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1.
Osteoporos Int ; 32(11): 2185-2192, 2021 Nov.
Article in English | MEDLINE | ID: mdl-34013459

ABSTRACT

This study examines the association between the ASA physical status classification score at hip fracture surgery and severe postoperative complications in patients aged 60 and older. Among both men and women, ASA scores consistently predict a wide range of complications including infections, cardiovascular complications, hospital readmissions, and death. INTRODUCTION: Hip fractures are common in aging populations and associated with poor prognosis. This study examines how the American Society of Anaesthesiologists (ASA) physical status classification is related to severe complications among hip fracture patients including infections, cardiovascular diseases, hospital readmissions, and death. METHODS: Based on a linkage of the Swedish National Inpatient Register with the Swedish National Registry for Hip Fractures (RIKSHÖFT), this study includes patients aged 60+ with first hip fracture between 1998 and 2017. We estimated associations between ASA score and complications during the hospital stay and during 1 year after hip fracture using multivariable-adjusted logistic regression and Cox proportional hazard regression. RESULTS: The study population included 170,193 hip fracture patients of which 24% died and 39% were readmitted to hospital within 1 year. The most common complications were urinary tract infections, pneumonia, second hip fractures, and heart failure. Among both men and women, higher ASA scores were consistently associated with higher risks for all complications included in this study. The strongest associations were observed for heart failure, myocardial infarction, pneumonia, and death. CONCLUSION: ASA scores are routinely assessed in clinical practice and predict a wide range of postoperative complications among hip fracture patients. Since many complications may be preventable through adequate drug treatment, rehabilitation, and risk awareness, future studies should examine the mechanisms linking ASA scores to complication risk in order to improve preventive strategies. Particularly, the high risk of cardiovascular complications among patients with high ASA scores deserves clinical and scientific attention.


Subject(s)
Cardiovascular Infections , Hip Fractures , Aged , Cohort Studies , Female , Hip Fractures/epidemiology , Hip Fractures/surgery , Humans , Male , Middle Aged , Patient Readmission , Postoperative Complications/epidemiology , Postoperative Complications/etiology , Retrospective Studies , Risk Factors
2.
Psychol Med ; 46(12): 2595-604, 2016 09.
Article in English | MEDLINE | ID: mdl-27353452

ABSTRACT

BACKGROUND: Many adults with autism spectrum disorder (ASD) remain undiagnosed. Specialist assessment clinics enable the detection of these cases, but such services are often overstretched. It has been proposed that unnecessary referrals to these services could be reduced by prioritizing individuals who score highly on the Autism-Spectrum Quotient (AQ), a self-report questionnaire measure of autistic traits. However, the ability of the AQ to predict who will go on to receive a diagnosis of ASD in adults is unclear. METHOD: We studied 476 adults, seen consecutively at a national ASD diagnostic referral service for suspected ASD. We tested AQ scores as predictors of ASD diagnosis made by expert clinicians according to International Classification of Diseases (ICD)-10 criteria, informed by the Autism Diagnostic Observation Schedule-Generic (ADOS-G) and Autism Diagnostic Interview-Revised (ADI-R) assessments. RESULTS: Of the participants, 73% received a clinical diagnosis of ASD. Self-report AQ scores did not significantly predict receipt of a diagnosis. While AQ scores provided high sensitivity of 0.77 [95% confidence interval (CI) 0.72-0.82] and positive predictive value of 0.76 (95% CI 0.70-0.80), the specificity of 0.29 (95% CI 0.20-0.38) and negative predictive value of 0.36 (95% CI 0.22-0.40) were low. Thus, 64% of those who scored below the AQ cut-off were 'false negatives' who did in fact have ASD. Co-morbidity data revealed that generalized anxiety disorder may 'mimic' ASD and inflate AQ scores, leading to false positives. CONCLUSIONS: The AQ's utility for screening referrals was limited in this sample. Recommendations supporting the AQ's role in the assessment of adult ASD, e.g. UK NICE guidelines, may need to be reconsidered.


Subject(s)
Autism Spectrum Disorder/diagnosis , Psychiatric Status Rating Scales/standards , Self Report/standards , Surveys and Questionnaires/standards , Adult , Autism Spectrum Disorder/epidemiology , Comorbidity , Female , Humans , Male , Predictive Value of Tests , Sensitivity and Specificity , Young Adult
3.
Science ; 287(5453): 655-8, 2000 Jan 28.
Article in English | MEDLINE | ID: mdl-10649999

ABSTRACT

Light generates reducing equivalents in chloroplasts that are used not only for carbon reduction, but also for the regulation of the activity of chloroplast enzymes by reduction of regulatory disulfides via the ferredoxin:thioredoxin reductase (FTR) system. FTR, the key electron/thiol transducer enzyme in this pathway, is unique in that it can reduce disulfides by an iron-sulfur cluster, a property that is explained by the tight contact of its active-site disulfide and the iron-sulfur center. The thin, flat FTR molecule makes the two-electron reduction possible by forming on one side a mixed disulfide with thioredoxin and by providing on the opposite side access to ferredoxin for delivering electrons.


Subject(s)
Chloroplasts/metabolism , Cyanobacteria/enzymology , Disulfides/metabolism , Oxidoreductases/chemistry , Oxidoreductases/metabolism , Amino Acid Motifs , Catalytic Domain , Crystallography, X-Ray , Cysteine/chemistry , Dimerization , Disulfides/chemistry , Electron Transport , Ferredoxins/metabolism , Hydrogen Bonding , Iron/chemistry , Iron-Sulfur Proteins , Models, Molecular , Oxidation-Reduction , Protein Structure, Secondary , Signal Transduction , Thioredoxins/metabolism
4.
Cell Mol Life Sci ; 65(24): 3907-17, 2008 Dec.
Article in English | MEDLINE | ID: mdl-19011749

ABSTRACT

In this report we describe the main features of the initially determined alcohol dehydrogenase, that of horse liver, relate this to the human enzyme structures and review recent structural studies on mutants and new complexes of the enzymes. We further review the structure of a bacterial alcohol dehydrogenase to arrive at a coherent picture of medium-chain dehydrogenase/reductase alcohol dehydrogenases in general.


Subject(s)
Alcohol Dehydrogenase/chemistry , Multigene Family , Alcohol Dehydrogenase/metabolism , Animals , Bacteria/enzymology , Catalysis , Humans , Protein Multimerization , Substrate Specificity
5.
Curr Opin Struct Biol ; 5(6): 758-66, 1995 Dec.
Article in English | MEDLINE | ID: mdl-8749363

ABSTRACT

Di-iron centers bridged by carboxylate residues and oxide/hydroxide groups have so far been seen in four classes of proteins involved in dioxygen chemistry or phosphoryl transfer reactions. The dinuclear iron centers in these proteins are coordinated by histidines and additional carboxylate ligands. Recent structural data on some of these enzymes, combined with spectroscopic and kinetic data, can now serve as a base for detailed mechanistic suggestions. The di-iron sites in the major class of hydroxylase-oxidase enzymes, which contains ribonucleotide reductase and methane monooxygenase, show significant flexibility in the geometry of their coordination of three or more carboxylate groups. This flexibility, combined with a relatively low coordination number, and a buried environment suitable for reactive oxygen chemistry, explains their efficient harnessing of the oxidation power of molecular oxygen.


Subject(s)
Bacterial Proteins/chemistry , Nonheme Iron Proteins/chemistry , Oxygenases/chemistry , Ribonucleotide Reductases/chemistry , Acid Phosphatase/chemistry , Acid Phosphatase/metabolism , Bacterial Proteins/metabolism , Cytochrome b Group/chemistry , Ferredoxins/chemistry , Ferredoxins/metabolism , Ferritins/chemistry , Glycoproteins/chemistry , Glycoproteins/metabolism , Hemerythrin , Iron/chemistry , Iron/metabolism , Nonheme Iron Proteins/metabolism , Oxygen/metabolism , Oxygenases/metabolism , Phosphoric Monoester Hydrolases/chemistry , Phosphoric Monoester Hydrolases/metabolism , Protein Conformation , Protein Structure, Secondary , Ribonucleotide Reductases/metabolism , Rubredoxins
6.
Structure ; 3(11): 1127-9, 1995 Nov 15.
Article in English | MEDLINE | ID: mdl-8591022

ABSTRACT

The first three-dimensional structure of copper amine oxidase demonstrates that one tyrosine residue is converted into 2,4,5-trihydroxyphenylalanine quinone (TPQ). TPQ binds to copper in the inactive form of the enzyme but not in the active form.


Subject(s)
Amine Oxidase (Copper-Containing)/chemistry , Bacterial Proteins/chemistry , Dihydroxyphenylalanine/analogs & derivatives , Protein Conformation , Tyrosine/chemistry , Amine Oxidase (Copper-Containing)/antagonists & inhibitors , Bacterial Proteins/antagonists & inhibitors , Binding Sites , Catalysis , Dihydroxyphenylalanine/chemistry , Escherichia coli/enzymology , Models, Chemical , Oxidation-Reduction , Quaternary Ammonium Compounds/pharmacology
7.
Structure ; 7(11): R257-62, 1999 Nov 15.
Article in English | MEDLINE | ID: mdl-10574800

ABSTRACT

The first structures of glycyl radical enzymes, the anaerobic ribonucleotide reductase from bacteriophage T4 and pyruvate formate lyase from Escherichia coli, have been recently determined. This work provides new insights into the structure and chemistry of glycyl radical sites.


Subject(s)
Acetyltransferases/chemistry , Glycine/chemistry , Ribonucleotide Reductases/chemistry , Free Radicals , Protein Conformation
8.
Structure ; 3(10): 1097-108, 1995 Oct 15.
Article in English | MEDLINE | ID: mdl-8590004

ABSTRACT

BACKGROUND: Thioredoxins are ubiquitous proteins that serve as reducing agents and general protein disulfide reductases. The structures of thioredoxins from a number of species, including man and Escherichia coli, are known. Cyanobacteria, such as Anabaena, contain two thioredoxins that exhibit very different activities with target enzymes and share little sequence similarity. Thioredoxin-2 (Trx-2) from Anabaena resembles chloroplast type-f thioredoxin in its activities and the two proteins may be evolutionarily related. We have undertaken structural studies of Trx-2 in order to gain insights into the structure/function relationships of thioredoxins. RESULTS: Anabaena Trx-2, like E. coli thioredoxin, consists of a five-stranded beta sheet core surrounded by four alpha helices. The active site includes a conserved disulfide ring (in the sequence 31WCGPC35). An aspartate (E. coli) to tyrosine (Trx-2) substitution alters the position of this disulfide ring relative to the central pleated sheet. However, loss of this conserved aspartate does not affect the disulfide geometry. In the Trx-2 crystals, the N-terminal residues make extensive contacts with a symmetry-related molecule with hydrogen bonds to residues 74-76 mimicking thioredoxin-protein interactions. CONCLUSIONS: The overall three-dimensional structure of Trx-2 is similar to E. coli thioredoxin and other related disulfide oxido-reductases. Single amino acid substitutions around the protein interaction area probably account for the unusual enzymatic activities of Trx-2 and its ability to discriminate between substrate and non-substrate peptides.


Subject(s)
Anabaena/chemistry , Thioredoxins/chemistry , Thioredoxins/metabolism , Amino Acid Sequence , Binding Sites , Chloroplasts/chemistry , Crystallography, X-Ray , Enzyme Stability , Escherichia coli/chemistry , Evolution, Molecular , Models, Molecular , Molecular Sequence Data , Plant Proteins/chemistry , Protein Conformation , Proteins/metabolism , Spinacia oleracea/chemistry
9.
Structure ; 4(9): 1053-64, 1996 Sep 15.
Article in English | MEDLINE | ID: mdl-8805591

ABSTRACT

BACKGROUND: Ribonucleotide reductases (RNRs) catalyze the formation of the deoxyribonucleotides that are essential for DNA synthesis. The R2 subunit of Escherichia coli RNR is a homodimer containing one dinuclear iron centre per monomer. A tyrosyl radical is essential for catalysis, and is formed via a reaction in which the reduced, diferrous form of the iron centre activates dioxygen. To help understand the mechanism of oxygen activation, we examined the structure of the diferrous form of R2. RESULTS: The crystal structures of reduced forms of both wild type R2 and a mutant of R2 (Ser211--> Ala) have been determined at 1.7 A and 2.2 A resolution, respectively. The diferrous iron centre was compared to the previously determined structure of the oxidized, diferric form of R2. In both forms of R2 the iron centre is coordinated by the same carboxylate dominated ligand sphere, but in the reduced form there are clear conformational changes in three of the carboxylate ligands and the bridging mu-oxo group and two water molecules are lost. In the reduced form of R2 the coordination number decreases from six to four for both ferrous ions, explaining their high reactivity towards dioxygen. The structure of the mutant Ser211--> Ala, known to have impaired reduction kinetics, shows a large conformational change in one of the neighbouring helices although the iron coordination is very similar to the wild type protein. CONCLUSIONS: Carboxylate shifts are often important for carboxylate coordinated metal clusters; they allow the metals to achieve different coordination modes in redox reactions. In the case of reduced R2 these carboxylate shifts allow the formation of accessible reaction sites for dioxygen. The Ser211--> Ala mutant displays a conformational change in the helix containing the mutation, explaining its altered reduction kinetics.


Subject(s)
Iron/metabolism , Oxygen/metabolism , Ribonucleotide Reductases/chemistry , Carboxylic Acids/chemistry , Crystallography, X-Ray , Kinetics , Molecular Sequence Data , Mutagenesis, Site-Directed , Oxidation-Reduction , Ribonucleotide Reductases/genetics , Ribonucleotide Reductases/metabolism
10.
Structure ; 6(5): 571-86, 1998 May 15.
Article in English | MEDLINE | ID: mdl-9634695

ABSTRACT

BACKGROUND: Pseudomonas sp. NCIB 9816-4 utilizes a multicomponent enzyme system to oxidize naphthalene to (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. The enzyme component catalyzing this reaction, naphthalene 1,2-dioxygenase (NDO), belongs to a family of aromatic-ring-hydroxylating dioxygenases that oxidize aromatic hydrocarbons and related compounds to cis-arene diols. These enzymes utilize a mononuclear non-heme iron center to catalyze the addition of dioxygen to their respective substrates. The present study was conducted to provide essential structural information necessary for elucidating the mechanism of action of NDO. RESULTS: The three-dimensional structure of NDO has been determined at 2.25 A resolution. The molecule is an alpha 3 beta 3 hexamer. The alpha subunit has a beta-sheet domain that contains a Rieske [2Fe-2S] center and a catalytic domain that has a novel fold dominated by an antiparallel nine-stranded beta-pleated sheet against which helices pack. The active site contains a non-heme ferrous ion coordinated by His208, His213, Asp362 (bidentate) and a water molecule. Asn201 is positioned further away, 3.75 A, at the missing axial position of an octahedron. In the Rieske [2Fe-2S] center, one iron is coordinated by Cys81 and Cys101 and the other by His83 and His104. CONCLUSIONS: The domain structure and iron coordination of the Rieske domain is very similar to that of the cytochrome bc1 domain. The active-site iron center of one of the alpha subunits is directly connected by hydrogen bonds through a single amino acid, Asp205, to the Rieske [2Fe-2S] center in a neighboring alpha subunit. This is likely to be the main route for electron transfer.


Subject(s)
Bacterial Proteins/chemistry , Iron-Sulfur Proteins/chemistry , Multienzyme Complexes/chemistry , Oxygenases/chemistry , Amino Acid Sequence , Bacterial Proteins/metabolism , Binding Sites , Crystallography , Dioxygenases , Electron Transport , Electron Transport Complex III/chemistry , Ferredoxins/metabolism , Hydroxylation , Iron-Sulfur Proteins/metabolism , Models, Molecular , Molecular Sequence Data , Multienzyme Complexes/metabolism , Naphthalenes/metabolism , Oxygenases/metabolism , Protein Conformation , Pseudomonas/enzymology
11.
Structure ; 5(8): 1077-92, 1997 Aug 15.
Article in English | MEDLINE | ID: mdl-9309223

ABSTRACT

BACKGROUND: Ribonucleotide reductase (RNR) is an essential enzyme in DNA synthesis, catalyzing all de novo synthesis of deoxyribonucleotides. The enzyme comprises two dimers, termed R1 and R2, and contains the redox active cysteine residues, Cys462 and Cys225. The reduction of ribonucleotides to deoxyribonucleotides involves the transfer of free radicals. The pathway for the radical has previously been suggested from crystallographic results, and is supported by site-directed mutagenesis studies. Most RNRs are allosterically regulated through two different nucleotide-binding sites: one site controls general activity and the other controls substrate specificity. Our aim has been to crystallographically demonstrate substrate binding and to locate the two effector-binding sites. RESULTS: We report here the first crystal structure of RNR R1 in a reduced form. The structure shows that upon reduction of the redox active cysteines, the sulfur atom of Cys462 becomes deeply buried. The more accessible Cys225 moves to the former position of Cys462 making room for the substrate. In addition, the structures of R1 in complexes with effector, effector analog and effector plus substrate provide information about these binding sites. The substrate GDP binds in a cleft between two domains with its beta-phosphate bound to the N termini of two helices; the ribose forms hydrogen bonds to conserved residues. Binding of dTTP at the allosteric substrate specificity site stabilizes three loops close to the dimer interface and the active site, whereas the general allosteric binding site is positioned far from the active site. CONCLUSIONS: Binding of substrate at the active site of the enzyme is structurally regulated in two ways: binding of the correct substrate is regulated by the binding of allosteric effectors and binding of the actual substrate occurs primarily when the active-site cysteines are reduced. One of the loops stabilized upon binding of dTTP participates in the formation of the substrate-binding site through direct interaction with the nucleotide base. The general allosteric effector site, located far from the active site, appears to regulate subunit interactions within the holoenzyme.


Subject(s)
Cysteine/chemistry , Ribonucleotide Reductases/chemistry , Allosteric Regulation , Amino Acid Sequence , Binding Sites , Conserved Sequence/genetics , Crystallography, X-Ray , Dimerization , Guanosine Diphosphate/chemistry , Models, Chemical , Models, Molecular , Molecular Sequence Data , Oxidation-Reduction , Sequence Alignment , Substrate Specificity , Thymine Nucleotides/chemistry
12.
Eur Psychiatry ; 35: 47-54, 2016 05.
Article in English | MEDLINE | ID: mdl-27077377

ABSTRACT

BACKGROUND: ADHD in childhood is associated with development of negative psychosocial and behavioural outcomes in adults. Yet, relatively little is known about which childhood and adulthood factors are predictive of these outcomes and could be targets for effective interventions. To date follow-up studies have largely used clinical samples from the United States with children ascertained at baseline using broad criteria for ADHD including all clinical subtypes or the use of DSM III criteria. AIMS: To identify child and adult predictors of comorbid and psychosocial comorbid outcomes in ADHD in a UK sample of children with DSM-IV combined type ADHD. METHOD: One hundred and eighteen adolescents and young adults diagnosed with DSM-IV combined type ADHD in childhood were followed for an average of 6years. Comorbid mental health problems, drug and alcohol use and police contact were compared for those with persistent ADHD, sub-threshold ADHD and population norms taken from the Adult Psychiatric Morbidity Study 2007. Predictors included ADHD symptomology and gender. RESULTS: Persistent ADHD was associated with greater levels of anger, fatigue, sleep problems and anxiety compared to sub-threshold ADHD. Comorbid mental health problems were predicted by current symptoms of hyperactivity-impulsivity, but not by childhood ADHD severity. Both persistent and sub-threshold ADHD was associated with higher levels of drug use and police contact compared to population norms. CONCLUSIONS: Young adults with a childhood diagnosis of ADHD showed increased rates of comorbid mental health problems, which were predicted by current levels of ADHD symptoms. This suggests the importance of the continuing treatment of ADHD throughout the transitional years and into adulthood. Drug use and police contact were more common in ADHD but were not predicted by ADHD severity in this sample.


Subject(s)
Attention Deficit Disorder with Hyperactivity/epidemiology , Health Status , Mental Health , Adolescent , Anxiety Disorders/epidemiology , Attention Deficit Disorder with Hyperactivity/psychology , Child , Comorbidity , Depression/epidemiology , Diagnostic and Statistical Manual of Mental Disorders , Female , Follow-Up Studies , Humans , Impulsive Behavior , Male , Quality of Life , Substance-Related Disorders/epidemiology , Young Adult
13.
Prog Biophys Mol Biol ; 77(3): 177-268, 2001 Nov.
Article in English | MEDLINE | ID: mdl-11796141

ABSTRACT

Ribonucleotide reductases (RNRs) catalyze all new production in nature of deoxyribonucleotides for DNA synthesis by reducing the corresponding ribonucleotides. The reaction involves the action of a radical that is produced differently for different classes of the enzyme. Class I enzymes, which are present in eukaryotes and microorganisms, use an iron center to produce a stable tyrosyl radical that is stored in one of the subunits of the enzyme. The other classes are only present in microorganisms. Class II enzymes use cobalamin for radical generation and class III enzymes, which are found only in anaerobic organisms, use a glycyl radical. The reductase activity is in all three classes contained in enzyme subunits that have similar structures containing active site cysteines. The initiation of the reaction by removal of the 3'-hydrogen of the ribose by a transient cysteinyl radical is a common feature of the different classes of RNR. This cysteine is in all RNRs located on the tip of a finger loop inserted into the center of a special barrel structure. A wealth of structural and functional information on the class I and class III enzymes can now give detailed views on how these enzymes perform their task. The class I enzymes demonstrate a sophisticated pattern as to how the free radical is used in the reaction, in that it is only delivered to the active site at exactly the right moment. RNRs are also allosterically regulated, for which the structural molecular background is now starting to be revealed.


Subject(s)
Ribonucleotide Reductases/chemistry , Ribonucleotide Reductases/metabolism , Allosteric Regulation , Amino Acid Sequence , Animals , Binding Sites , Catalysis , Drug Design , Humans , Iron/metabolism , Molecular Sequence Data , Oxidation-Reduction , Protein Conformation , Ribonucleotide Reductases/antagonists & inhibitors , Ribonucleotide Reductases/classification
14.
J Mol Biol ; 232(1): 123-64, 1993 Jul 05.
Article in English | MEDLINE | ID: mdl-8331655

ABSTRACT

The crystal structure of the ribonucleotide reductase free radical protein R2 from Escherichia coli has been determined by multiple isomorphous replacement and twofold molecular averaging. The structure has been refined at 2.2 A resolution to R = 0.175. The subunit structure of the R2 protein has a novel fold where the basic motif is a bundle of eight long helices. The R2 dimer has two equivalent dinuclear iron centers. Each iron center is well buried in the subunit. The iron atoms have both histidine and carboxyl acid ligands and are bridged by an oxide ion and the carboxylate group of Glu115. One iron atom is octahedrally coordinated with small deviations from ideal values, while the coordination of the other iron ion is more distorted, mainly due to the fact that Asp84 is a bidental ligand to this iron atom. The oxidation of the enzymatically essential tyrosine residue (Tyr122) and the dinuclear iron center by molecular oxygen is suggested to take part in a suitable conserved oxygen-binding pocket between the iron center and the tyrosine zeta-oxygen 5.3 A away from the closest iron ion. The tyrosine proton can be abstracted by the dioxygen and the deprotonated tyrosine residue is then more easily oxidized to a radical species. Tyr122 is buried inside the protein about 10 A from the surface. This has the consequence that the tyrosyl radical cannot participate directly in hydrogen abstraction from the substrate ribose at the active site of the holoenzyme located on the R1 subunit. The radical must then be indirectly involved in the mechanism of the enzyme and an electron transfer reaction between the active site and the tyrosine must take place. Based on the analysis of the available ribonucleotide reductase sequences, the binding surface for the large ribonucleotide reductase protein R1, and a possible route for an electron transport between the buried radical and this surface is described.


Subject(s)
Escherichia coli/enzymology , Ribonucleotide Reductases/metabolism , Amino Acid Sequence , Animals , Consensus Sequence , Crystallography , Cytochrome P-450 Enzyme System/chemistry , Free Radicals , Hemerythrin/analogs & derivatives , Hemerythrin/chemistry , Humans , Hydrogen Bonding , Iron/chemistry , Mercury , Mice , Models, Molecular , Molecular Sequence Data , Protein Structure, Secondary , Protein Structure, Tertiary , Sequence Alignment , Structure-Activity Relationship , Water , X-Ray Diffraction
15.
J Mol Biol ; 262(3): 358-69, 1996 Sep 27.
Article in English | MEDLINE | ID: mdl-8845001

ABSTRACT

The large subunit of ribonucleotide reductase (RNR) contains a ten-stranded beta/alpha barrel of a new type consisting of two antiparallel halves. The two halves of the barrel are pseudo 2-fold-related, have similar folds but different additional intervening secondary structure elements and loops. The inner diameter of the RNR barrel, 15 A to 20 A, is significantly larger than for the (beta alpha)3 barrels. The larger barrel forms a stable framework which holds an inserted hairpin loop rigidly and exposes active site residues at its tip. The barrel organization allows three cysteine residues to be positioned close to each other without forming unfavorable disulfide bridges between Cys439 on the tip of the inserted loop and the redox-active cysteine residues on the barrel strands. Redox-active cysteine residues separated by more than 200 residues are held in close proximity to each other on adjacent barrel strands.


Subject(s)
Ribonucleotide Reductases/chemistry , Amino Acid Sequence , Binding Sites , Crystallography, X-Ray , Energy Transfer , Hydrogen Bonding , Models, Molecular , Molecular Sequence Data , Protein Conformation , Ribonucleotide Reductases/metabolism , Triose-Phosphate Isomerase/chemistry , Triose-Phosphate Isomerase/metabolism
16.
J Mol Biol ; 268(1): 147-57, 1997 Apr 25.
Article in English | MEDLINE | ID: mdl-9149148

ABSTRACT

Flavodoxin reductase from Escherichia coli is an FAD-containing oxidoreductase that transports electrons between flavodoxin or ferredoxin and NADPH. Together with flavodoxin, the enzyme is involved in the reductive activation of three E. coli enzymes: cobalamin-dependent methionine synthase, pyruvate formate lyase and anaerobic ribonucleotide reductase. An additional function for the oxidoreductase appears to be to protect the bacteria against oxygen radicals. The three-dimensional structure of flavodoxin reductase has been solved by multiple isomorphous replacement, and has been refined at 1.7 A to an R-value of 18.4% and Rfree 24.8%. The monomeric molecule contains one beta-sandwich FAD domain and an alpha/beta NADP domain. The overall structure is similar to other reductases of the NADP-ferredoxin reductase family in spite of the low sequence similarities within the family. Flavodoxin reductase lacks the loop which is involved in the binding of the adenosine moiety of FAD in other FAD binding enzymes of the superfamily but is missing in the FMN binding phthalate dioxygenase reductase. Instead of this loop, the adenine interacts with an extra tryptophan at the C terminus. The FAD in flavodoxin reductase has an unusual bent conformation with a hydrogen bond between the adenine and the isoalloxazine. This is probably the cause of the unusual spectrum of the enzyme. There is a pronounced cleft close to the isoalloxazine that appears to be well suited for binding of flavodoxin/ferredoxin. Two extra short strands of the NADP-binding domain probably act as an anchor point for the binding of flavodoxin.


Subject(s)
Escherichia coli/enzymology , Flavodoxin/metabolism , Oxidoreductases/chemistry , Oxidoreductases/metabolism , Adenosine/metabolism , Amino Acid Sequence , Binding Sites , Conserved Sequence , Crystallography, X-Ray , Ferredoxin-NADP Reductase/chemistry , Ferredoxin-NADP Reductase/metabolism , Flavodoxin/chemistry , Models, Molecular , Molecular Sequence Data , NADP/metabolism , Nitrate Reductase , Nitrate Reductases/chemistry , Nitrate Reductases/metabolism , Protein Conformation , Protein Folding , Protein Structure, Secondary , Sequence Homology, Amino Acid
17.
J Mol Biol ; 197(4): 685-94, 1987 Oct 20.
Article in English | MEDLINE | ID: mdl-3123698

ABSTRACT

The binding to liver alcohol dehydrogenase of the inhibitor 2,4-(4-pyrazolyl)-butylisothiourea has been studied both by modelling experiments using computer graphics with interactive energy minimization and by X-ray crystallographic structure determination. For the modelling experiments, we used the program system TOM, which was developed in our laboratory as an extension of the program FRODO. Different strategies for using computer graphics with interactive energy minimization were tested. Two essentially different binding modes were found. One of these was favoured from energy minimizations using a potential energy function which was the sum of a Coulomb interaction term and two different van der Waals' interaction terms for non-bonded and torsional interactions. This binding mode was close to the crystallographic observed structure. The results show that flexibility of both ligand and receptor side-chains as well as main-chain conformations are important for docking to the active site of liver alcohol dehydrogenase.


Subject(s)
Alcohol Dehydrogenase/antagonists & inhibitors , Computer Simulation , Models, Molecular , Pyrazoles/pharmacology , Thiourea/analogs & derivatives , Amino Acid Sequence , Binding Sites , Computer Graphics , Crystallography , Liver/enzymology , Thiourea/pharmacology
18.
J Mol Biol ; 212(1): 167-84, 1990 Mar 05.
Article in English | MEDLINE | ID: mdl-2181145

ABSTRACT

The crystal structure of thioredoxin from Escherichia coli has been refined by the stereochemically restrained least-squares procedure to a crystallographic R-factor of 0.165 at 1.68 A resolution. In the final model, the root-mean-square deviation from ideality for bond distances is 0.015 A and for angle distances 0.035 A. The structure contains 1644 protein atoms from two independent molecules, two Cu2+, 140 water molecules and seven methylpentanediol molecules. Ten residues have been modeled in two alternative conformations. E. coli thioredoxin is a compact molecule with 90% of its residues in helices, beta-strands or reverse turns. The molecule consists of two conformational domains, beta alpha beta alpha beta and beta beta alpha, connected by a single-turn alpha-helix and a 3(10) helix. The beta-sheet forms the core of the molecule packed on either side by clusters of hydrophobic residues. Helices form the external surface. The active site disulfide bridge between Cys32 and Cys35 is located at the amino terminus of the second alpha-helix. The positive electrostatic field due to the helical dipole is probably important for stabilizing the anionic intermediate during the disulfide reductase function of the protein. The more reactive cysteine, Cys32, has its sulfur atom exposed to solvent and also involved in a hydrogen bond with a backbone amide group. Residues 29 to 37, which include the active site cysteine residues, form a protrusion on the surface of the protein and make relatively fewer interactions with the rest of the structure. The disulfide bridge exhibits a right-handed conformation with a torsion angle of 81 degrees and 72 degrees about the S-S bond in the two molecules. Twenty-five pairs of water molecules obey the noncrystallographic symmetry. Most of them are involved in establishing intramolecular hydrogen-bonding interactions between protein atoms and thus serve as integral parts of the folded protein structure. Methylpentanediol molecules often pack against the loops and stabilize their structure. Cu2+ used for crystallization exhibit a distorted octahedral square bipyramid co-ordination and provide essential packing interactions in the crystal. The two independent protein molecules are very similar in conformation but distinctly different in atomic detail (root-mean-square = 0.94 A). The differences, which may be related to the crystal contacts, are localized mostly to regions far from the active site.


Subject(s)
Bacterial Proteins , Escherichia coli , Thioredoxins , Amino Acids , Binding Sites , Computer Graphics , Copper , Glycols , Hydrogen Bonding , Models, Molecular , Protein Conformation , Water , X-Ray Diffraction
19.
J Mol Biol ; 262(5): 706-20, 1996 Oct 11.
Article in English | MEDLINE | ID: mdl-8876648

ABSTRACT

The three-dimensional structure of mouse ribonucleotide reductase R2 has been determined at 2.3 A resolution using molecular replacement and refined to an R-value of 19.1% (Rfree = 25%) with good stereo-chemistry. The overall tertiary structure architecture of mouse R2 is similar to that from Escherichia coli R2. However, several important structural differences are observed. Unlike the E. coli protein, the mouse dimer is completely devoid of beta-strands. The sequences differ significantly between the mouse and E. coli R2s, but there is high sequence identity among the eukaryotic R2 proteins, and the identities are localized over the whole sequence. Therefore, the three-dimensional structures of other mammalian ribonucleotide reductase R2 proteins are expected to be very similar to that of the mouse enzyme. In mouse R2 a narrow hydrophobic channel leads to the proposed binding site for molecular oxygen near to the iron-radical site in the interior of the protein. In E. coli R2 this channel is blocked by the phenyl ring of a tyrosine residue, which in mouse R2 is a serine. These structural variations may explain the observed differences in sensitivity to radical scavengers. The structure determination is based on diffraction data from crystals grown at pH 4.7. Unexpectedly, the protein is not iron-free, but contains one iron ion bound at one of the dinuclear iron sites. This ferric ion is bound with partial occupancy and is coordinated by three glutamic acids (one bidentate) and one histidine in a bipyramidal coordination that has a free apical coordination position. Soaking of crystals in a solution of ferrous salt at pH 4.7 increased the occupancy on the already occupied site, but without any detectable binding at the second site.


Subject(s)
Bacterial Proteins/ultrastructure , Ribonucleotide Reductases/ultrastructure , Animals , Crystallography, X-Ray , Escherichia coli/chemistry , Free Radical Scavengers/chemistry , Hydroxyurea/chemistry , Iron/chemistry , Mice , Models, Molecular , Oxidation-Reduction , Protein Conformation , Protein Structure, Secondary , Ribonucleotide Reductases/chemistry , Sequence Alignment , Sequence Homology, Amino Acid , Tyrosine/chemistry
20.
J Mol Biol ; 264(5): 1044-57, 1996 Dec 20.
Article in English | MEDLINE | ID: mdl-9000629

ABSTRACT

Thioredoxin exists in all organisms and is responsible for the hydrogen transfer to important enzymes for ribonucleotide reduction and the reduction of methionine sulphoxide and sulphate. Thioredoxins have also been shown to regulate enzyme activity in plants and are also involved in the regulation of transcription factors and several other regulatory activities. Thioredoxin is reduced by the flavoenzyme thioredoxin reductase using NADPH. We have now determined the first structure of a eukaryotic thioredoxin reductase, from the plant Arabidopsis thaliana, at 2.5 A resolution. The dimeric A. thaliana thioredoxin reductase is structurally similar to that of the Escherichia coli enzyme, and most differences occur in the loops. Because the plant and E. coli enzymes have the same architecture, with the same dimeric structure and the same position of the redox active disulphide bond, a similar mechanism that involves very large domain rotations is likely for the two enzymes. The subunit is divided into two domains, one that binds FAD and one that binds NADPH. The relative positions of the domains in A. thaliana thioredoxin reductase differ from those of the E. coli reductase. When the FAD domains are superimposed, the NADPH domain of A. thaliana thioredoxin reductase must be rotated by 8 degrees to superimpose on the corresponding domain of the E. coli enzyme. The domain rotation we now observe is much smaller than necessary for the thioredoxin reduction cycle.


Subject(s)
Arabidopsis/enzymology , Thioredoxin-Disulfide Reductase/chemistry , Amino Acid Sequence , Arabidopsis/genetics , Binding Sites , Crystallography, X-Ray , Escherichia coli/enzymology , Escherichia coli/genetics , Flavin-Adenine Dinucleotide/metabolism , Models, Molecular , Molecular Sequence Data , Molecular Structure , NADP/metabolism , Protein Conformation , Sequence Homology, Amino Acid , Species Specificity , Thioredoxin-Disulfide Reductase/genetics , Thioredoxin-Disulfide Reductase/metabolism
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