1.1.1.205: IMP dehydrogenase

This is an abbreviated version, for detailed information about IMP dehydrogenase, go to the full flat file.

Reaction

IMP
+
NAD+
+
H2O
=
XMP
+
NADH
+
H+

Synonyms

A1S_3321, BTH_I2056, class I IMPDH, class II IMPDH, dehydrogenase, inosinate, DR63_268, EC 1.2.1.14, GBAA_0008, guaB, guaB2, IMD2, IMD3, IMD4, IMP dehydrogenase, IMP DH, IMP oxidoreductase, IMP-DH, IMP:NAD oxidoreductase, IMP:NAD+ oxidoreductase, IMPD, IMPDH, IMPDH II, IMPDH-1, IMPDH-B, IMPDH-S, IMPDH1, IMPDH2, IMPDHab, IMPDHba, IMPDHbt, IMPDHI, IMPDHII, IMPDHkp, IMPDHlpp, IMPDHnm, IMPDHpa, inosinate dehydrogenase, inosine 5' monophosphate dehydrogenase, inosine 5'-monophosphate dehydrogenase, inosine 5'-monophosphate dehydrogenase 2, inosine 5'-phosphate dehydrogenase, inosine 5-monophosphate dehydrogenase, inosine 5-monophosphate dehydrogenase type I, inosine 5’ -monophosphate dehydrogenase, inosine 5’-monophosphate dehydrogenase 2, inosine monophosphate dehydrogenase, inosine monophosphate oxidoreductase, inosine-5'-monophosphate dehydrogenase, inosine-5'-phosphate dehydrogenase, inosinic acid 5’-monophosphate dehydrogenase, inosinic acid dehydrogenase, lpg1723, mpaF, NMC1103, Raspberry protein, Rv3411c, SOI12, Superoxide-inducible protein 12, type 1 inosine monophosphate, type 2 inosine monophosphate dehydrogenase

ECTree

     1 Oxidoreductases
         1.1 Acting on the CH-OH group of donors
             1.1.1 With NAD+ or NADP+ as acceptor
                1.1.1.205 IMP dehydrogenase

Crystallization

Crystallization on EC 1.1.1.205 - IMP dehydrogenase

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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
in a phosphate ion-bound form and in complex with its substrate, inosine 5'-monophosphate, and product, xanthosine 5'-monophosphate, to 2.38-2.65 A resolution. The enzyme monomer has a typical two-domain structure, the catalytic domain, which is a TIM barrel, and the CBS domain. In all structures, each monomer contains a ligand bound in the active site, i.e.phosphate anion in the apo structure and IMP and XMP in the substrate and product-bound structures, respectively. In all the structures, the CBS domains are partially disordered
purified recombinant short enzyme mutant BaIMPDHDELTAS in apoform from 0.2 M sodium chloride, 0.1 M sodium cacodylate, pH 6.5, and 2 M ammonium sulfate, 16°C, and purified recombinant long enzyme mutant BaIMPDHDELTAL in complex with IMP and with inhibitors 4-[(1R)-[1-(4-chlorophenyl)-1H-1,2,3-triazol-4yl]ethoxy]quinoline-1-oxide, ((alpha-methyl-)N-2-naphthalenyl-2-(2-pyridinyl)-1H-benzimidazole-)1-acetamide, 3,4-dihydro-3-methyl-4-oxo-N-(6,7,8,9-tetrahydro2-dibenzofuranyl)-1-phthalazineacetamide, 2-chloro-N-methyl-5-[[[1-methyl-1-[3-(1-methylethenyl)phenyl]ethyl]amino]carbonyl]aminobenzamide, N-(4-bromophenyl)-N-[1-[3-[1-(hydroxyimino)ethyl]phenyl]-1-methylethyl] urea, and 2-(1-naphthalenyloxy)-N-[(2-(4-pyridinyl)-5-benzoxazolyl)]-(2S)-propanamide in several conformations and under different conditions resulting in 6 different crystal structures, X-ray diffraction structure determination and analysis at resolutions of 1.93-2.85 A, respectively, overview
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at 2.4 A resolution
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in complex with sulfate, at 2.4 A resolution
-
purified recombinant short enzyme mutant CjIMPDHDELTAS in complex with IMP and with inhibitor 2 from 1.6 M ammonium sulfate, 0.1 M MES, pH 6.5, 10% dioxane, 16 °C, or with inhibitor 4 from 0.2 M lithium sulfate, 0.1 M CAPS, pH 10.5, 1.2 M sodium/0.8 M potassium phosphate, 16 °C, X-ray diffraction structure determination and analysis at resolutions of 2.44 and 2.54 A, respectively
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purified recombinant long enzyme mutant ClpIMPDHDELTAL in complex with IMP and with inhibitor 1 from 5% tacsimate, pH 7.0, 0.1 M HEPES, pH 7.0, 10% PEG MME 5000, 16°C, or with inhibitor 2 from 0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 17% PEG 10000, 16°C, X-ray diffraction structure determination and analysis at resolutions of 2.95 and 2.85 A, respectively
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in complex with inosine 5'-phosphate and mycophenolic acid at 2.6 A resolution
-
in complex with xanthosine 5'-phosphate, inhibitor mycophenolic acid and K+, at 2.6 A resolution
-
in complex with NAD+ and IMP, to 2.5 A resolution. Space group I422
hanging drop vapour diffusion method, to 3.2 A resolution, space group P21212. In complex with inhibitor N-(4-bromophenyl)-2-[2-(1,3-thiazol-2-yl)-1H-benzimidazol-1-yl]acetamide, to 2.8 A resolution. The thiazole ring of the inhibitor stacks against the purine ring of IMP perpendicularly, and the remainder of the inhibtor extends across the subunit interface into a pocket in the adjacent monomer, where the bromoaniline moiety interacts with Tyr358 from the adjacent subunit. This residue forms a hydrogen-bonding network involving Glu329, Ser354, Thr221, and possibly the amide nitrogen of N-(4-bromophenyl)-2-[2-(1,3-thiazol-2-yl)-1H-benzimidazol-1-yl]acetamide. Residues Ser22, Pro26, Gly357 of the adjacent subunit and Ala165 form the remainder of the inhibitor binding pocket. With the exception of Thr221, all of these residues are different in human IMPDHs
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purified recombinant enzyme in complex with substrate IMP and inhibitor P131, sitting drop vapor diffusion method, mixing of 400 nl of 13.4 mg/ml protein in 20 mM HEPES, pH 8.0, 150 mM KCl, and 1.5 mM TCEP with 400 nl of reservoir solution containing 0.1 M bicine-NaOH, pH 9.0, and 20% PEG 6000, and equilibration against 0.134 ml of reservoir solution, at 16°C, X-ray diffraction structure determination and analysis at 2.053 A resolution, molecular replacement using the structure of CpIMPDH, PDB ID 3ffs, as search model, modelling
-
purified recombinant mutant apoenzyme AgIMPDH-DELTABateman, vapor diffusion method, mixing 23 mg/ml protein 10 mM Tris-HCl, 100 mM KCl, 0.25 mM TCEP, pH 8.0, with an equal volume of mother liquor consisting of 0.1 M HEPES, pH 7.5, 40% PEG 300 v/v, and 0.2 M NaCl, for the enzyme mutant complex with IMP and NAD+ up to 5 mM XMP and 5 mM NAD+ are added to the protein solution, at room temperature, harvest of crystals of AgIMPDH-DELTABateman with a mixture of about 80% of the covalent intermediate E-XMP* and about 20% IMP bound to the active site, X-ray diffraction structure determination and analysis
enzyme type II complexed with 6-Cl-IMP and selenazole-4-carboxamide adenine dinucleotide, no method mentioned
modeling of complex with inhibitor 9-(5-O-[hydroxy[([hydroxy[2-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydro-2-benzofuran-5-yl)ethoxy]phosphoryl]oxy)methyl]phosphoryl]-b-L-ribofuranosyl)-9H-purin-6-amine; modeling of complex with inhibitor 9-(5-O-[hydroxy[([hydroxy[2-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydro-2-benzofuran-5-yl)ethoxy]phosphoryl]oxy)methyl]phosphoryl]-b-L-ribofuranosyl)-9H-purin-6-amine
-
molecular modeling of type II enzyme in complex with inhibitor 1_1_1.205_2.3
-
type 1 in complex with inhibitor 6-Cl-inosine 5'-phosphate, at 2.6 A resolution, type 2 in complex with inhibitor 6-Cl-inosine 5'-phosphate and SAD or NAD, at 2.9 A resolution, and with inhibitors ribavirin-monophosphate and C2-mycophenolic adenine nucleotide, at 2.65 A resolution
-
type II isoform, in complex with 6-chloropurine riboside 5'-monophosphate and selenazole-4-carboxyamide-adenine dinucleotide at 2.9 A resolution, in complex with ribavirin monophosphate and phosphonic acidmono-[2-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydro-isobenzofuran-5-yl)-ethyl] ester at 2.65 resolution, in complex with with 6-chloropurine riboside 5'-monophosphate and NAD+ at 2.9 A resolution; type I isoform, in complex with 6-chloropurine riboside 5'-monophosphate at 2.5 A resolution
-
modeling of enzyme in complex with eicosadienoic acid. Eicosadienoic acid binds to residue C331 in the active site
-
modeling of complex with inhibitor 9-(5-O-[hydroxy[([hydroxy[2-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydro-2-benzofuran-5-yl)ethoxy]phosphoryl]oxy)methyl]phosphoryl]-b-L-ribofuranosyl)-9H-purin-6-amine
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purified recombinant MtbIMPDH2DELTACBS enzyme mutant in apofomr or complexed with IMP/NAD+, or with inhibitors MAD1/IMP, P41/IMP, or Q67/IMP, the crystallization conditions are for the apoform mutant 0.1 M sodium/potassium phosphate, pH 6.2, 25% 1,2-propandiol, 10% glycerol, 16°C, for the MAD1/IMP-enzyme mutant complex 0.1 M sodium/potassium phosphate, pH 6.2, 25% 1,2-propandiol, 10% glycerol, 16°C, for the P41/IMP-enzyme mutant complex 0.3 M magnesium formate, 0.1 M Tris, pH 8.5, 16°C, for the Q67/IMP-enzyme mutant complex 0.1 M sodium/potassium phosphate, pH 6.2, 25% 1,2-propandiol, 10% glycerol, 16°C, and for the NAD+/IMP-enzyme mutant complex 0.4 M magnesium formate, 0.1M Tris-HCl, pH 8.5, 20% sucrose, 16°C, crystals are soaked with 200 mM ligand solutions, X-ray diffraction structure determination and analysis at 1.60-2.00 A resolution. Analysis of the crystal structure of the enzyme mutant in complex with XMP and NAD+, detailed overview
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purified recombinant IMPDH enzyme mutant DELTACBS in the apo form and in complex with IMP, sitting drop vapour diffusion method, mixing of 0.0015 ml of 9.2 mg/ml protein in 20 mM potassium phosphate, pH 8.0, 25 mM KCl, with 0.0015 ml reservoir solution consisting of either 4.3 M sodium chloride, 100 mM HEPES, pH 7.5, or 10 mM sodium citrate, and 33% PEG 8000 for the apoenzyme and containing 1.26 M ammonium sulfate, 100 mM HEPES, pH 7.5, for the IMP-complexed enzyme, equilibration against 0.15 ml or reservoir solution. For the D199N variant in complex with IMP, the optimized crystals are obtained by mixing 0.0015 ml of 11.7 mg/ml protein in solution in 20 mM potassium phosphate, pH 8.0, 25 mM KCl, and 10 mM IMP, with 0.0015 ml of reservoir solution containing 10% w/v PEG 4000, 200 mM magnesium chloride, 100 mM MES pH 6.5, and equilibration against 0.15 ml or reservoir solution, 18°C, X-ray diffraction structure determination and analysis at 1.65-1.95 A resolution, molecular replacement using a previously solved structure of wild-type IMPDHpa, PDB ID 4dqw, as a template
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to 2.25 A resolution. Strucuture is a homotetramer of subunits dominated by a (beta/alpha)8-barrel fold. The cystathionine beta-synthase domains, residues 92-204, are not present in the model owing to disorder. A loop that creates part of the active site is composed of residues 297-315, links alpha8 and beta9 and carries the catalytic Cys304
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in complex with xanthosine 5'-phosphate at 2.1 A resolution
-
in complex with inosine 5'-phosphate at 1.9 A resolution
-
in complex with inosine 5'-phosphate, at 1.9 A resolution
-
tetramer structure of IMPDH shows square planar geometry
-
vapor diffusion method using hanging drops
-
at 2.18 A resolution
-
analysis of crystal structures. The Cys319 loop has different conformations during the dehydrogenase and hydrolase reactions as suggested by the crystal structures. The structure of the Cys319 loop modulates the closure of themobile flap. This conformational change converts the enzyme from a dehydrogenase into hydrolase, suggesting that the conformation of the Cys319 loop may gate the catalytic cycle
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at 2.3 A resolution, in complex with inosine 5'-phosphate and beta-methylene-thiazole-4-carboxyamide-adenine dinucleotide at 2.2 A resolution, in complex with xanthosine 5'-phosphate and NAD+ at 2.15 A resolution, in complex with xanthosine 5'-phosphate and mycophenolic acid at 2.2 A resolution, in complex with RVP and mycophenolic acid at 2.15 A resolution, in complex with 4-carbamoyl-1-beta-D-ribofuranosylimidazolium-5-olate-5'-phosphate at 2.0 A resolution
-
no method mentioned
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purified recombinant full-length enzyme and alphabeta core domain in complex with inosine 5'-phosphate and beta-methylene-thiazole-4-carboxamide adenine dinucleotide, X-ray diffraction structure determination and analysis at 2.2 A resolution, molecular replacement
-
wild-type at 2.3 A resolution, in complex with xanthosine 5'-phosphate, at 2.6 A resolution, in complex with inhibitor ribavirin-monophosphate, at 1.9 A resolution, in complex with inhibitors ribavirin-monophosphate and mycophenolic acid, at 2.5 A resolution, in complex with inosine 5'-phosphate, at 2.2 A resolution, in complex with inosine 5'-phosphate and inhibitor mycophenolic acid, at 1.95 A resolution, in complex with xanthosine 5'-phosphate and inhibitor mycophenolic acid, at 2.2 A resolution, in complex with xanthosine 5'-phosphate and NAD+, at 2.15 A resolution. Mutant DELTA(101-226) in complex with inosine 5'-phosphate and inhibitor beta-CH2-tiazofurin adenine dinucletoide, at 2.2 A resolution or in complex with inhibitor mizoribine monophosphate, at 2 A resolution
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purified recombinant long enzyme mutant VcIMPDHDELTAL in complex with IMP and NAD+ from 0.77 M sodium/potassium phosphate, 0.15 M Tris-HCl, pH 8.0, 6% MPD, 16°C, followed by soaking with 200 mM NAD+ solution for 15 min at 20°C, or enzyme mutant VcIMPDHDELTAL in complex with XMP and NADH from 1.03 M sodium/potassium phosphate, pH 5.0, 0.15 M sodium malate, 3% PEG 300, 16°C, followed by soaking with 200 mM NAD+ solution for 5 days at 16°C, X-ray diffraction structure determination and analysis at resolutions of 2.38 and 1.66 A, respectively
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