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3.2.2.22: rRNA N-glycosylase

This is an abbreviated version!
For detailed information about rRNA N-glycosylase, go to the full flat file.

Word Map on EC 3.2.2.22

Reaction

A4324 in 28S rRNA
+
H2O
=
deadenylated 28S rRNA
 +
adenine

Synonyms

(ribosome-inactivating protein)-like protein, abelesculin, ABRaA, abrin, abrin-a A chain, Abrus precatorius agglutinin, alpha-MC, alpha-momorcharin, alpha-pisavin, antiviral protein DAP-30, aralin, B-32, balsamin, BBAP1, BE27, beta-momorcharin, beta-pisavin, Bougainvillea xbuttiana antiviral protein 1, bouganin, camphorin, CAP30, cinnamomin, Cochinin B, cytotoxic ribosome-inactivating lectin, D6D54_07625, D6D54_08385, D6D54_08880, depurinating rRNA N-glycosidase, dianthin 30, dianthin 32, dianthin-30, diphtheria toxin, ebulin b, ebulitin alpha, ebulitin beta, ebulitin gamma, gelonin, gysophilin, hispin, IRAb, IRIP, Iris agglutinin b, Iris ribosome-inactivating protein, JIP60, karasurin-A, KML, lamjapin, luffaculin I, luffin P1, lychnin, MAP, marmorin, ME1, Mirabilis antiviral protein, mistletoe lectin I, mistletoe lectin II, mistletoe lectin III, ML-I, MLI, MLII, MLIII, MOD, modeccin, momorcochin, momorcochin-S, momordin, momordin I, momordin II, momorgrosvin, More, N-glycosidase, n-TCS, neo-trichosanthin, nigrin b, nigritin f1, nigritin f2, PAG, PAGase, PAP, PAP-I, PAP-II, PAP-III, PAP-R, PAP-S, PD-L, PD-L1, PD-L4, pepocin, PGase, pokeweed anti-viral protein, pokeweed antiviral protein, polynucleotide:adenosine glycosidase, polynucleotide:adenosine glycosylase, porrectin, RA, RCA-II, ribosomal inactivating protein, ribosomal ribonucleate N-glycosidase, ribosome inactivating protein, ribosome-inactivating protein, ribosome-inactivating protein 3, ribosome-inactivating protein type II, ribosome-inactivating proteins, ribosome-inactivating type II protein, ribosome-specific N-glycosidase, ricin, ricin A, ricin A chain, ricin A-chain, ricin toxin A-chain, ricin-A-chain, ricin-like protein, Ricinus communis agglutinin, Ricinus communis agglutinin II, RIP, RIP-1, RIP1, RIP2, RIPII, riproximin, RLP1, RLP2, RLP3, RLP4, RLP5, RLP6, RNA N-glycosidase, RNA-NGA, RNA-specific N-glycosidase, RNase Bo, Rpx, rRNA N-glycosidase, RTA, Sambucus nigra agglutinin, Sambucus nigra agglutinin I, SAP, saporin, saporin 6, saporin S-6, saporin S6, saporin-6, saporin-L1, saporin-S6, saporins, SBA, SCO7092, SEPIN, Shiga toxin, Shiga toxin 1, Shiga toxin 1 subunit A, Shiga toxin 2, Shiga toxin 2 subunit A, Shiga toxin type 1, Shiga toxin type 2, Shiga toxin-1, shiga-like toxin, shiga-like toxin I, sieboldin-b, single-chain ribosome-inactivating protein, SLT-I, SLT-II, SLT-IIv, SNA, SNA-I, SNA-V, SnaI, SNAIf, SNAV, SNLRP, SoRIP1, SoRIP2, stenodactylin, Stx, Stx type 1, Stx-1, Stx1, Stx1A, Stx2, Stx2A, Stx2dact, StxB, TCS, trichoanguin, trichomaglin, trichosanthin, Trichosanthrip, trichosnathin, TRIP, tritin-L, tritin-S, TYchi, type 1 ribosome inactivating protein, type 1 ribosome-inactivating protein, type 1 RIP, type 2 ribosome inactivating protein, type 2 ribosome-inactivating protein, type 2 RIP, type 2RIP, type 3 RIP, type I ribosome inactivating protein, type I ribosome-inactivating protein, type I RIP, type II ribosome inactivating protein, type II ribosome-inactivating protein, type II RIP, type III ribosome-inactivating protein, type III RIP, type-1 ribosome-inactivating protein, type-1 RIP, type-2 ribosome-inactivating protein, type-2 RIP, VAA-I, viscinum, Viscum album agglutinin I, viscumin, volkensin

ECTree

     3 Hydrolases
         3.2 Glycosylases
             3.2.2 Hydrolysing N-glycosyl compounds
                3.2.2.22 rRNA N-glycosylase

Crystallization

Crystallization on EC 3.2.2.22 - rRNA N-glycosylase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified native stenodactylin, sitting drop vapour diffusion technique, mixing of 0.004 ml of 1.4-1.5 M sodium malonate, pH 6.8-7.5, reservoir solution with 0.004 ml of protein solution containing with 5.76 mg/ml protein in 5 mM sodium phosphate buffer, pH 7.0, 0.14 M NaCl and 4 mM galactose, equilibration against 0.75 ml of reservoir solution, 20°C, 3 weeks, X-ray diffraction structure determination and analysis at 2.15 A resolution
-
2.8 A resolution, space group P212121, two molecules per asymmetric unit
-
in presence of adenosine and adenine, resolution to 1.8 A. Adenine is positioned in the active site, adenosine is cleaved
-
at 1.4 A resolution. Assignment of sequence by improved X-ray sequencing. Residues Y70, Y110, E159 and R162 define the active site. Residues N77 and N84 carry N-acetylglucosamine moieties
-
hanging drop vapor diffusion method, using 16% (w/v) polyethylene glycol 6000 and 0.1 M sodium phosphate buffer at pH 6.5
vapor diffusion method, using 0.1 M sodium phosphate buffer pH 6.5 and 16% (w/v) polyethylene glycol 6000
modeling and docking analysis on interaction of residue S211 with W207 located within the active site
space group C2, two molecules per asymmetric unit
-
coarse-grained latice simulation model of sequence-structure modifications of the ricin A chain protein fold. Calculation of unfolding-folding transition temperature and evaluation of a possible unfolding model
-
determination of the coupling of tyrosine residues, presence of energy transfer from tyrosine to tryptophan residues. The molar absorption coefficient of ricin in phosphate-buffered saline is 93900 per mol and cm
-
dynamics calculations suggest that steric factors cause the nucleoside to bind in an orientation where the enzyme destabilizes the formation of the oxacarbeniumion and thus precludes catalysis
purified recombinant mutant RTAs N122A and R213D, sitting drop vapour diffusion method using microbridges, X-ray diffraction structure determination and analysis at 1.4 A and 1.9 A resolution, respectively
-
ricin A chain in complex with inhibitor 7-carboxy pterin, hanging drop vapor diffusion method, using 75 mM Tris-HCl pH 8.9, 10 mM BME, 1 mM EDTA, 4.1% (w/v) PEG MW 8000
-
RTA with 4-(3-(2-amino-4,6-dihydroxy-5-pyrimidinyl)propyl) benzoic acid
sitting drop vapor diffusion method, using 100 mM N,N-bis(2-hydroxyethyl)glycine (pH 8.5) and 20% (w/v) polyethylene glycol (PEG) 6000 (in complex with antigen binding domain E5 of single-chain monoclonal antibody) or 100 mM Na acetate (pH 4.5), 200 mM zinc acetate and 10% (w/v) PEG 3000 (in complex with antigen binding domain D10 of single-chain monoclonal antibody) or 100 mM Na-Hepes (pH 7.5) and 20% (w/v) PEG 8000 (in complex with antigen binding domain G12 of single-chain monoclonal antibody) or 100 mM Na acetate (pH 4.5), 200 mM NaCl and 40% (w/v) PEG 300 (in complex with antigen binding domain G11 of single-chain monoclonal antibody)
structure of ricin-A chain in a complex with the C-terminal domain of the human ribosomal protein P2. The Phe111, Leu113 and Phe114 residues of P2 insert into a hydrophobic pocket formed by the Tyr183, Arg235, Phe240 and Ile251 residues of ricin A-chain, while Asp115 of P2 forms hydrogen bonds with Arg235 of ricin A-chain. The interaction with P stalk proteins is essential for the inhibition of protein synthesis by ricin A-chain
the smallest ligand stabilizing an open conformer of the ricin A chain active site pocket is an amide group, bound weakly by only a few hydrogen bonds to the protein. Complexes with small amide-containing molecules also reveal a switch in geometry from a parallel towards a splayed arrangement of an arginine-tryptophan cation-pi interaction that was associated with an increase and redshift in tryptophan fluorescence upon ligand binding. Urea binding has a favorable enthalpy change and unfavorable entropy change. The side-chain position of residue >80 in a complex with adenine suggests a smaller role for aromatic stacking at the ricin active site
the total helical content of ricin is 53.6%
-
in complex with 11-mer of P-protein C-terminal end (c11-P)
crystal structures of several E85 mutant TCS complexes with adenosine-5'-monophosphate, E85A, space group P2(1)2(1)2(1), unit cell constants a = 38.3, b = 76.7, c= 79.2
-
crystals of n-TCS, space group P2(1)2(1)2(1), unit cell constants a = 3.839 nm, b = 7.652 nm, c = 7.963 nm and mutant Y70A, space group P2(1)2(1)2(1), a = 3.830, b = 7.646, c = 7.943
-
E85Q, space group P2(1)2(1)2(1), unit cell constants a = 38.0, b = 75.9, c= 78.4
-
E85R, space group P2(1)2(1)2(1), unit cell constants a = 38.0, b = 75.3, c= 78.4
-
high quality crystals of the ML-I complex obtained by vapor diffusion
homology modeling of both A and B chain protein and comparison with European mistletoe lectin-1, Himalayan mistletoe lectin, and ricin
-
crystallization of precursor protein and active form, at 2.4 and 2.5 A resolution, respectively. In the precursor, the inactivation region is found on the protein surface and consists of a flexible loop followed by a long alpha-helix. Presence of this region diminishes both the interaction with ribosome and cytotoxicity, but not cellular uptake. The active site of the enzyme is too small to accomodate two glutamate residues
-