Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: C30B5 .7
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Pig muscle phosphoglycerate kinase has been crystallized from polyethyleneglycol in the presence of its substrate 3-phospho-D-glycerate (3-PG) and the structure has been determined at 2.0 A resolution. The structure was solved using the known structure of the substrate-free horse muscle enzyme and has been refined to a crystallographic R-factor of 21.5%. 3-Phospho-D-glycerate is bound to the N-domain of the enzyme through a network of hydrogen bonds to a cluster of basic amino acid residues and by electrostatic interactions between the negatively charged phosphate and these basic protein side chains. This binding site is in good agreement with earlier proposals [Banks et al., Nature (London) 279:773-777, 1979]. The phosphate oxygen atoms are hydrogen bonded to His-62, Arg-65, Arg-122, and Arg-170. The 2-hydroxyl group, which defines the D-isomer of 3PG, is hydrogen bonded to Asp-23 and Asn-25. The carboxyl group of 3-PG points away from the N-domain towards the C-domain and is hydrogen bonded via a water molecule to main chain nitrogen atoms of helix-14. The present structure of the 3-PG-bound pig muscle enzyme is compared with the structure of the substrate-free horse enzyme. Major changes include an ordering of helix-13 and a domain movement, which brings the N-domain closer to the ATP-binding C-domain. This domain movement consists of a 7.7 degree rotation, which is less than previously estimated for the ternary complex. Local changes close to the 3-PG binding site include an ordering of Arg-65 and a shift of helix-5.
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PMID:Crystal structure of the binary complex of pig muscle phosphoglycerate kinase and its substrate 3-phospho-D-glycerate. 160 3

Asp222 is an invariant residue in all known sequences of aspartate aminotransferases from a variety of sources and is located within a distance of strong ionic interaction with N(1) of the coenzyme, pyridoxal 5'-phosphate (PLP), or pyridoxamine 5'-phosphate (PMP). This residue of Escherichia coli aspartate aminotransferase was replaced by Ala, Asn, or Glu by site-directed mutagenesis. The PLP form of the mutant enzyme D222E showed pH-dependent spectral changes with a pKa value of 6.44 for the protonation of the internal aldimine bond, slightly lower than that (6.7) for the wild-type enzyme. In contrast, the internal aldimine bond in the D222A or D222N enzyme did not titrate over the pH range 5.3-9.5, and a 430-nm band attributed to the protonated aldimine persisted even at high pH. The binding affinity of the D222A and D222N enzymes for PMP decreased by 3 orders of magnitude as compared to that of the wild-type enzyme. Pre-steady-state half-transamination reactions of all the mutant enzymes with substrates exhibited anomalous progress curves comprising multiphasic exponential processes, which were accounted for by postulating several kinetically different enzyme species for both the PLP and PMP forms of each mutant enzyme. While the replacement of Asp222 by Glu yielded fairly active enzyme species, the replacement by Ala and Asn resulted in 8600- and 20,000-fold decreases, respectively, in the catalytic efficiency (kmax/Kd value for the most active species of each mutant enzyme) in the reactions of the PLP form with aspartate. In contrast, the catalytic efficiency of the PMP form of the D222A or D222N enzyme with 2-oxoglutarate was still retained at a level as high as 2-10% of that of the wild-type enzyme. The presteady-state reactions of these two mutant enzymes with [2-2H]aspartate revealed a deuterium isotope effect (kH/kD = 6.0) greater than that [kH/kD = 2.2; Kuramitsu, S., Hiromi, K., Hayashi, H., Morino, Y., & Kagamiyama, H. (1990) Biochemistry 29, 5469-5476] for the wild-type enzyme. These findings indicate that the presence of a negatively charged residue at position 222 is particularly critical for the withdrawal of the alpha-proton of the amino acid substrate and accelerates this rate-determining step by about 5 kcal.mol-1. Thus it is concluded that Asp222 serves as a protein ligand tethering the coenzyme in a productive mode within the active site and stabilizes the protonated N(1) of the coenzyme to strengthen the electron-withdrawing capacity of the coenzyme.
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PMID:Role of Asp222 in the catalytic mechanism of Escherichia coli aspartate aminotransferase: the amino acid residue which enhances the function of the enzyme-bound coenzyme pyridoxal 5'-phosphate. 161 Aug 31

We identify His381 of Pseudomonas mevalonii 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase as the basic residue functional in catalysis. The catalytic domain of 20 HMG-CoA reductases contains a single conserved histidine (His381 of the P. mevalonii enzyme). Diethyl pyrocarbonate inactivated the P. mevalonii enzyme, and hydroxylamine partially restored activity. We changed His381 to alanine, lysine, asparagine, and glutamine. The mutant proteins were overexpressed, purified to homogeneity, and characterized. His381 mutant enzymes were not inactivated by diethyl pyrocarbonate. All four mutant enzymes exhibited wild-type crystal morphology and chromatographed on substrate affinity supports like wild-type enzyme. The mutant enzymes had low catalytic activity (Vmax 0.06-0.5% that of wild-type enzyme), but Km values approximated those for wild-type enzyme. For wild-type enzyme and mutant enzymes H381A, H381N, and H381Q, Km values at pH 8.1 were 0.45, 0.27, 3.7, and 0.71 mM [(R,S)-mevalonate]; 0.05, 0.03, 0.20, and 0.11 mM [coenzyme A]; 0.22, 0.14, 0.81, and 0.62 mM [NAD+]. Km values at pH 11 for wild-type enzyme and mutant enzyme H381K were 0.32 and 0.75 mM [(R,S)-mevalonate]; 0.24 and 0.50 mM [coenzyme A]; 0.15 and 1.23 mM [NAD+]. Both pK values for the enzyme-substrate complex increased relative to wild-type enzyme (by 1-2.5 pH units for pK1 and by 0.5-1.3 pH units for pK2). For mutant enzyme H381K, the pK1 of 10.2 is consistent with lysine acting as a general base at high pH. His381 of P. mevalonii HMG-CoA reductase, and consequently the histidine of the consensus Leu-Val-Lys-Ser-His-Met-Xaa-Xaa-Asn-Arg-Ser motif of the catalytic domain of eukaryotic HMG-CoA reductases, thus is the general base functional in catalysis.
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PMID:Identification of the catalytically important histidine of 3-hydroxy-3-methylglutaryl-coenzyme A reductase. 163 43

Mutations of the two ionizable residues, GluL212 and AspL213, in the secondary quinone (QB) binding site of reaction centers (RCs) from Rhodobacter sphaeroides cause major dysfunctions in the proton transfer processes leading to the formation of quinol. Mutant RCs with AspL213----Asn are especially severely blocked, and the rate of the proton-limited transfer of the second electron is at least 10(4) times slower than in the wild-type. Small, weak acids, such as azide/hydrazoic acid (N3-/HN3;pK approximately 4.7) accelerated the electron transfer rate in mutant RCs in a pH and concentration-dependent manner, consistent with their functioning as protein-penetrating protonophores, delivering protons to the QB site in a non-specific, diffusive process. Other small weak acids acted similarly with efficacies dependent on their size and pK values. In terms of the concentration of protonated species, the relative effectiveness was: nitrite greater than cyanate approximately formate greater than azide much greater than acetate. The behavior of bacterial RCs containing the AspL213----Asn mutation resembles that of bicarbonate-depleted photosystem II, and the mutational block is partially alleviated by bicarbonate. The possibility is discussed that bicarbonate acts in PS II as an analogue to the carboxylic acid residues of the bacterial proton conduction pathway.
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PMID:Small weak acids stimulate proton transfer events in site-directed mutants of the two ionizable residues, GluL212 and AspL213, in the QB-binding site of Rhodobacter sphaeroides reaction center. 164 93

A family with one homozygote and three heterozygotes for hemoglobin Stanleyville II (alpha 78 Asn----Lys) has been analyzed by alpha-globin gene mapping. The pattern of restriction fragments with the enzymes BamHI and BglII demonstrated that the alpha globin variant is associated with a 3.7-kb alpha-globin gene deletion.
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PMID:Hemoglobin Stanleyville II (alpha 78 Asn----Lys) is associated with a 3.7-kb alpha-globin gene deletion. 167 72

We used the expression of chimeric proteins and point mutants to identify amino acids of the hepatic progesterone 21-hydroxylase P450IIC5 which are part of an epitope recognized by an inhibitory monoclonal antibody and which affect substrate binding. Three amino acids of P450IIC5 at positions 113, 115, and 118 were introduced into P450IIC4, which is 95% identical to P450IIC5. The resultant chimeric protein acquired binding of the monoclonal antibody 1F11, which is highly specific and inhibitory for P450IIC5. Point mutants in P450IIC4 showed that two of the three changes, T115S and N118K, contribute to the epitope recognized by this antibody. The T115S mutant bound the antibody weakly (Kd greater than 30 nM) whereas the N118K mutant bound the antibody as tightly as P450IIC5 (Kd less than or equal to 0.7 nM). Thus, residues 115 and 118 are located on the surface of these enzymes, and the Lys/Asn difference at amino acid 118 is largely responsible for the high degree of discrimination which this antibody exhibits between P450IIC5 and P450IIC4. The valine to alanine mutation at position 113 conferred to P450IIC4 a lower apparent Km for progesterone 21-hydroxylation. Because antibody binding was not affected by this mutation, it is tempting to speculate that this residue is buried in the protein where it exerts its effect on the catalytic activity by interaction with the substrate or alters the positions of residues of the active site. The close proximity of the epitope at positions 115 and 118 to Ala113 suggests that the inhibitory monoclonal antibody interferes with substrate binding.
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PMID:An inhibitory monoclonal antibody binds in close proximity to a determinant for substrate binding in cytochrome P450IIC5. 170 11

The activity and kinetics of acid-stable protease inhibitor (ASPI) were investigated in the chronic phase of carrageenin-induced inflammation in rats. The ASPI activity was 19.6 +/- 3.1 units/ml in the plasma and 15.4 +/- 2.1 units/ml in the inflammatory exudate. The plasma value was significantly higher than that of the control (11.6 +/- 1.3 units/ml). A kinetics study was performed using purified and radiolabeled rat plasma ASPI, whose NH2-terminal amino acid sequence was Ala-Val-Leu-Pro-Gln-Glu-Asn-Glu-Gly-X-Gly-Ser-Glu-Pro-Leu-Ile-Thr-Gly-Th r-Leu- Lys-Lys-Glu-Asp-Ser-Asn-Gln-Leu-Lys-Tyr-Ser-Glu-Gly-Pro. The half-life of the distributive phase was 4.3 +/- 0.4 min and that of the postdistributive phase (biological half-life) was 42.2 +/- 9.2 min in inflammation. There was no significant difference compared with the values in the control (3.9 +/- 0.4 min and 40.7 +/- 6.5 min, respectively). It appeared that the increase in ASPI in inflammation was not due to prolonged excretion of the inhibitor but to an increased production of it, and ASPI was rapidly distributed to the fluids and tissues.
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PMID:Acid-stable protease inhibitor in chronic phase of carrageenin-induced inflammation in rats. 176 32

Among the vitamin K-dependent plasma proteins, only protein S contains the post-translationally modified amino acid erythro-beta-hydroxyasparagine (Hyn). Protein S also contains erythro-beta-hydroxyaspartic acid (Hya). The function of these unusual amino acids, located in the epidermal growth factor-like domains, is unknown. To determine if these post-translational modifications contribute to the functional integrity of human protein S (HPS), recombinant human protein S lacking Hya and Hyn (rHPSdesHya/Hyn) was purified from the medium of human kidney 293 cells that were transfected with HPS cDNA and grown in the presence of the hydroxylase inhibitor 2,2'-dipyridyl. Solution-phase equilibrium binding studies revealed that rHPSdesHya/Hyn binds C4b-binding protein (C4BP) in a manner indistinguishable from recombinant HPS and plasma-derived HPS, exhibiting a Kd in the presence of 2 mM CaCl2 of approximately 0.7 nM and a Kd in the presence of 4 mM EDTA approximately 10-fold higher. In a purified component system, rHPSdesHya/Hyn displayed normal anticoagulant cofactor activity in the activated protein C-catalyzed inactivation of coagulation factor Va bound in the prothrombinase complex. In addition, digestion of rHPSdesHya/Hyn with thrombin in the presence of EDTA appeared normal, and 2 mM CaCl2 prevented the cleavage. Together these results suggest that the post-translational modifications of Asn and Asp residues are not necessary for the macromolecular or Ca2+ interactions associated with the anticoagulant and C4BP binding characteristics of HPS.
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PMID:beta-Hydroxyaspartic acid and beta-hydroxyasparagine residues in recombinant human protein S are not required for anticoagulant cofactor activity or for binding to C4b-binding protein. 183 48

The pH dependence of the peptidolytic reaction of recombinant human immunodeficiency virus type 1 protease has been examined over a pH range of 3-7 for four oligopeptide substrates and two competitive inhibitors. The pK values obtained from the pKis vs pH profiles for the unprotonated and protonated active-site aspartyl groups, Asp-25 and Asp-25', in the monoprotonated enzyme form were 3.1 and 5.2, respectively. Profiles of log V/K vs pH for all four substrates were "bell-shaped" in which the pK values for the unprotonated and protonated aspartyl residues were 3.4-3.7 and 5.5-6.5, respectively. Profiles of log V vs pH for these substrates were "wave-shaped" in which V was shifted to a constant lower value upon protonation of a residue of pK = 4.2-5.2. These results indicate that substrates bind only to a form of HIV-1 protease in which one of the two catalytic aspartyl residues is protonated. Solvent kinetic isotope effects were measured over a pH (D) range of 3-7 for two oligopeptide substrates, Ac-Arg-Ala-Ser-Gln-Asn-Tyr-Pro-Val-Val-NH2 and Ac-Ser-Gln-Asn-Tyr-Pro-Val-Val-NH2. The pH-independent value for DV/K was 1.0 for both substrates, and DV = 1.5-1.7 and 2.2-3.2 at low and high pH (D), respectively. The attentuation of both V and DV at low pH (D) is consistent with a change in rate-limiting step from a chemical one at high pH (D) to one in which a product release step or an enzyme isomerization step becomes partly rate-limiting at low pH (D). Proton inventory data is in accord with the concerted transfer of two protons in the transition state of a rate-limiting chemical step in which the enzyme-bound amide hydrate adduct collapses to form the carboxylic acid and amine products.
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PMID:Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism. 188 31

Heteronuclear 2D and 3D NMR experiments were carried out on recombinant Drosophila calmodulin (CaM), a protein of 148 residues and with molecular mass of 16.7 kDa, that is uniformly labeled with 15N and 13C to a level of greater than 95%. Nearly complete 1H and 13C side-chain assignments for all amino acid residues are obtained by using the 3D HCCH-COSY and HCCH-TOCSY experiments that rely on large heteronuclear one-bond scalar couplings to transfer magnetization and establish through-bond connectivities. The secondary structure of this protein in solution has been elucidated by a qualitative interpretation of nuclear Overhauser effects, hydrogen exchange data, and 3JHNH alpha coupling constants. A clear correlation between the 13C alpha chemical shift and secondary structure is found. The secondary structure in the two globular domains of Drosophila CaM in solution is essentially identical with that of the X-ray crystal structure of mammalian CaM [Babu, Y., Bugg, C. E., & Cook, W.J. (1988) J. Mol. Biol. 204, 191-204], which consists of two pairs of a "helix-loop-helix" motif in each globular domain. The existence of a short antiparallel beta-sheet between the two loops in each domain has been confirmed. The eight alpha-helix segments identified from the NMR data are located at Glu-6 to Phe-19, Thr-29 to Ser-38, Glu-45 to Glu-54, Phe-65 to Lys-77, Glu-82 to Asp-93, Ala-102 to Asn-111, Asp-118 to Glu-127, and Tyr-138 to Thr-146. Although the crystal structure has a long "central helix" from Phe-65 to Phe-92 that connects the two globular domains, NMR data indicate that residues Asp-78 to Ser-81 of this central helix adopt a nonhelical conformation with considerable flexibility.
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PMID:Secondary structure and side-chain 1H and 13C resonance assignments of calmodulin in solution by heteronuclear multidimensional NMR spectroscopy. 190 92


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