Abstract:
:d-2-Hydroxyglutarate dehydrogenase from Pseudomonas aeruginosa PAO1 (PaD2HGDH) catalyzes the oxidation of d-2-hydroxyglutarate to 2-ketoglutarate, which is a necessary step in the serine biosynthetic pathway. The dependence of P. aeruginosa on PaD2HGDH makes the enzyme a potential therapeutic target against P. aeruginosa. In this study, recombinant His-tagged PaD2HGDH was expressed and purified to high levels from gene PA0317, which was previously annotated as an FAD-binding PCMH-type domain-containing protein. The enzyme cofactor was identified as FAD with fluorescence emission after phosphodiesterase treatment and with mass spectrometry analysis. PaD2HGDH had a kcat value of 11 s-1 and a Km value of 60 μM with d-2-hydroxyglutarate at pH 7.4 and 25 °C. The enzyme was also active with d-malate but did not react with molecular oxygen. Steady-state kinetics with d-malate and phenazine methosulfate as an electron acceptor established a mechanism that was consistent with ping-pong bi-bi steady-state kinetics at pH 7.4. A comparison of the kcat/Km values with d-2-hydroxyglutarate and d-malate suggested that the C5 carboxylate of d-2-hydroxyglutarate is important for the substrate specificity of the enzyme. Other homologues of the enzyme have been previously grouped in the VAO/PMCH family of flavoproteins. PaD2HGDH shares fully conserved residues with other α-hydroxy acid oxidizing enzymes, and these conserved residues are found in the active site of the PaD2HDGH homology model. An Enzyme Function Initiative-Enzyme Similarity Tool Sequence Similarity Network analysis suggests a functional difference between PaD2HGDH and human D2HGDH, and no relationship with VAO. A phylogenetic tree analysis of PaD2HGDH, VAO, and human D2HGDH establishes genetic diversity among these enzymes.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Quaye JA,Gadda Gdoi
10.1021/acs.biochem.0c00832subject
Has Abstractpub_date
2020-12-29 00:00:00pages
4833-4844issue
51eissn
0006-2960issn
1520-4995journal_volume
59pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Mistic is an unusual membrane protein from Bacillus subtilis. It appears to fold and insert autonomously into a lipid bilayer and has been suggested as a tool that aids the targeting of eukaryotic membrane proteins to bacterial membranes. The NMR structure of Mistic in detergent (LDAO) micelles has revealed it to be a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0608818
更新日期:2006-08-01 00:00:00
abstract::Taurine/alpha-ketoglutarate (alphaKG) dioxygenase (TauD), an archetype alphaKG-dependent hydroxylase, is a non-heme mononuclear Fe(II) enzyme that couples the oxidative decarboxylation of alphaKG with the conversion of taurine to aminoacetaldehyde and sulfite. The crystal structure of taurine-alphaKG-Fe(II)TauD is kno...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi048746n
更新日期:2005-03-15 00:00:00
abstract::The isolated N-terminal Src homology 3 (SH3) domain of Drosophila drk exists in equilibrium between folded and unfolded states in aqueous buffer near neutral pH. Nuclear magnetic resonance spectra recorded on both states simultaneously exhibit an approximate 1:1 ratio of protein conformations. The folded form is simil...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00020a025
更新日期:1995-05-23 00:00:00
abstract::The role of lateral diffusion in mitochondrial electron transport has been investigated by measuring the diffusion coefficients for lipid, cytochrome c, and cytochrome oxidase in membranes of giant mitoplasts from cuprizone-fed mice using the technique of fluorescence redistribution after photobleaching (FRAP). The di...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00331a017
更新日期:1985-05-07 00:00:00
abstract::The trifunctional dinuclear platinum compounds 1,2/c,c [[cis-PtCl(NH(3))(2)]mu-H(2)N(CH(2))(6)NH(2)[cis-PtCl(2)(NH(3))]](+) and 1,2/t,c [[trans-PtCl(NH(3))(2)]mu-H(2)N(CH(2))(6)NH(2)[cis-PtCl(2)(NH(3))]](+) contain a monofunctional platinum coordination sphere linked to a cis-[PtCl(2)(amine)(2)] moiety. The compounds ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi030243e
更新日期:2004-06-22 00:00:00
abstract::Rapid freeze-quench (RFQ) Mössbauer and stopped-flow absorption spectroscopy were used to monitor the ferritin ferroxidase reaction using recombinant (apo) frog M ferritin; the initial transient ferric species could be trapped by the RFQ method using low iron loading (36 Fe2+/ferritin molecule). Biphasic kinetics of f...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi980847w
更新日期:1998-07-14 00:00:00
abstract::Fatty acid-induced upregulation of death receptor 5 (DR5) and its cognate ligand, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), promotes hepatocyte lipoapoptosis, which is a key mechanism in the progression of fatty liver disease. Accordingly, inhibition of DR5 signaling represents an attractive str...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.0c00529
更新日期:2020-10-13 00:00:00
abstract::Molecular imaging is an important new direction in medical diagnosis; however, its success is dependent upon molecular probes that demonstrate selective tissue targeting. We report the design and chemical synthesis of a derivative of human amyloid-beta (Abeta) peptide that is capable of selectively targeting individua...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0359574
更新日期:2004-05-25 00:00:00
abstract::We have studied the hydrogen-exchange kinetics of hemoglobin A0 as a function of ligand, CO, saturation. In the noncooperative system, azide binding to methemoglobin, the alterations in exchange kinetics are proportional to the average degree of ligation. However, in the case of CO binding to deoxyhemoglobin the chang...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00297a015
更新日期:1984-01-17 00:00:00
abstract::NMR spectroscopy has been used to study the interaction of aminoglycoside antibiotics with an aminoglycoside antibiotic 3'-phosphotransferase [APH(3')-IIIa]. APH(3')-IIIa is an enterococcal enzyme that is responsible for the ATP-dependent O-phosphorylation of a broad range of aminoglycoside antibiotics. The NMR method...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9626822
更新日期:1997-03-04 00:00:00
abstract::RS1, also known as retinoschisin, is an extracellular discoidin domain-containing protein that has been implicated in maintaining the cellular organization and synaptic structure of the vertebrate retina. Mutations in the gene encoding RS1 are responsible for X-linked retinoschisis, a retinal degenerative disease char...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi800938g
更新日期:2008-09-02 00:00:00
abstract::DNA-DNA interstrand cross-links are thought to be important for the cytotoxicity of many chemotherapeutic agents. To study this more definitively, adduct site-specific methods are used to construct a plasmid with a single nitrogen mustard interstrand cross-link (inter-HN2-pTZSV28). Replication efficiency (RE = [coloni...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi962778w
更新日期:1997-03-25 00:00:00
abstract::Oxidative damage by transition metals bound to proteins may be an important pathogenic mechanism. Ceruloplasmin (Cp) is a Cu-containing plasma protein thought to be involved in oxidative modification of lipoproteins. We have previously shown that Cp increased cell-mediated low-density lipoprotein (LDL) oxidation by a ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi981137t
更新日期:1998-10-06 00:00:00
abstract::The mechanism of wild-type and R37A mutant Pseudomonas dacunhae aspartate beta-decarboxylase (ABDC) was studied by rapid-scanning stopped-flow spectrophotometry. Mixing wild-type ABDC with 50 mM disodium l-Asp resulted in the formation of a 325 nm absorption peak within the dead time of the stopped-flow instrument, li...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi100272g
更新日期:2010-06-22 00:00:00
abstract::We review signaling by reactive oxygen species, which is emerging as a major physiological process. However, among the reactive oxygen species, H(2)O(2) best fulfills the requirements of being a second messenger. Its enzymatic production and degradation, along with the requirements for the oxidation of thiols by H(2)O...
journal_title:Biochemistry
pub_type: 杂志文章,评审
doi:10.1021/bi9020378
更新日期:2010-02-09 00:00:00
abstract::We report the first experimental characterization of the full thermodynamic profile for binding of urea to a native protein. We measured the volumetric parameters of lysozyme at pH 7.0 as a function of urea within a temperature range of 18-45 °C. At neutral pH, lysozyme retains its native conformation between 0 and 8 ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b00805
更新日期:2016-11-29 00:00:00
abstract::The Rieske protein from Thermus thermophilus (TtRp) and a truncated version of the protein (truncTtRp), produced to achieve a low-pH crystallization condition, have been characterized using UV-visible and circular dichroism spectroscopies. TtRp and truncTtRp undergo a change in the UV-visible spectra with increasing p...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi901126u
更新日期:2009-10-20 00:00:00
abstract::The kinetics of the slow folding and unfolding reactions of barstar, a bacterial ribonuclease inhibitor protein, have been studied at 23(+/-1) degrees C, pH 8, by the use of tryptophan fluorescence, far-UV circular dichroism (CD), near-UV CD, and transient mixing (1)H nuclear magnetic resonance (NMR) spectroscopic mea...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi990285w
更新日期:1999-07-13 00:00:00
abstract::The relationship between steroid binding and protein subunit interactions of rabbit sex steroid binding protein (rSBP) has been studied by steady-state and time-resolved fluorescence spectroscopy. The high-affinity (Ka approximately 10(8) M-1 at 4 degrees C), fluorescent estrogen d-1,3,5(10),6,8-estrapentaene-3,17 bet...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00492a005
更新日期:1990-10-09 00:00:00
abstract::Comparative primary structural analyses have begun to elucidate polymorphic residues and segments of the class I antigens of the major histocompatibility complex, at least some of which presumably contribute to determinants important in immune recognition events. HLA-A2 structural variants have been described which ar...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00267a042
更新日期:1982-11-23 00:00:00
abstract::The bifunctional enzyme dehydroquinate dehydratase-shikimate dehydrogenase (DHQ-SDH) catalyzes the dehydration of dehydroquinate to dehydroshikimate and the reduction of dehydroshikimate to shikimate in the shikimate pathway. We report the first crystal structure of Arabidopsis DHQ-SDH with shikimate bound at the SDH ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi060366+
更新日期:2006-06-27 00:00:00
abstract::To shed more light on the molecular requirements for recognition of thyroid response elements (TREs) by thyroid receptors (TRs), we compared the specific aspects of DNA TRE recognition by different TR constructs. Using fluorescence anisotropy, we performed a detailed and hierarchical study of TR-TRE binding. This was ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi901282s
更新日期:2010-02-09 00:00:00
abstract::The beta(2) subunit of a class Ia or Ib ribonucleotide reductase (RNR) is activated when its carboxylate-bridged Fe(2)(II/II) cluster reacts with O(2) to oxidize a nearby tyrosine (Y) residue to a stable radical (Y(*)). During turnover, the Y(*) in beta(2) is thought to reversibly oxidize a cysteine (C) in the alpha(2...
journal_title:Biochemistry
pub_type: 杂志文章,评审
doi:10.1021/bi8017625
更新日期:2008-12-30 00:00:00
abstract::The kinetic parameters (kpol, Kd app) for all possible correct and incorrect pairing between the A, T, G, and C bases were determined for wild-type (WT) rat DNA polymerase beta (pol beta) and the R283A mutant under pre-steady-state kinetic assay conditions. The base substitution fidelities of these two proteins were t...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi961653o
更新日期:1997-02-04 00:00:00
abstract::The presence of a N-(2-deoxy-D-erythro pentofuranosyl)urea (henceforth referred to as deoxyribosylurea) residue, ring fragmentation product of a thymine, in a frameshift situation in the sequence 5'd(AGGACCACG).d(CGTGGurTCCT) has been studied by 1H and 31P nuclear magnetic resonance and molecular dynamics. At equilibr...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi971202j
更新日期:1998-01-27 00:00:00
abstract::The properties of the nucleotide binding sites in the isolated beta and alpha subunits of H(+)-ATPase from Bacillus PS3 (TF1) have been examined by studying the EPR properties of bound VO(2+), which is a paramagnetic probe for the native Mg2+ cation cofactor. The amino acid ligands of the VO2+ complexes with the isola...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9910732
更新日期:1999-11-16 00:00:00
abstract::The inactivation of excited rhodopsin in the presence of ATP, rhodopsin kinase, and/or arrestin has been studied from its effect on the two subsequent steps in the light-induced enzymatic cascade: metarhodopsin II catalyzed activation of G-protein and G-protein-dependent activation of cGMP phosphodiesterase. The inact...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00405a049
更新日期:1988-03-08 00:00:00
abstract::In order to more clearly define the structure of human plasma fibronectin (PFn) under physiologic buffer conditions, we determined the mean harmonic rotational relaxation times (rho H) of PFn and the thrombin-derived 190/170-kDa PFn fragment using steady-state fluorescence polarization. These measurements utilized the...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00464a027
更新日期:1990-03-27 00:00:00
abstract::Genomic clones encompassing all the translated sequences, the 3' untranslated sequence, and 1 kb flanking the ATG translation initiation codon of bovine tropoelastin have been obtained and characterized by restriction enzyme analysis and extensive DNA sequencing. These analyses demonstrated that functionally distinct ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00432a003
更新日期:1989-03-21 00:00:00
abstract::Studies reveal that it is possible to design a palladium(II)-containing porphyrin to bind exclusively by intercalation to double-stranded DNA while simultaneously enhancing the ability to sensitize the formation of singlet oxygen. The comparisons revolve around the cations [5,10,15,20-tetra(N-methylpyridinium-4-yl)por...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi401610t
更新日期:2014-02-04 00:00:00