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:254
 aligned with RIP0_DIACA | P24476 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:254
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273    
           RIP0_DIACA    24 ATAYTLNLANPSASQYSSFLDQIRNNVRDTSLIYGGTDVAVIGAPSTTDKFLRLNFQGPRGTVSLGLRRENLYVVAYLAMDNANVNRAYYFKNQITSAELTALFPEVVVANQKQLEYGEDYQAIEKNAKITTGDQSRKELGLGINLLITMIDGVNKKVRVVKDEARFLLIAIQMTAEAARFRYIQNLVTKNFPNKFDSENKVIQFQVSWSKISTAIFGDCKNGVFNKDYDFGFGKVRQAKDLQMGLLKYLGRPK 277
               SCOP domains d1lp8a_ A: Dianthin 30                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1lp8A01 A:1-181 Ricin (A subunit), domain 1                                                                                                                                          1lp8A02 A:182-254 Ricin (A Subunit), domain 2                             CATH domains
               Pfam domains ----RIP-1lp8A01 A:5-219                                                                                                                                                                                                    ----------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhh...........ee.........eeeeeeee..eeeeeeee.....eeeeeee.....eeeee.....hhhhhhhhh...hhh.eee.....hhhhhhhhhh......hhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhee..eeeeeee....eeee.hhhh..ee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lp8 A   1 ATAYTLNLANPSASQYSSFLDQIRNNVRDTSLIYGGTDVEVIGAPSTTDKFLRLNFQGPRGTVSLGLRRENLYVVAYLAMDNANVNRAYYFKNQITSAELTALFPEVVVANQKQLEYGEDYQAIEKNAKITTGDQSRKELGLGINLLITMIDGVNKKVRVVKDEARFLLIAIQMTAEAARFRYIQNLVTKNFPNKFDSENKVIQFQVSWSKISTAIFGDCKNGVFNKDYDFGFGKVRQAKDLQMGLLKYLGRPK 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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  (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   (RIP0_DIACA | P24476)
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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  Cis Peptide Bonds
    Phe A:192 - Pro A:193   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIP0_DIACA | P24476: 1lpc 1lpd 1rl0

(-) Related Entries Specified in the PDB File

1lpc HIGH RESOLUTION STRUCTURE OF RECOMBINANT DIANTHIN ANTIVIRAL PROTEIN-POTENT ANTI-HIV AGENT (COMPLEX WITH CYCLIC AMP)
1lpd HIGH RESOLUTION STRUCTURE OF RECOMBINANT DIANTHIN ANTIVIRAL PROTEIN-POTENT ANTI-HIV AGENT (COMPLEX WITH ADENINE)