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.

Reaction

hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes =

Synonyms

(ribosome-inactivating protein)-like protein, abelesculin, ABRaA, abrin, abrin-a A chain, Abrus precatorius agglutinin, Agglutinin, alpha-MC, alpha-momorcharin, alpha-pisavin, aralin, B-32, balsamin, BBAP1, beta-momorcharin, beta-pisavin, Bougainvillea xbuttiana antiviral protein 1, bouganin, camphorin, CAP30, cinnamomin, Cochinin B, cytotoxic ribosome-inactivating lectin, depurinating rRNA N-glycosidase, dianthin 30, dianthin 32, 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 glycosidase activity, 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, 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, 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
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2.8 A resolution, space group P212121, two molecules per asymmetric unit
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in presence of adenosine and adenine, resolution to 1.8 A. Adenine is positioned in the active site, adenosine is cleaved
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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
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hanging drop vapor diffusion method, using 16% (w/v) polyethylene glycol 6000 and 0.1 M sodium phosphate buffer at pH 6.5
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vapor diffusion method, using 0.1 M sodium phosphate buffer pH 6.5 and 16% (w/v) polyethylene glycol 6000
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modeling and docking analysis on interaction of residue S211 with W207 located within the active site
space group C2, two molecules per asymmetric unit
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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
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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
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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
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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
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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
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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)
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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%
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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; E85Q, space group P2(1)2(1)2(1), unit cell constants a = 38.0, b = 75.9, c= 78.4
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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; 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
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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; 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; E85Q, space group P2(1)2(1)2(1), unit cell constants a = 38.0, b = 75.9, c= 78.4
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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
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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
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