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(-) Description

Title :  BRYODIN TYPE I RIP
 
Authors :  H. E. Klei, C. Y. Chang
Date :  14 Feb 97  (Deposition) - 04 Mar 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  Y,Z
Biol. Unit 1:  Y  (1x)
Biol. Unit 2:  Z  (1x)
Keywords :  Ribosome-Inactivating Protein, Immunotoxin, Bryodin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. L. Gawlak, M. Neubauer, H. E. Klei, C. Y. Chang, H. M. Einspahr, C. B. Siegall
Molecular, Biological, And Preliminary Structural Analysis Of Recombinant Bryodin 1, A Ribosome-Inactivating Protein From The Plant Bryonia Dioica.
Biochemistry V. 36 3095 1997
PubMed-ID: 9115985  |  Reference-DOI: 10.1021/BI962474+
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BRYODIN I
    Chains: Y, Z
    EC Number: 3.2.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSE 13.0
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Variant: LAMBDA DE3
    Fragment: RESIDUES 1 - 247
    Organ: LEAF
    Organism Common: RED BRYONY
    Organism Scientific: BRYONIA DIOICA
    Organism Taxid: 3652
    Other Details: CDNA SEQUENCE ISOLATED FROM BRYONIA DIOICA LEAF MRNA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : YZ
Biological Unit 1 (1x): Y 
Biological Unit 2 (1x):  Z

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1BRY)

(-) Sites  (0, 0)

(no "Site" information available for 1BRY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIP1_BRYDI178-194
 		  2Y:155-171
Z:155-171
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIP1_BRYDI178-194
 		  1Y:155-171
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIP1_BRYDI178-194
 		  1-
Z:155-171

(-) Exons   (0, 0)

(no "Exon" information available for 1BRY)

(-) Sequences/Alignments

Asymmetric 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 Y from PDB  Type:PROTEIN  Length:247
 aligned with RIP1_BRYDI | P33185 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:247
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       
           RIP1_BRYDI    24 DVSFRLSGATTTSYGVFIKNLREALPYERKVYNIPLLRSSISGSGRYTLLHLTNYADETISVAVDVTNVYIMGYLAGDVSYFFNEASATEAAKFVFKDAKKKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLYYYTASSAASALLVLIQSTAESARYKFIEQQIGKRVDKTFLPSLATISLENNWSALSKQIQIASTNNGQFESPVVLIDGNNQRVSITNASARVVTSNIALLLNRNNIA 270
               SCOP domains d1bryy_ Y: Bryodin                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1bryY01 Y:1-162 Ricin (A subunit), domain 1                                                                                                                       1bryY02 Y:163-247 Ricin (A Subunit), domain 2                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhh..eeeee..eeee.....hhhheeeeeee.....eeeeeee....eeeeeee..eeee...hhhhhhhh.......eeee......hhhhhhhh...hhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.........hhhhhhhh.hhhhhhhhhhhhh........eeee.....eeee.....hhhh........hhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ---------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bry Y   1 DVSFRLSGATTTSYGVFIKNLREALPYERKVYNIPLLRSSISGSGRYTLLHLTNYADETISVAVDVTNVYIMGYLAGDVSYFFNEASATEAAKFVFKDAKKKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLYYYTASSAASALLVLIQSTAESARYKFIEQQIGKRVDKTFLPSLATISLENNWSALSKQIQIASTNNGQFESPVVLIDGNNQRVSITNASARVVTSNIALLLNRNNIA 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       


Chain Z from PDB  Type:PROTEIN  Length:247
 aligned with RIP1_BRYDI | P33185 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:247
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       
           RIP1_BRYDI    24 DVSFRLSGATTTSYGVFIKNLREALPYERKVYNIPLLRSSISGSGRYTLLHLTNYADETISVAVDVTNVYIMGYLAGDVSYFFNEASATEAAKFVFKDAKKKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLYYYTASSAASALLVLIQSTAESARYKFIEQQIGKRVDKTFLPSLATISLENNWSALSKQIQIASTNNGQFESPVVLIDGNNQRVSITNASARVVTSNIALLLNRNNIA 270
               SCOP domains d1bryz_ Z: Bryodin                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1bryZ01 Z:1-162 Ricin (A subunit), domain 1                                                                                                                       1bryZ02 Z:163-247 Ricin (A Subunit), domain 2                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhh..eeeee..eeee.....hhhheeeeeee.....eeeeeee....eeeeeee..eeee...hhhhhhhh.......eeee......hhhhhhhh...hhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.........hhhhhhhh.hhhhhhhhhhhhh........eeee.....eeee.....hhhh........hhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ---------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bry Z   1 DVSFRLSGATTTSYGVFIKNLREALPYERKVYNIPLLRSSISGSGRYTLLHLTNYADETISVAVDVTNVYIMGYLAGDVSYFFNEASATEAAKFVFKDAKKKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLYYYTASSAASALLVLIQSTAESARYKFIEQQIGKRVDKTFLPSLATISLENNWSALSKQIQIASTNNGQFESPVVLIDGNNQRVSITNASARVVTSNIALLLNRNNIA 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BRY)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain Y,Z   (RIP1_BRYDI | P33185)
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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