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(-) Description

Title :  CRYSTAL STRUCTURE OF THE S211A MUTANT OF THE RIBOSOME INACTIVATING PROTEIN PDL4 FROM P. DIOICA LEAVES
 
Authors :  R. Berisio, A. Ruggiero
Date :  27 Jun 07  (Deposition) - 26 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.29
Chains :  Asym./Biol. Unit :  A
Keywords :  Crystal, Ribosome Inactivating Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ruggiero, A. Chambery, A. Di Maro, A. Parente, R. Berisio
Atomic Resolution (1. 1 A) Structure Of The Ribosome-Inactivating Protein Pd-L4 From Phytolacca Dioica L. Leaves
Proteins V. 71 8 2008
PubMed-ID: 17963235  |  Reference-DOI: 10.1002/PROT.21712
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOME-INACTIVATING PROTEIN PD-L4
    Chains: A
    EC Number: 3.2.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PHYTOLACCA DIOICA
    Organism Taxid: 29725
    Synonym: RRNA N- GLYCOSIDASE PD-L3/PD-L4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:72 , SER A:120 , ILE A:170 , HOH A:515 , HOH A:550 , HOH A:625BINDING SITE FOR RESIDUE EDO A 501
2AC2SOFTWARESER A:77 , ASP A:78 , HOH A:531 , HOH A:555BINDING SITE FOR RESIDUE EDO A 502

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:34 -A:258
2A:84 -A:105

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:46 -Pro A:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z53)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIPL2_PHYDI170-186  1A:170-186

(-) Exons   (0, 0)

(no "Exon" information available for 2Z53)

(-) 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:261
 aligned with RIPL2_PHYDI | P84854 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    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 
          RIPL2_PHYDI     1 VNTITFDVGNATINKYATFMESLRNEAKDPTLKCYGIPMLPDSNLTPKYVLVKLQDASSKTITLMLRRNNLYVMGYSDLYNGKCRYHIFNDISSTESTDVENTLCPNSNSREKKAINYNSQYSTLQNKAGVSSRSQVQLGIQILNSDIGKISGVSTFTDKTEAEFLLVAIQMVSEAARFKYIENQVKTNFNRAFNPNPKVLSLEENWGKISLAIHNAKNGALTSPLELKNADDTKWIVLRVDEIKPDMGLLNYVSGTCQTT 261
               SCOP domains d2z53a_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2z53A01 A:1-177 Ricin (A subunit), domain 1                                                                                                                                      2z53A02 A:178-258 Ricin (A Subunit), domain 2                                    --- CATH domains
               Pfam domains ----RIP-2z53A01 A:5-217                                                                                                                                                                                                  -------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhh....ee..ee..........eeeeeee.....eeeeeee.....eeeeeeee..eeeeee....hhhhhhhhhhhhh.....eee.......hhhhhhhhhh..hhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeehhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z53 A   1 VNTITFDVGNATINKYATFMESLRNEAKDPTLKCYGIPMLPDSNLTPKYVLVKLQDASSKTITLMLRRNNLYVMGYSDLYNGKCRYHIFNDISSTESTDVENTLCPNSNSREKKAINYNSQYSTLQNKAGVSSRSQVQLGIQILNSDIGKISGVSTFTDKTEAEFLLVAIQMVSEAARFKYIENQVKTNFNRAFNPNPKVLSLEENWGKIALAIHNAKNGALTSPLELKNADDTKWIVLRVDEIKPDMGLLNYVSGTCQTT 261
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RIPL2_PHYDI | P84854)
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.

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  2z53
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  3.2.2.22
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIPL2_PHYDI | P84854: 2qes 2qet 2z4u

(-) Related Entries Specified in the PDB File

2qes 2qet 2z4u