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(-) Description

Title :  1.6A CRYSTAL STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN-III (PAP-III) WITH METHYLATED LYSINES
 
Authors :  I. V. Kurinov, F. M. Uckun
Date :  29 Apr 02  (Deposition) - 17 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Pokeweed Antiviral Protein, Ribosome Inactivating Protein, Polynucleotide:Adenosine, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. V. Kurinov, F. M. Uckun
High Resolution X-Ray Structure Of Potent Anti-Hiv Pokeweed Antiviral Protein-Iii
Biochem. Pharm. V. 65 1709 2003
PubMed-ID: 12754107  |  Reference-DOI: 10.1016/S0006-2952(03)00144-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIVIRAL PROTEIN 3
    Chains: A
    EC Number: 3.2.2.22
    Organism Common: AMERICAN POKEWEED
    Organism Scientific: PHYTOLACCA AMERICANA
    Organism Taxid: 3527
    Other Details: LATE SUMMER LEAVES
    Synonym: PAP-II, RIBOSOME-INACTIVATING PROTEIN, RRNA N- GLYCOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric/Biological Unit (1, 14)
No.NameCountTypeFull Name
1MLY14Mod. Amino AcidN-DIMETHYL-LYSINE

(-) Sites  (0, 0)

(no "Site" information available for 1LLN)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:32 -A:259
2A:81 -A:98

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:44 -Pro A:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIP2_PHYAM192-208  1A:167-183

(-) Exons   (0, 0)

(no "Exon" information available for 1LLN)

(-) 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:262
 aligned with RIP2_PHYAM | Q40772 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:262
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  
           RIP2_PHYAM    26 NIVFDVENATPETYSNFLTSLREAVKDKKLTCHGMIMATTLTEQPKYVLVDLKFGSGTFTLAIRRGNLYLEGYSDIYNGKCRYRIFKDSESDAQETVCPGDKSKPGTQNNIPYEKSYKGMESKGGARTKLGLGKITLKSRMGKIYGKDATDQKQYQKNEAEFLLIAVQMVTEASRFKYIENKVKAKFDDANGYQPDPKAISLEKNWDSVSKVIAKVGTSGDSTVTLPGDLKDENNKPWTTATMNDLKNDIMALLTHVTCKVK 287
               SCOP domains d1llna_ A: Antiviral protein 3                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1llnA01 A:1-175 Ricin (A subunit), domain 1                                                                                                                                    1llnA02 A:176-262 Ricin (A Subunit), domain 2                                           CATH domains
               Pfam domains --RIP-1llnA01 A:3-216                                                                                                                                                                                                   ---------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhheeeeeee..eeee........eeeeeeee..eeeeeeee.....eeeeeeee..eeeee.......hhhhhhh.................hhhhhhhhhhhhhhh..hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh......eee..............eeehhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lln A   1 NIVFDVENATPETYSNFLTSLREAVkDkKLTCHGMIMATTLTEQPkYVLVDLkFGSGTFTLAIRRGNLYLEGYSDIYNGKCRYRIFkDSESDAQETVCPGDKSKPGTQNNIPYEkSYKGMESKGGARTKLGLGkITLKSRMGkIYGKDATDQKQYQKNEAEFLLIAVQMVTEASRFkYIENkVkAKFDDANGYQPDPkAISLEKNWDSVSkVIAKVGTSGDSTVTLPGDLkDENNKPWTTATMNDLKNDIMALLTHVTCKVK 262
                                    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       260  
                                                    26-MLY              46-MLY 53-MLY                            87-MLY                     115-MLY            134-MLY  143-MLY                           177-MLY| |           198-MLY      211-MLY             231-MLY                           
                                                      28-MLY                                                                                                                                                   182-MLY                                                                            
                                                                                                                                                                                                                 184-MLY
   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   (RIP2_PHYAM | Q40772)
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:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    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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    Gln A:44 - Pro A:45   [ RasMol ]  
 

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  3.2.2.22
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1qcg LOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN, WILD-TYPE ISOFORM (PAP-I)