Functional annotation and three-dimensional structure of an incorrectly annotated dihydroorotase from cog3964 in the amidohydrolase superfamily.

Abstract:

:The substrate specificities of two incorrectly annotated enzymes belonging to cog3964 from the amidohydrolase superfamily were determined. This group of enzymes are currently misannotated as either dihydroorotases or adenine deaminases. Atu3266 from Agrobacterium tumefaciens C58 and Oant2987 from Ochrobactrum anthropi ATCC 49188 were found to catalyze the hydrolysis of acetyl-(R)-mandelate and similar esters with values of k(cat)/K(m) that exceed 10(5) M(-1) s(-1). These enzymes do not catalyze the deamination of adenine or the hydrolysis of dihydroorotate. Atu3266 was crystallized and the structure determined to a resolution of 2.62 Å. The protein folds as a distorted (β/α)(8) barrel and binds two zincs in the active site. The substrate profile was determined via a combination of computational docking to the three-dimensional structure of Atu3266 and screening of a highly focused library of potential substrates. The initial weak hit was the hydrolysis of N-acetyl-D-serine (k(cat)/K(m) = 4 M(-1) s(-1)). This was followed by the progressive identification of acetyl-(R)-glycerate (k(cat)/K(m) = 4 × 10(2) M(-1) s(-1)), acetyl glycolate (k(cat)/K(m) = 1.3 × 10(4) M(-1) s(-1)), and ultimately acetyl-(R)-mandelate (k(cat)/K(m) = 2.8 × 10(5) M(-1) s(-1)).

journal_name

Biochemistry

journal_title

Biochemistry

authors

Ornelas A,Korczynska M,Ragumani S,Kumaran D,Narindoshvili T,Shoichet BK,Swaminathan S,Raushel FM

doi

10.1021/bi301483z

subject

Has Abstract

pub_date

2013-01-08 00:00:00

pages

228-38

issue

1

eissn

0006-2960

issn

1520-4995

journal_volume

52

pub_type

杂志文章
  • Analysis of the backbone dynamics of interleukin-1 beta using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy.

    abstract::The backbone dynamics of uniformly 15N-labeled interleukin-1 beta are investigated by using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy. 15N T1, T2, and NOE data at a spectrometer frequency of 600 MHz are obtained for 90% of the backbone amide groups. The data provide evidence for motions on...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00484a006

    authors: Clore GM,Driscoll PC,Wingfield PT,Gronenborn AM

    更新日期:1990-08-14 00:00:00

  • Conformational changes of an exchangeable apolipoprotein, apolipophorin III from Locusta migratoria, at low pH: correlation with lipid binding.

    abstract::Locusta migratoria apolipophorin III (apoLp-III) is a helix bundle exchangeable apolipoprotein that reversibly binds to lipoprotein surfaces. Structural reorganization of its five amphipathic alpha-helices enables the transition from the lipid-free to lipid-bound state. ApoLp-III-induced transformation of dimyristoylp...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi010410f

    authors: Weers PM,Kay CM,Ryan RO

    更新日期:2001-06-26 00:00:00

  • Discovery of a Kojibiose Phosphorylase in Escherichia coli K-12.

    abstract::The substrate profiles for three uncharacterized enzymes (YcjM, YcjT, and YcjU) that are expressed from a cluster of 12 genes ( ycjM-W and ompG) of unknown function in Escherichia coli K-12 were determined. Through a comprehensive bioinformatic and steady-state kinetic analysis, the catalytic function of YcjT was dete...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.8b00392

    authors: Mukherjee K,Narindoshvili T,Raushel FM

    更新日期:2018-05-15 00:00:00

  • Hydrogen bonds of water and C==O groups coordinate long-range structural changes in the L photointermediate of bacteriorhodopsin.

    abstract::Fourier transform infrared spectra of light-adapted bacteriorhodopsin exhibit a band at 1618 cm(-1) that shifts to 1625 cm(-1) upon formation of the L intermediate. It is assigned to the peptide C==O of Val49 from the fact that it shifts in [1-(13)C]valine-labeled bacteriorhodopsin and appears perturbed in the Val49--...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9524530

    authors: Yamazaki Y,Tuzi S,Saitô H,Kandori H,Needleman R,Lanyi JK,Maeda A

    更新日期:1996-04-02 00:00:00

  • A General Mechanism for the Propagation of Mutational Effects in Proteins.

    abstract::Mutations in the hydrophobic interior of proteins are generally thought to weaken the interactions only in their immediate neighborhood. This forms the basis of protein engineering-based studies of folding mechanism and function. However, mutational work on diverse proteins has shown that distant residues are thermody...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00798

    authors: Rajasekaran N,Suresh S,Gopi S,Raman K,Naganathan AN

    更新日期:2017-01-10 00:00:00

  • Structures of apolipoprotein A-II and a lipid-surrogate complex provide insights into apolipoprotein-lipid interactions.

    abstract::Apolipoproteins A-I and A-II form the major protein constituents of high-density lipid particles (HDL), the concentration of which is inversely correlated with the frequency of heart disease in humans. Although the physiological role of apolipoprotein A-II is unclear, evidence for its involvement in free fatty acid me...

    journal_title:Biochemistry

    pub_type: 杂志文章,收录出版

    doi:10.1021/bi026069w

    authors: Kumar MS,Carson M,Hussain MM,Murthy HM

    更新日期:2002-10-01 00:00:00

  • Identification of essential tyrosine and lysine residues in angiotensin converting enzyme: evidence for a single active site.

    abstract::Inactivation of rabbit lung angiotensin converting enzyme (ACE) by 1-fluoro-2,4-dinitrobenzene (Dnp-F) has been shown to be due primarily to the modification of a tyrosine residue [Bünning, P., Kleeman, S.G., & Riordan, J.F. (1990) Biochemistry (preceding paper in this issue)]. Rabbit testicular ACE is also inactivate...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00498a011

    authors: Chen YN,Riordan JF

    更新日期:1990-11-20 00:00:00

  • Chromatin condensing functions of the linker histone C-terminal domain are mediated by specific amino acid composition and intrinsic protein disorder.

    abstract::Linker histones bind to the nucleosomes and linker DNA of chromatin fibers, causing changes in linker DNA structure and stabilization of higher order folded and oligomeric chromatin structures. Linker histones affect chromatin structure acting primarily through their approximately 100-residue C-terminal domain (CTD). ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801636y

    authors: Lu X,Hamkalo B,Parseghian MH,Hansen JC

    更新日期:2009-01-13 00:00:00

  • Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn.

    abstract::The hairpin ribozyme is an RNA enzyme that performs site-specific phosphodiester bond cleavage between nucleotides A-1 and G+1 within its cognate substrate. Previous functional studies revealed that the minimal hairpin ribozyme exhibited "gain-of-function" cleavage properties resulting from U39C or U39 to propyl linke...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi051550i

    authors: Alam S,Grum-Tokars V,Krucinska J,Kundracik ML,Wedekind JE

    更新日期:2005-11-08 00:00:00

  • Kinetic mechanism of the inhibition of cathepsin G by alpha 1-antichymotrypsin and alpha 1-proteinase inhibitor.

    abstract::Uncontrolled proteolysis due to cathepsin G (cat G) may cause severe pathological disorders. Cat G is inhibited by alpha 1-antichymotrypsin (ACT) and alpha 1-proteinase inhibitor (alpha 1PI), two members of the serpin superfamily of proteins. To see whether these two inhibitors play a physiological proteolysis-prevent...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi980223q

    authors: Duranton J,Adam C,Bieth JG

    更新日期:1998-08-11 00:00:00

  • Stereochemistry and deuterium isotope effects in camphor hydroxylation by the cytochrome P450cam monoxygenase system.

    abstract::Bacterial cytochrome P450cam catalyzes the hydroxylation of camphor to yield 5-exo-hydroxycamphor in vivo and in a reconstituted system with oxygen, pyridine nucleotide, flavoprotein dehydrogenase, and putidaredoxin. Product is also formed when the ferric form of the hemoprotein is mixed with the exogenous oxidants io...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00531a026

    authors: Gelb MH,Heimbrook DC,Mälkönen P,Sligar SG

    更新日期:1982-01-19 00:00:00

  • Spin-label detection of hemoglobin-membrane interaction at physiological pH.

    abstract::The interaction between hemoglobin and the cytoplasmic surface of human erythrocyte membranes at physiological pH was studied by monitoring the electron paramagnetic resonance (EPR) signal of spin-labeled membrane ghosts in hemoglobin solutions of various concentrations. The EPR spectra indicate the existence of a sig...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00528a017

    authors: Fung LW

    更新日期:1981-12-08 00:00:00

  • Functional groups at the catalytic site of BF1 adenosinetriphosphatase from Escherichia coli.

    abstract::The rates of inactivation of BF1 adenosinetriphosphatase (BF1-ATPase) from Escherichia coli by 7-chloro-4-nitro-2,1,3-benzoxadiazole, 1-fluoro-2,4-dinitrobenzene, 2,4,6-trinitrobenzenesulfonate, phenylglyoxal, and N,N'-dicyclohexylcarbodiimide have been measured in the presence and absence of various concentrations of...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00531a011

    authors: Ting LP,Wang JH

    更新日期:1982-01-19 00:00:00

  • Orientation and motion of spin-labels in rabbit small intestinal brush border vesicle membranes.

    abstract::The temperature dependence of the packing (order) and fluidity (microviscosity) of rabbit small, intestinal brush border vesicle membranes and of liposomes made from their extracted lipids has been investigated by using a variety of lipid spin probes. The lipids in the brush border membrane are present essentially as ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00265a036

    authors: Hauser H,Gains N,Semenza G,Spiess M

    更新日期:1982-10-26 00:00:00

  • Ethanol-perturbed amyloidogenic self-assembly of insulin: looking for origins of amyloid strains.

    abstract::A model cosolvent, ethanol, has profound and diversified effects on the amyloidogenic self-assembly of insulin, yielding spectroscopically and morphologically distinguishable forms of beta-aggregates. The alcohol reduces hydrodynamic radii of insulin molecules, decreases enthalpic costs associated with aggregation-pro...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi050281t

    authors: Dzwolak W,Grudzielanek S,Smirnovas V,Ravindra R,Nicolini C,Jansen R,Loksztejn A,Porowski S,Winter R

    更新日期:2005-06-28 00:00:00

  • Oxy intermediates of homoprotocatechuate 2,3-dioxygenase: facile electron transfer between substrates.

    abstract::Substrates homoprotocatechuate (HPCA) and O(2) bind to the Fe(II) of homoprotocatechuate 2,3-dioxygenase (FeHPCD) in adjacent coordination sites. Transfer of an electron(s) from HPCA to O(2) via the iron is proposed to activate the substrates for reaction with each other to initiate aromatic ring cleavage. Here, rapid...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi201436n

    authors: Mbughuni MM,Chakrabarti M,Hayden JA,Meier KK,Dalluge JJ,Hendrich MP,Münck E,Lipscomb JD

    更新日期:2011-11-29 00:00:00

  • Acidic residues involved in cation and substrate interactions in the Na+/dicarboxylate cotransporter, NaDC-1.

    abstract::The role of acidic amino acid residues in cation recognition and selectivity by the Na+/dicarboxylate cotransporter, NaDC-1, was investigated by site-directed mutagenesis and expression in Xenopus oocytes. Four of the residues tested, Asp-52, Glu-74, Glu-101, and Glu-332, were found to be unimportant for transport act...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi990076b

    authors: Griffith DA,Pajor AM

    更新日期:1999-06-08 00:00:00

  • Organization of the human protein S genes.

    abstract::Human genomic clones that span the entire protein S expressed gene (PS alpha) and the 3' two-thirds of the protein S pseudogene (PS beta) have been isolated and characterized. The PS alpha gene is greater than 80 kilobases in length and contains 14 introns and 15 exons, as well as 6 repetitive "Alu" sequences. Exons I...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00486a010

    authors: Schmidel DK,Tatro AV,Phelps LG,Tomczak JA,Long GL

    更新日期:1990-08-28 00:00:00

  • Diepoxybutane cross-links DNA at 5'-GNC sequences.

    abstract::Epoxides are cancer-causing agents chemically analogous to the nitrogen mustards, a family of powerful antitumor drugs. We found that the DNA interstrand cross-linking sequence preference of diepoxybutane is the same as that of the mustard mechlorethamine: 5'-GNC. Therefore, the genomic site of cross-linking alone can...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00059a034

    authors: Millard JT,White MM

    更新日期:1993-03-02 00:00:00

  • Primary structure of Escherichia coli ribosomal protein L31.

    abstract::Protein L31 from the 50S ribosomal subunit of Escherichia coli was manually sequenced by the dansyl-Edman method. Owing to the availability of only small quantities of purified L31, sequencing methods were scaled down such that the entire primary structure could be determined with 700 microgram of protein. The techniq...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00596a020

    authors: Brosius J

    更新日期:1978-02-07 00:00:00

  • Comparison of N-glycosides of fetuins from different species and human alpha 2-HS-glycoprotein.

    abstract::Complex type N-glycosides of commercial bovine fetuin preparations from pooled fetal calf serum have been shown to contain comparable amounts of Gal4,4,4TRI (see structure A below) and Gal4,4,3TRI (structure B) as major asialo-structures. To investigate whether there is a clear genetic specificity for synthesis of the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00135a024

    authors: Hayase T,Rice KG,Dziegielewska KM,Kuhlenschmidt M,Reilly T,Lee YC

    更新日期:1992-05-26 00:00:00

  • Dynamics and binding mode of Hoechst 33258 to d(GTGGAATTCCAC)2 in the 1:1 solution complex as determined by two-dimensional 1H NMR.

    abstract::We have investigated the interaction of the bisbenzimidazole derivative Hoechst 33258 with the self-complementary dodecadeoxynucleotide duplex d(GTGGAATTCCAC)2 using one-dimensional (1D) and two-dimensional (2D) proton nuclear magnetic resonance (1H NMR) spectroscopy. To monitor the extent of complex formation, we use...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00112a004

    authors: Fede A,Labhardt A,Bannwarth W,Leupin W

    更新日期:1991-12-03 00:00:00

  • Affinity labeling of the active site and the reactive sulfhydryl associated with activation of rat liver phenylalanine hydroxylase.

    abstract::A pterin analogue, 5-[(3-azido-6-nitrobenzylidene)amino]-2,6-diamino-4-pyrimidinone (ANBADP), was synthesized as a probe of the pterin binding site of phenylalanine hydroxylase. The photoaffinity label has been found to be a competitive inhibitor of the enzyme with respect to 6,7-dimethyltetrahydropterin, having a Ki ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00241a024

    authors: Gibbs BS,Benkovic SJ

    更新日期:1991-07-09 00:00:00

  • Manganese(II)-dependent extradiol-cleaving catechol dioxygenase from Arthrobacter globiformis CM-2.

    abstract::A manganese-dependent 3,4-dihydroxyphenylactate 2,3-dioxygenase from Arthrobacter globiformis strain CM-2 (MndD) cloned in Escherichia coli has been purified to homogeneity. Sedimentation equilibrium analysis indicates an alpha 4 homotetrameric holoenzyme structure (4 x 38,861 Da). Steady-state kinetic analysis of Mnd...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi951979h

    authors: Whiting AK,Boldt YR,Hendrich MP,Wackett LP,Que L Jr

    更新日期:1996-01-09 00:00:00

  • Cofactor Complexes of DesD, a Model Enzyme in the Virulence-related NIS Synthetase Family.

    abstract::The understudied nonribosomal-peptide-synthetase-independent siderophore (NIS) synthetase family has been increasingly associated with virulence in bacterial species due to its key role in the synthesis of hydroxamate and carboxylate "stealth" siderophores. We have identified a model family member, DesD, from Streptom...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.9b00899

    authors: Hoffmann KM,Goncuian ES,Karimi KL,Amendola CR,Mojab Y,Wood KM,Prussia GA,Nix J,Yamamoto M,Lathan K,Orion IW

    更新日期:2020-09-22 00:00:00

  • Characterization of recombinant human erythropoietin produced in Chinese hamster ovary cells.

    abstract::Physicochemical properties of recombinant human erythropoietin were examined. This protein, produced in Chinese hamster ovary cells, showed a conformation apparently identical with the natural product isolated from human urine when examined by circular dichroism, UV absorbance, and fluorescence spectroscopy. Sedimenta...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00383a034

    authors: Davis JM,Arakawa T,Strickland TW,Yphantis DA

    更新日期:1987-05-05 00:00:00

  • Mechanism of autophosphorylation of mycobacterial PknB explored by molecular dynamics simulations.

    abstract::Mycobacterial Ser/Thr kinase, PknB, is essential for the growth of the pathogen. Unphosphorylated PknB is catalytically inactive, and its activation requires autophosphorylation of Thr residues on the activation loop. Autophosphorylation can in principle take place via two distinct mechanisms. Intermolecular trans aut...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi500245v

    authors: Damle NP,Mohanty D

    更新日期:2014-07-22 00:00:00

  • Calmodulin-dependent protein phosphatase: a developmental study.

    abstract::Calmodulin-dependent protein phosphatase, one of the major calmodulin-binding proteins in bovine brain, dephosphorylates casein with a specific activity of 15 nmol mg-1 min-1 at 30 degrees C. The stimulation of phosphatase activity by calmodulin is reversed by ethylene glycol bis (beta-aminoethyl ether)-N,N,N',N'-tetr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00284a014

    authors: Tallant EA,Cheung WY

    更新日期:1983-07-19 00:00:00

  • Membrane binding kinetics of protein kinase C betaII mediated by the C2 domain.

    abstract::Conventional isoforms of protein kinase C (PKC) are activated when their two membrane-targeting modules, the C1 and C2 domains, bind the second messengers diacylglycerol (DG) and Ca2+, respectively. This study investigates the mechanism of Ca2+-induced binding of PKC betaII to anionic membranes mediated by the C2 doma...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi010761u

    authors: Nalefski EA,Newton AC

    更新日期:2001-11-06 00:00:00

  • Iron-sulfur cluster biosynthesis: functional characterization of the N- and C-terminal domains of human NFU.

    abstract::Human NFU (also known as HIRIP5) has been implicated in cellular iron-sulfur cluster biosynthesis. Bacterial and yeast forms are smaller than the human protein and are homologous to the C-terminal domain of the latter. This C-terminal domain contains a pair of redox active cysteines and demonstrates thioredoxin-like a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801645z

    authors: Liu Y,Qi W,Cowan JA

    更新日期:2009-02-10 00:00:00