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1.1.1.22: UDP-glucose 6-dehydrogenase

This is an abbreviated version!
For detailed information about UDP-glucose 6-dehydrogenase, go to the full flat file.

Word Map on EC 1.1.1.22

Reaction

UDP-alpha-D-glucose
+ 2 NAD+ +
H2O
=
UDP-alpha-D-glucuronate
 + 2 NADH + 2 H+

Synonyms

ADH-like UDP-glucose dehydrogenase, AglM, BceC, Cj1441c, dehydrogenase, uridine diphosphoglucose, dual specificity UDP-glucose dehydrogenase, GbUGD, GH_D12G1806, HasB, HasB2, HVO_1531, jekyll m151, kfiD, PA2022, PA3559, PH02Gene21682, sqv-4, Sugarless protein, UDG1, UDP-alpha-D-glucose:NAD oxidoreductase, UDP-D-glucose dehydrogenase, UDP-GDH, UDP-Glc dehydrogenase, UDP-Glc DH, UDP-GlcDH, UDP-GlcDHase, UDP-glucose dehydrogenase, UDPDH, UDPG dehydrogenase, UDPG-DH, UDPG:NAD oxidoreductase, UDPGD, UDPGDH, UDPGDH-A, UDPGDH-B, UDPGlc dehydrogenase, UDPglucose dehydrogenase, UDPglucose:NAD+ oxidoreductase, Ugd, UGD1, Ugd2, UgdG, UGDH, UGDH4, uridine diphosphate D-glucose dehydrogenase, uridine diphosphate glucose dehydrogenase, uridine diphosphate glucose-6-dehydrogenase, uridine diphosphate-glucose dehydrogenase, uridine diphosphoglucose dehydrogenase, uridine-5'-diphosphoglucose dehydrogenase, uridyl phosphate dehydrogenase, VNG1048G, VNG_1048G

ECTree

     1 Oxidoreductases
         1.1 Acting on the CH-OH group of donors
             1.1.1 With NAD+ or NADP+ as acceptor
                1.1.1.22 UDP-glucose 6-dehydrogenase

Crystallization

Crystallization on EC 1.1.1.22 - UDP-glucose 6-dehydrogenase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant His6-tagged BceC, 0.001 ml of protein solution containing 5 mg/ml protein in 25 mM Tris-HCl, pH 8.3, 50 mM NaCl, 2.5 mM DTT, 0.25 mM UDP-GlcA, and 0.5 mM NAD+, is mixed with 0.001 ml of precipitant solution containing 200 mM ammonium sulfate, 100 mM sodium acetate, pH 4.5, 11% w/v PEG 4000, and 50 mM NaF, method optimiization, X-ray diffraction structure determination and analysis at 2.09 A resolution, molecular replacement
-
to 1.75 A resolution
structures of unliganded and UDP-xylose bound UGDH. The A109P substitution that differs human and Caenorhabditis elgans enzymes is accommodated by an Asn-to-Ser substitution at position 290. The allosteric transition is conserved in UGDH, and UDP-Xyl binding induces formation of the Eomega hexamer. The enzyme also exhibits hysteresis in progress curves and negative cooperativity with respect to NAD+ binding
structure in the presence of NAD+ and UDP-glucose bound in the active site
2.3 A resolution crystal structure of the deletion construct DELTA132 reveals an open conformation that relaxes steric constraints and facilitates repacking of the protein core. The open conformation stabilizes the deletion construct as a hexamer with point group symmetry 32, similar to that of the active complex. In contrast, the UDP-alpha-D-xylose-inhibited enzyme forms a lower-symmetry, horseshoe-shaped hexameric complex. The DELTA132 and the UDP-alpha-D-xylose-inhibited structures have similar hexamer-building interfaces
alternate crystal structure of human enzyme in complex with UDP-glucose at 2.8 A resolution. The substrate-bound protein complex consists of the open homohexamer. In all subunits of the open structure, residue Thr131 has translocated into the active site occupying the volume vacated by the absent active water and partially disordered NAD+ molecule. This conformation suggests a mechanism by which the enzyme may exchange NADH for NAD+ and repolarize the catalytic water molecule bound to Asp280 while protecting the reaction intermediates
crystallized from a solution of 0.2 M ammonium sulfate, 0.1 M Na cacodylate, pH 6.5, and 21% PEG 8000. Diffraction data are collected to a resolution of 2.8 A. The crystals belong to the orthorhombic space group P2(1)2(1)2(1) with unit-cell parameters a = 173.25, b = 191.16, c = 225.94 A and alpha = beta = gamma = 90.0°
-
in mutant E161Q, the hydrolysis step becomes completely rate-limiting so that a thioester enzyme intermediate accumulates at steady state. Crystallization of mutant E161Q in the presence of 5 mM UDP-glucose and 2 mM NAD results in trapping a thiohemiacetal enzyme intermediate. Residue Cys276 is covalently modified in the structure, establishing its role as catalytic nucleophile of the reaction
mutant A104L, structure reveals a reduced cavity C-1 volume. The allosteric switch still adopts the E and E* states, albeit with a more rigid protein core
mutant A136M at 2.05 A resolution, the A136M substitution has stabilized the active conformation of the T131-loop/alpha6 allosteric switch
mutant K94E, to 2.08 A resolution. Cofactor binding triggers the formation of the 32 symmetry hexamer, but substrate UDP-alpha-D-glucose is needed for the stability of the complex. Loop88-110 is the cofactor-responsive allosteric switch that drives hexamer formation, loop88-110 directly links cofactor binding to the stability of the hexamer-building interface. In the interface, loop88-110 packs against the Thr131-loop/alpha6 helix, the allosteric switch that responds to the feedback inhibitor UDP-alpha-D-xylose
the structure of UGDH in the crystal form reveals a hexameric arrangement, composed a trimer of dimers of six subunits
sitting-drop vapour-diffusion method, diffraction quality crystals (maximum dimensions of 0.1 * 0.1 * 0.1 mm) are obtained within one week at 273°C using reservoir solution composed of 4.0 M NaCl, 100 mM HEPES pH 7.5. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 117.7, b = 76.7, c = 75.6 A, beta = 125.8°. Crystal structure is at a resolution of 2.0 A. The overall fold is comprised of an N-terminal NAD+ dinucleotide binding domain and a C-terminal UDP-sugar binding domain connected by a long alpha-helix
purified recombinant wild-type and selenomethionine-labeled UgdG at 4.5 and 5.5 mg/ml, respectively, in 25 mM Tris-HCl, pH 8.3, 50 mM NaCl, 2.5 mM DTT and 1 mM NAD+, or 0.5 mM UDP-GlcA and 1 mM NAD+, 0.0005 ml of each protein and precipitant solution are mixed at 20°C, 24 h, the precipitant solution contains 200 mM Li2SO4, 100 mM Tris-HCl, pH 8.5, and 30% v/v PEG 4000, or 100 mM sodium citrate, pH 5.6, 20% 2-propanol, and 20% v/v PEG 4000, vapour diffusion method, method optimization, X-ray diffraction structure determination and analysis at 2.4 A resolution for the wild-type enzyme, and at 3.4 A resolution for the SeMet-UDG