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3.4.23.16: HIV-1 retropepsin

This is an abbreviated version!
For detailed information about HIV-1 retropepsin, go to the full flat file.

Word Map on EC 3.4.23.16

Reaction

specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro =

Synonyms

CRF01_AE protease, Gag protease, HIV aspartyl protease, HIV PR, HIV protease, HIV-1 aspartyl protease, HIV-1 PR, HIV-1 protease, HIV-1 proteinase, HIV-1PR, HIV-2 protease, HIVPR, human immunodeficiency virus 1 protease, human immunodeficiency virus 1 retropepsin, human immunodeficiency virus protease, human immunodeficiency virus type 1 protease, human immunodeficiency virus type I protease, More, PR, PR1, PR2, retropepsin, retroproteinase

ECTree

     3 Hydrolases
         3.4 Acting on peptide bonds (peptidases)
             3.4.23 Aspartic endopeptidases
                3.4.23.16 HIV-1 retropepsin

Crystallization

Crystallization on EC 3.4.23.16 - HIV-1 retropepsin

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
complex of the inactive enzyme variant D25N and a long substrate peptide KARVLAEAMS
computer simulation of subtype AE HIV-1 protease with the drugs lopinavir and nelfinavir. Comparison of the interactive mechanisms of lopinavir and nelfinavir with HIV-1 protease shows that the presence of a dodecahydroisoquinoline ring at the P10 subsite, a [2-(2,6-dimethylphenoxy)acetyl]amino group at the P20 subsite, and an N2 atom at the P2 subsite could improve the binding affinity of the drug with AE HIV-1 protease
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crystal of HIV1 protease complexed with KNI-272
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crystal structure of a synthetic HIV-1 protease
crystal structure of the protease/DMP323 complex shows that the carboxyl oxygens of the catalytic aspartic acid residues, Asp25/25' and the diol oxygens of the inhibitor are positioned to form a network of hydrogen bonds
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crystal structures of HIV-1 protease mutants, D30N, K45I, and L90M complexed with peptide inhibitor analogues of CA-p2 and p2-NC cleavage sites in the gal-pol precursor
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crystal structures of HIV-1 protease with N-[(1S,2R)-1-benzyl-2-hydroxy-3-[[(3-methoxyphenyl)sulfonyl](thiophen-2-ylmethyl)amino]propyl]-3-fluoro-2-methylbenzamide, C11c, N2-acetyl-N-[(1S,2R)-1-benzyl-2-hydroxy-3-[(thiophen-2-ylmethyl)[(2,4,5-trifluorophenyl)sulfonyl]amino]propyl]-L-alaninamide, (2E)-N-[(1S,2R)-1-benzyl-2-hydroxy-3-[(thiophen-2-ylmethyl)[(2,4,5-trifluorophenyl)sulfonyl]amino]propyl]-4,4,4-trifluoro-3-methylbut-2-enamide, N-[(1S,2R)-1-benzyl-2-hydroxy-3-[[(4-methoxyphenyl)sulfonyl][(2S)-2-methylbutyl]amino]propyl]-4-oxohexanamide, N-[(1S,2R)-3-[(1,3-benzothiazol-6-ylsulfonyl)[(2S)-2-methylbutyl]amino]-1-benzyl-2-hydroxypropyl]-3-hydroxybenzamide, (2S)-N-[(1S,2R)-3-[(1,3-benzothiazol-6-ylsulfonyl)[(2S)-2-methylbutyl]amino]-1-benzyl-2-hydroxypropyl]-2-hydroxy-3-methylbutanamide, N2-acetyl-N-[(1S,2R)-3-[(1,3-benzothiazol-6-ylsulfonyl)(pentyl)amino]-1-benzyl-2-hydroxypropyl]-L-valinamide or N-[(1S,2R)-3-[(1,3-benzothiazol-6-ylsulfonyl)(2-methylpropyl)amino]-1-benzyl-2-hydroxypropyl]-3-hydroxybenzamide
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crystallization of a complex between the chemically synthesized HIV-1 protease and the peptide inhibitor N-acetyl-Thr-Ile-Nle-PSI[CH2-NH]-Nle-Gln-Arg-amide
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crystallization of a protein-inhibitor complex
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crystallization of variants of HIV proteinase with or without insertions at positions 33 and 35
crystallographic-based structural studies of HIV-1 protease inhibitors with reduced response to the V82A mutation
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determination of the crystal structures of three chimeric HIV proteases complexed with SB203386. The chimeras are constructed by substituting amino acid residues in the HIV type 1 protease sequence with the corresponding residues from HIV type 2 in the region spanning residues 31-37 and in the active site cavity. Crystallographic analysis reveals that substitution of residues 31-37 (30's loop) with those of HIV-2 protease renders the chimera similar to HIV-2 protease in both the inhibitor binding affinity and mode of binding (two inhibitor molecules per protease dimer). However, further substitution of active site residues 47 and 82 has a compensatory effect which restores the HIV-1-like inhibitor binding mode
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docking study of inhibitors (3R,4aR,8aR)-N-tert-butyl-2-[(R)-2-hydroxy-3-(N-isobutyl-4-aminophenylsulfonamido)propyl]decahydroisoquinoline-3-carboxamide, (3R,4aR,8aR)-N-tert-butyl-2-[(R)-2-hydroxy-3-(N-isobutyl-3-aminophenylsulfonamido)propyl]decahydroisoquinoline-3-carboxamide, (3R,4aR,8aR)-N-tert-butyl-2-[(R)-2-hydroxy-3-(N-propyl-4-aminophenylsulfonamido)propyl]decahydroisoquinoline-3-carboxamide, (3R,4aR,8aR)-N-tert-butyl-2-[(R)-2-hydroxy-3-(N-(2-phenylethyl)-4-aminophenylsulfonamido)propyl]decahydroisoquinoline-3-carboxamide based on crystal structure of HIV-1 protease and comparative molecular field analysis study
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enzyme in complex with GADIFYLDGA, GAEVFYVDGA or GAQTFYVDGA
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hanging drop method, crystal structures of complexes of an inactive variant D25N of HIV-1 protease with six peptides that correspond to the natural substrate cleavage site
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hanging drop method, mutant enzyme G48V/L90M in complex with saquinavir
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hanging drop vapor diffusion method
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hanging drop vapor diffusion method at 20°C, A28S mutant enzyme in complex with the peptide inhibitor U-89360E
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hanging drop vapor diffusion method, using 0.25 M sodium citrate pH 6.0, 10% (v/v) DMSO, and 40%-60% (w/v) saturated ammonium sulfate
hanging drop vapor diffusion method, using 126 mM phosphate buffer at pH 6.2, 63 mM sodium citrate, and 24-29% (w/v) ammonium sulfate
hanging drop vapor diffusion technique, crystal structures of nelfinavir-resistant HIV protease mutants (D30N, D30N/A71V, D30N/N88D, and D30N/L90M) with nelfinavir
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hanging drop vapor diffusion, a hexapeptide substrate (containing two macrocyclic tripeptides constrained to mimic alpha/beta-strand conformation, linked by a scissile peptide bond, to probe the structural mechanism of proteolysis) is cocrystallized with catalytically active synthetic HIV-1 protease and an inactive isosteric D25N mutant, and three-dimensional structures are determined by 1.6 A
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hanging-drop vapor diffusion method
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hanging-drop vapor diffusion method, high-resolution crystal structures of wild-type enzyme and the multidrug-resistant variant with the I54V mutation in complex with a peptide at 1.46 and 1.50 A resolution, respectively
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hanging-drop vapor diffusion method, two high-resolution crystal structures of wild-type enzyme and the multidrug-resistant variant with the I54V mutation in complex with a peptide at 1.46 and 1.50 A resolution, respectively
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hanging-drop vapour diffusion method, crystallization of an tethered dimer that has a mutation in only one subunit at position 95
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HIV-1 protease in complex with inhibitor tert-butyl N-[(1R,2S)-1-benzyl-3-[(4S)-7-fluoro-4-methyl-1,1-dioxo-1,3,4,5-tetrahydro-2H-1lambda6,2-benzothiazepin-2-yl]-2-hydroxypropyl]carbamate, hanging drop vapor diffusion method, in 0.5 M NaCl, acetate buffer, pH 5.5
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in complex with substrate Arg-Pro-Gly-Asn-Phe-Leu-Gln-Ser-Arg-Pro, to 2.8 A resolution. Hydrogen bonding between the flap hinge and the protease core regions shows significant structural rearrangements in CRF01_AE protease compared to the clade B protease structure
mutant enzyme D25N in complex with SGIFLETS, vapor diffusion method, using 100 mM sodium acetate buffer pH 5.0 containing 1.0 M NaCl
mutant enzyme V32I/I47V/V82I in complex with amprenavir, sitting drop vapor diffusion method, using 0.1M MES, 0.9 M NaCl, pH 6.0 in H2O
mutant enzyme V32I/I47V/V82I in complex with inhibitors darunavir, amprenavir or saquinavir, hanging drop vapor diffusion method, using 0.1 M sodium acetate buffer, pH 4.6 and 2 M NaCl as precipitant (darunavir), 1.5 M NaCl with 0.6 M imidazole/0.12 M zinc acetate buffer at pH 6 (amprenavir), or 0.1 M sodium acetate buffer, pH 5.0, 0.4 M potassium chloride as precipitant (saquinavir)
mutant enzymes G86A and G86S in complex with darunavir or DMP323, hanging drop vapor diffusion method, using 10% (w/v) sodium chloride and 0.1 M MES buffer at pH 6.5 and 4°C
mutant enzymes R8Q, K45I and L90M are crystallized with the inhibitor RVL-(reduced peptide bond)-FEA-Nle-NH2
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mutants I50V and I84 V in complex with inhibitor N,N'-(3S,4S)-pyrrolidine-3,4-diylbis(4-amino-N-benzylbenzenesulfonamide), to 1.58 A and 1.92 a resolution, respectively
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mutants I50V, I54V, I54M in complex with saquinavir, and mutants G48V, I54V, and I54M in complex with darunavir, at resolutions of 1.05-1.40 A. The mutants show changes in conformation of the flap region, interactions with adjacent residues, inhibitor binding, and the conformation of the 80s loop relative to the wild-type protease
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PRS17-D25N alone and in complex with substrate analogues RVLrFEANle and Ace-TINlerNleQR , hanging drop vapor diffusion method, using 1.95 M sodium chloride and 0.1 M bis-Tris pH 7.5 (inhibitor-free), 2.1 M sodium chloride and 0.1 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid at pH 7.6 (with RVLrFEANle) or 29.5% (w/v) poly(ethylene glycol) 4000, 0.2 M ammonium acetate, and 0.1 M sodium acetate buffer at pH 4.6 (with Ace-TINlerNleQR)
purified recombinant enzyme free or in complex with inhibitor rac-(2S,4S)-N-[4-([benzenesulfonyl-isobutyl-amino]-methyl)-pyrrolidine-3-ylmethyl]-N-benzyl-2-(2,6-dimethyl-phenoxy)-acetamide, 18°C, 3 M NaCl, 0.1 M BisTris, pH 6.5, cryoprotection by 20% glycerol, X-ray diffraction structure determination and analysis at 1.5-1.85 A resolution
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purified recombinant mutant enzymes Q7K/L33I/L63I/C67A/C95A, V82A, and I84V in complex with inhibitor UIC-94017, hanging drop vapour diffusion method, for mutant enzyme Q7K/L33I/L63I/C67A/C95A: 2:1 or 5:1 ratios inhibitor to protein, the well solution contains 30 mM sodium acetate, pH 4.8, 10% w/v NaCl, 10% v/v glycerol, 10% v/v DMSO, and 10% dioxane at room temperature, slightly altered conditions for mutant enzymes V82A and I84V, X-ray diffraction structure determination and analysis at 1.1-1.5 A resolution, overview
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purified recombinant mutant F53L, hanging drop vapour diffusion method, X-ray diffraction and analysis at 1.35 A resolution
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purified recombinant wild-type enzyme in complex with inhibitors ritonavir or indinavir, hanging drop vapour diffusion method, 3 mg/ml protein in 50 mM sodium acetate, pH 4.7, is mixed in a ratio of 10:1 with inhibitor ritonavir or indinavir solubilized in 100% DMSO, protein-inhibitor slution is mixed with an equal volume of reservoir solution, containing 1.5 M ammonium sulfate and 20 mM sodium acetate at pH 6.0 giving hanging drops of 0.004 ml, room temperature, one week, X-ray diffraction and analysis at 1.9-2.5 A resolution
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purified recombinant wild-type enzyme, mutant V82A enzyme, and mutant I84V enzyme in complex with substrate analogue inhibitors, 5 mg/ml protein mixed with inhibitor in a 20fold molar excess, incubation at 4°C for 1 h, hanging drop vapour diffusion method, 24°C, equal volumes of protein and reservoir solutions, the latter containing 0.1 M sodium acetate/citrate phosphate buffer, pH 4.2-5.0, 5% v/v DMSO, 0-5% v/v dioxane, 0.4-1.2 M sodium chloride, and 15-40% w/v saturated ammonium sulfate, X-ray diffraction structure determination and analysis at 1.10-1.54 A resolution
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purified refolded recombinant wild-type and mutant enzymes in complex with inhibitors, hanging drop vapour diffusion method, room temperature, preincubation of 1.8-3.5 mg/ml protein with inhibitor in a ratio of 1:5 - 1:20, for mutant L24I: the reservoir solution contains 0.2 M sodium phosphate, pH 5.0-6.0, 10% v/v DMSO, and 20-40% saturated ammonium sulfate, for mutants I50V and G73S: the reservoir solution contains 0.1 M sodium citrate/0.2 M sodium phosphate, pH 5.4-5.8, 8-13% DMSO and 6-20% saturated ammonium sulfate, protein and reservoir solutions are mixed in ratio of 1:1, X-ray diffraction structure determination snd analysis at 1.1-1.5 A resolution
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substrate binding pocket structure analysis
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the structure of the HIV-1 protease in complex with A79285, a pseudo-C2 symmetric inhibitor, which contains a central difluoroketone motif determined with X-ray diffraction data extending to 1.7 A resolution. Crystals are grown at room temperature by hanging drop method with 37% w/v ammonium sulfate, 63 mM citrate and 126 mM sodium phosphate, pH 6.2
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three-dimensional structure of a bi-product complex between HIV-1 protease and the two cleavage product peptides AETF and YVDGAA. The structure, refined against synchrotron data to 1.65 A resolution, shows the occurrence of the cleavage reaction in the crystal, with the product peptides still held in the enzyme active site
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three-dimensional structures of HIV-1 protease product complexes
vapor diffusion hanging drop method, mutant enzyme complexed to darunavir or acetyl-Thr-Ile-Nle-r-Nle-Gln-Arg-NH2
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vapor diffusion method
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wild-type and mutant A71V/V82T/I84V enzymes in complex with inhibitors SE, and SQ, hanging drop vapour diffusion method, 25°C, the reservoir solution contains 0.1 M sodium citrate, pH 4.4, 0.5 M sodium chloride, and 10% v/v glycerol, X-ray diffraction structure determination and analysis at 1.93-2.38 A resolution
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X-ray crystallographic analysis of HIV-1 protease in complex with transframe peptide FLREDLAF and the tripeptide EDL
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X-ray crystallographic structures of two mutant HIV-1 proteases, G48H and A28S, in complex with a peptidic inhibitor U-89360E
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