Outcomes of complex abdominal wall reconstruction in patients with connective tissue disorders: a single center experience

INTRODUCTION

Individuals diagnosed with connective tissue disorders (CTD) are known to be predisposed to incisional hernia formation. However, there is a scarcity of data on outcomes for these patients undergoing hernia repair. We sought to describe our outcomes in performing abdominal wall reconstructions in these complex patients.

METHODS

Adult patients with CTD undergoing open, elective, posterior component separation with permanent synthetic mesh at our institution from January 2018 to October 2022 were queried from a prospectively collected database in the Abdominal Core Health Quality Collaborative. We evaluated 30-day wound morbidity, perioperative complications, long-term hernia recurrence, and patient-reported quality of life.

RESULTS

Twelve patients were identified. Connective tissue disorders included Marfan's n = 7 (58.3%), Loeys-Dietz syndrome n = 2 (16.7%), Systemic Lupus Erythematosus n = 2 (16.7%), and Scleroderma n = 1 (8.3%). Prior incisions included three midline laparotomies and nine thoracoabdominal, mean hernia width measured 14 cm, and 9 were recurrent hernias. Surgical site occurrences (SSOs) were observed in 25% of cases, and 16.7% necessitated procedural intervention. All twelve patients were available for long-term follow-up, with a mean of 34 (12-62) months. There were no instances of reoperation or mesh excision related to the TAR procedure. One patient developed a recurrence after having his mesh violated for repair of a new visceral aneurysm. Mean HerQLes scores at 1 year were 70 and 89 at ≥ 2 years; Mean scaled PROMIS scores were 30.7 at 1 year and 36.3 at ≥ 2 years.

CONCLUSION

Ventral hernia repair with TAR is feasible in patients with connective tissue disorder and can be a suitable alternative in patients with large complex hernias.

Association of active smoking on 30-day wound events and additional morbidity and mortality following inguinal hernia repair with mesh: an analysis of the ACHQC database

BACKGROUND

To date, there is limited data on the association of active smoking and 30-day wound events following inguinal hernia repair (IHR) with mesh. We aimed to determine if active smoking at the time of IHR with mesh was associated with worse 30-days wound events and additional morbidity outcomes using the Abdominal Core Health Quality Collaborative (ACHQC) database.

METHODS

All adult patients undergoing elective, IHR with mesh who had 30-day follow-up data available were identified within the ACHQC database. Smokers were defined as having used nicotine within the 30 days prior to surgery. A 1:1 propensity score matched analysis was performed comparing smokers to non-smokers, controlling for factors previously shown to be associated with postoperative wound events. The effect of smoking on 30-day wound events and additional morbidity outcomes following IHR with mesh was investigated using Chi-square or Fisher's exact test for categorical data and Wilcoxon ranked test for continuous data.

RESULTS

A total of 17,543 patients met inclusion criteria; 1855 (11%) were active smokers at the time of minimally invasive IHR with mesh. A total of 3694 patients were used for the matched analysis. There were no statistically significant differences between the non-smokers and smokers with respect to the incidence of surgical site infection (p = 0.10), surgical site occurrences (p = 0.22), or surgical site occurrences requiring procedural intervention (p = 0.64). Non-smokers were significantly more likely to be readmitted to the hospital and had significantly less improvement in all pain domains following IHR with mesh.

CONCLUSIONS

Active smoking at the time of IHR with mesh is not associated with worse 30-day wound or additional morbidity and mortality outcomes. Based on these results, preoperative smoking cessation for all patients undergoing IHR may not reduce 30-day morbidity.

Frequency of endoscopic surveillance for Barrett's esophagus is influenced by health insurance status: results from a population-based analysis

Factors that influence the frequency of surveillance endoscopy for nondysplastic Barrett's esophagus are not well understood. The objective of this study is to assess factors which influence the frequency of endoscopic surveillance for Barrett's esophagus, including health insurance/third-party payer status. Cases of nondysplastic Barrett's esophagus undergoing esophagogastroduodenoscopy with biopsy were identified using longitudinal data from the Healthcare Utilization Project database in 2005-2006 and followed through 2011. The threshold for appropriate surveillance utilization was defined as two to four surveillance esophagogastroduodenoscopies over a standardized 5-year period. Patients' insurance status was designated as either Medicare, Medicaid, private, or noninsured. 36,676 cases of nondysplastic Barrett's esophagus were identified. Among these, 4,632 patients (12.6%) underwent between two and four surveillance esophagogastroduodenoscopies in 5 years of follow-up versus 31,975 patients (87.3%) who underwent fewer than two esophagogastroduodenoscopies during follow-up. Multivariate analysis found that Barrett's patients insured through Medicaid (OR 1.273; 95% CI = 1.065-1.522) or without insurance (OR = 2.453; 95% CI = 1.67-3.603) were at increased likelihood of being under-surveilled. This study identified a difference in frequency of surveillance esophagogastroduodenoscopy for Barrett's esophagus by payer status. Patients without health insurance and those whose primary insurance was Medicaid were at increased odds for under-surveillance. These data suggest that a more robust system for tracking and ensuring longitudinal follow-up of patients with Barrett's esophagus, with attention to the uninsured and underinsured population, may be needed to ensure optimal surveillance.

Norepinephrine transporter expression is inversely associated with glycaemic indices: a pilot study in metabolically diverse persons with overweight and obesity

Objective

The objective of this study was to examine the cross‐sectional relationship between the expression of norepinephrine transporter (NET), the protein responsible for neuronal uptake‐1, and indices of glycaemia and hyperinsulinaemia, in overweight and obese individuals.

Methods

Thirteen non‐medicated, non‐smoking subjects, aged 58 ± 1 years (mean ± standard error of the mean), body mass index (BMI) 31.4 ± 1.0 kg m⁻², with wide‐ranging plasma glucose and haemoglobin A1c (HbA1c, range 5.1% to 6.5%) participated. They underwent forearm vein biopsy to access sympathetic nerves for the quantification of NET by Western blot, oral glucose tolerance test (OGTT), euglycaemic hyperinsulinaemic clamp, echocardiography and assessments of whole‐body norepinephrine kinetics and muscle sympathetic nerve activity.

Results

Norepinephrine transporter expression was inversely associated with fasting plasma glucose (r = −0.62, P = 0.02), glucose area under the curve during OGTT (AUC_0–120, r = −0.65, P = 0.02) and HbA1c (r = −0.67, P = 0.01), and positively associated with steady‐state glucose utilization during euglycaemic clamp (r = 0.58, P = 0.04). Moreover, NET expression was inversely related to left ventricular posterior wall dimensions (r = −0.64, P = 0.02) and heart rate (r = −0.55, P = 0.05). Indices of hyperinsulinaemia were not associated with NET expression. In stepwise linear regression analysis adjusted for age, body mass index and blood pressure, HbA1c was an independent inverse predictor of NET expression, explaining 45% of its variance.

Conclusions

Hyperglycaemia is associated with reduced peripheral NET expression. Further studies are required to identify the direction of causality.

Blood pressure as a predictor of cardiovascular events in the elderly: the William Hale Research Program

This study evaluates the association between blood pressure (BP) and the risk of developing cardiovascular disease (CVD) events in the elderly. The Morton Plant Mease Foundation has followed 4,008 elderly patients >64 years of age for at least 5 years. Systolic and diastolic blood pressure (SBP and DBP) was divided into categories. Cardiovascular disease events were classified as myocardial infarction, stroke, and CVD-related deaths reported from the National Death Index. Cox proportional hazard ratios were used to assess the relationship between BP and CVD events and controlled for weight, gender, smoker, and alcohol use. Ages <75 and >or=75 years were assessed separately. After 11.1 years of follow-up, elevated SBP (P=<0.0001) is strongly associated with developing a future CVD event; the relationship is linear and graded and holds for ages above and below 75 years. The frequency of CVD events was lowest in the SBP <120 mm Hg group. In subjects <75 years of age, DBP elevations were not a significant risk factor for CVD events. (relative risk (RR): DBP 70 to <80 mm Hg=0.92; DBP 80 to <90 mm Hg=0.88; DBP >or=90 mm Hg=1.02.) With subjects >or=75 years of age, a DBP between 80 and 90 is associated with the lowest significant risk for CVD (RR: DBP 70 to <80 mm Hg=0.74; DBP 80 to <90 mm Hg=0.59; DBP >or=90=0.71). In conclusion, these findings support the Joint National Committee on Hypertension recommendations for SBP in the elderly. Further studies are warranted to identify optimal DBP for the elderly at various ages.

Crystallization and preliminary X-ray diffraction studies of the Saccharomyces cerevisiae phospholipid-transfer protein Sec14p

The Saccharomyces cerevisiae phosphatidylinositol-transfer protein Secl4p catalyzes the exchange of phosphatidylinositol or phosphatidylcholine between membrane bilayers in vitro, and is an essential protein required for the budding of secretory vesicles from the yeast Golgi complex in vivo. At issue is the fundamental question of how the dual phospholipid ligand specificity of Sec 14p translates to in vivo function. In an attempt to determine the structural basis for how Secl4p binds each of its phopholipid ligands, Secl4p occupied with phosphatidylcholine has been purified and the complex crystallized in the presence of the mild detergent n-octyl beta-D-glucopyranoside. The Secl4p crystals diffract to 2.7 A and belong to space group P3(1)21 or P3(2)21 with unit-cell dimensions of a = b = 88.79, c = 111.21 A, alpha = beta = 90, gamma = 120 degrees. As Secl4p exhibits significant primary sequence homology to mammalian retinaldehyde binding proteins and the noncatalytic domain of human MEG2 protein tyrosine phosphatase, is is anticipated that solution of the Secl4p crystal structure will provide new functional insights for a family of interesting proteins.

Crystallization and initial X-ray analysis of beta-crustacyanin, the dimer of apoproteins A2 and C1, each with a bound astaxanthin molecule

Crystals of beta-crustacyanin, a carotenoid-binding protein from lobster carapace, have been grown under oil from solutions containing sodium potassium phosphate as precipitant. They grow slowly over a period of months to reach maximal dimensions of 0.5 x 0.1 x 0.1 mm, and belong to space group P622 with cell dimensions: a = b = 124.39, c = 188.86 A and gamma = 120 degrees. The crystals diffract to beyond 3 A but are very radiation sensitive, limiting the resolution of usable data. The unit-cell volume suggests that there are two beta-crustacyanin molecules per asymmetric unit.

Copper amine oxidase: cunning cofactor and controversial copper

Copper amine oxidases have a complex reaction cycle that converts a primary amine and molecular oxygen into the aldehyde, ammonia and hydrogen peroxide. Coupling structural studies of freeze-trapped reaction intermediates in crystals with kinetic and spectroscopic experiments in solution has generated a detailed molecular picture of catalysis. Although dioxygen has been directly observed bound to the copper at a late stage in the reaction cycle, whether copper is the initial binding site remains controversial.

Crystal structure of the precursor of galactose oxidase: an unusual self-processing enzyme

Galactose oxidase (EC ) is a monomeric enzyme that contains a single copper ion and catalyses the stereospecific oxidation of primary alcohols to their corresponding aldehydes. The protein contains an unusual covalent thioether bond between a tyrosine, which acts as a radical center during the two-electron reaction, and a cysteine. The enzyme is produced in a precursor form lacking the thioether bond and also possessing an additional 17-aa pro-sequence at the N terminus. Previous work has shown that the aerobic addition of Cu(2+) to the precursor is sufficient to generate fully processed mature enzyme. The structure of the precursor protein has been determined to 1.4 A, revealing the location of the pro-sequence and identifying structural differences between the precursor and the mature protein. Structural alignment of the precursor and mature forms of galactose oxidase shows that five regions of main chain and some key residues of the active site differ significantly between the two forms. The precursor structure provides a starting point for modeling the chemistry of thioether bond formation and pro-sequence cleavage.

Conserved tyrosine-369 in the active site of Escherichia coli copper amine oxidase is not essential

Copper amine oxidases are homodimeric enzymes that catalyze two reactions: first, a self-processing reaction to generate the 2,4,5-trihydroxyphenylalanine (TPQ) cofactor from an active site tyrosine by a single turnover mechanism; second, the oxidative deamination of primary amine substrates with the production of aldehyde, hydrogen peroxide, and ammonia catalyzed by the mature enzyme. The importance of active site residues in both of these processes has been investigated by structural studies and site-directed mutagenesis in enzymes from various organisms. One conserved residue is a tyrosine, Tyr369 in the Escherichia coli enzyme, whose hydroxyl is hydrogen bonded to the O4 of TPQ. To explore the importance of this site, we have studied a mutant enzyme in which Tyr369 has been mutated to a phenylalanine. We have determined the X-ray crystal structure of this variant enzyme to 2.1 A resolution, which reveals that TPQ adopts a predominant nonproductive conformation in the resting enzyme. Reaction of the enzyme with the irreversible inhibitor 2-hydrazinopyridine (2-HP) reveals differences in the reactivity of Y369F compared with wild type with more efficient formation of an adduct (lambda(max) = 525 nm) perhaps reflecting increased mobility of the TPQ adduct within the active site of Y369F. Titration with 2-HP also reveals that both wild type and Y369F contain one TPQ per monomer, indicating that Tyr369 is not essential for TPQ formation, although we have not measured the rate of TPQ biogenesis. The UV-vis spectrum of the Y369F protein shows a broader peak and red-shifted lambda(max) at 496 nm compared with wild type (480 nm), consistent with an altered electronic structure of TPQ. Steady-state kinetic measurements reveal that Y369F has decreased catalytic activity particularly below pH 6.5 while the K(M) for substrate beta-phenethylamine increases significantly, apparently due to an elevated pK(a) (5.75-6.5) for the catalytic base, Asp383, that should be deprotonated for efficient binding of protonated substrate. At pH 7.0, the K(M) for wild type and Y369F are similar at 1.2 and 1.5 microM, respectively, while k(cat) is decreased from 15 s(-1) in wild type to 0.38 s(-1), resulting in a 50-fold decrease in k(cat)/K(M) for Y369F. Transient kinetics experiments indicate that while the initial stages of enzyme reduction are slower in the variant, these do not represent the rate-limiting step. Previous structural and solution studies have implicated Tyr369 as a component of a proton shuttle from TPQ to dioxygen. The moderate changes in kinetic parameters observed for the Y369F variant indicate that if this is the case, then the absence of the Tyr369 hydroxyl can be compensated for efficiently within the active site.

Phosphatidylinositol transfer proteins and protein kinase C make separate but non-interacting contributions to the phosphorylation state necessary for secretory competence in rat mast cells

Mast cells permeabilized by streptolysin O undergo exocytosis when stimulated with Ca(2+) and guanosine 5'-[gamma-thio]triphosphate but become progressively refractory to this stimulus if it is delayed. This run-down of responsiveness occurs over a period of 20-30 min, during which the cells leak soluble and tethered proteins. We show here that withdrawal of ATP during the process of run-down is strongly inhibitory but that as little as 25 microM ATP can extend responsiveness significantly; this effect is maximal at 50 microM. When phosphatidylinositol transfer proteins (PITPs) are provided to cells at the time of permeabilization, run-down is retarded. We conclude that in the presence of ATP they convey substrates for phosphorylation that are essential for exocytosis and thus interact with the regulatory machinery. Furthermore, we show that PITPalpha and PITPbeta have additive effects in this mechanism, suggesting that they are not functionally redundant. Alternatively, secretion from run-down cells can be inhibited by the aminoglycoside antibiotic neomycin, which is understood to bind to phosphoinositide headgroups, and by a PH (pleckstrin homology) domain polypeptide that binds phosphoinositides. The apparent displacement of neomycin by exogenous PITPs suggests that these proteins screen essential lipids. Secretion from run-down cells is also inhibited by 1-O-hexadecyl-2-O-methyl-rac-glycerol (AMG-C(16)), an inhibitor of protein kinase C. The lack of synergy between neomycin and AMG-C(16) suggests that protein kinase C independently provides a second essential component through protein phosphorylation and that there are two independent phosphorylation pathways necessary for secretion competence.

The active site of the junction-resolving enzyme T7 endonuclease I

Endonuclease I is a junction-resolving enzyme encoded by bacteriophage T7, that selectively binds and cleaves four-way DNA junctions. We have recently solved the structure of this dimeric enzyme at atomic resolution, and identified the probable catalytic residues. The putative active site comprises the side-chains of three acidic amino acids (Glu20, Asp55 and Glu65) together with a lysine residue (Lys67), and shares strong similarities with a number of type II restriction enzymes. However, it differs from a typical restriction enzyme as the proposed catalytic residues in both active sites are contributed by both polypeptides of the dimer. Mutagenesis experiments confirm the importance of all the proposed active site residues. We have carried out in vitro complementation experiments using heterodimers formed from mutants in different active site residues, showing that Glu20 is located on a different monomer from the remaining amino acid residues comprising the active site. These experiments confirm that the helix-exchanged architecture of the enzyme creates a mixed active site in solution. Such a composite active site structure should result in unilateral cleavage by the complemented heterodimer; this has been confirmed by the use of a cruciform substrate. Based upon analogy with closely similar restriction enzyme active sites and our mutagenesis experiments, we propose a two-metal ion mechanism for the hydrolytic cleavage of DNA junctions.

Crystal structure of the Holliday junction resolving enzyme T7 endonuclease I

We have solved the crystal structure of the Holliday junction resolving enzyme T7 endonuclease I at 2.1 A resolution using the multiwavelength anomalous dispersion (MAD) technique. Endonuclease I exhibits strong structural specificity for four-way DNA junctions. The structure shows that it forms a symmetric homodimer arranged in two well-separated domains. Each domain, however, is composed of elements from both subunits, and amino acid side chains from both protomers contribute to the active site. While no significant structural similarity could be detected with any other junction resolving enzyme, the active site is similar to that found in several restriction endonucleases. T7 endonuclease I therefore represents the first crystal structure of a junction resolving enzyme that is a member of the nuclease superfamily of enzymes.

Direct and indirect readout in mutant Met repressor-operator complexes

BACKGROUND

The methionine repressor, MetJ, represses the transcription of genes involved in methionine biosynthesis by binding to arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. Naturally occurring operators differ from the consensus sequence to a greater extent as the number of metboxes increases. MetJ, while accommodating this sequence variation in natural operators, is very sensitive to particular base changes, even where bases are not directly contacted in the crystal structure of a complex formed between the repressor and consensus operator.

RESULTS

Here we report the high-resolution structure of a MetJ mutant, Q44K, bound to the consensus operator sequence (Q44Kwt19) and two related sequences containing mutations at sites believed to be important for indirect readout at non-contacted bases. The overall structure of the Q44Kwt19 complex is very similar to the wild-type complex, but there are small variations in sugar-phosphate backbone conformation and direct contacts to the DNA bases. The mutant complexes show a mixture of direct and indirect readout of sequence variations, with differences in direct contacts and DNA conformation.

CONCLUSIONS

Comparison of the wild-type and mutant repressor-operator complexes shows that the repressor makes sufficiently strong interactions with the sugar-phosphate backbone to accommodate some variation in operator sequence with minor changes in direct bases contacts. The reduction in repressor affinity for the two mutant repressor complexes can be partially attributed to a loss in direct contacts to the DNA. In one case, however, the replacement of a flexible TA base-step leads to an unfavourable DNA conformation that reduces the stability of the repressor-operator complex.

Leishmania pyruvate kinase: the crystal structure reveals the structural basis of its unique regulatory properties

Glycolysis occupies a central role in cellular metabolism, and is of particular importance for the catabolic production of ATP in protozoan parasites such as Leishmania and Trypanosoma. In these organisms pyruvate kinase plays a key regulatory role, and is unique in responding to fructose 2,6-bisphosphate as allosteric activator. The determination of the crystal structure of the first eukaryotic pyruvate kinase in the T-state (the inactive or 'tense' conformation of allosteric enzymes) is described. A comparison of the effector sites of the Leishmania and yeast enzymes reveals the structural basis for the different effector specificity. Two loops, comprising residues 443-453 and 480-489, adopt very different conformations in the two enzymes, and Lys-453 and His-480 that are a feature of trypanosomatid enzymes provide probable ligands for the 2-phospho group of the effector molecule. These and other differences offer an opportunity for the design of drugs that would exploit regulatory differences between parasite and host.

Visualization of dioxygen bound to copper during enzyme catalysis

X-ray crystal structures of three species related to the oxidative half of the reaction of the copper-containing quinoprotein amine oxidase from Escherichia coli have been determined. Crystals were freeze-trapped either anaerobically or aerobically after exposure to substrate, and structures were determined to resolutions between 2.1 and 2.4 angstroms. The oxidation state of the quinone cofactor was investigated by single-crystal spectrophotometry. The structures reveal the site of bound dioxygen and the proton transfer pathways involved in oxygen reduction. The quinone cofactor is regenerated from the iminoquinone intermediate by hydrolysis involving Asp383, the catalytic base in the reductive half-reaction. Product aldehyde inhibits the hydrolysis, making release of product the rate-determining step of the reaction in the crystal.

The structure of pyruvate kinase from Leishmania mexicana reveals details of the allosteric transition and unusual effector specificity

Glycolysis occupies a central role in cellular metabolism, and is of particular importance for the catabolic production of ATP in protozoan parasites such as Leishmania and Trypanosoma. In these organisms pyruvate kinase plays a key regulatory role, and is unique in responding to fructose 2,6-bisphosphate as allosteric activator. The determination of the first eukaryotic pyruvate kinase crystal structure in the T-state is reported. A comparison of the leishmania and yeast R-state enzymes reveals fewer differences than the previous comparison of Escherichia coli T-state and rabbit muscle non-allosteric enzymes. Structural changes related to the allosteric transition can therefore be distinguished from those that are a consequence of the inherent wide structural divergence between bacterial and mammalian proteins. The allosteric transition involves significant changes in a tightly packed array of eight alpha helices at the interface near the catalytic site. At the other interface the allosteric transition appears to be accompanied by the bending of a ten-stranded intersubunit beta sheet adjacent to the effector site. Helix Calpha1 makes contacts to the N-terminal helical domain and bridges both interfaces. A comparison of the effector sites of the leishmania and yeast enzymes reveals the structural basis for the different effector specificity. Two loops comprising residues 443-453 and 480-489 adopt very different conformations in the two enzymes, and Lys453 and His480 that are a feature of trypanosomatid enzymes provide probable ligands for the 2-phospho group of the effector molecule. These differences offer an opportunity for the design of drugs that would bind to the trypanosomatid enzymes but not to those of the mammalian host.

Yeast Sec14p deficient in phosphatidylinositol transfer activity is functional in vivo

Yeast phosphatidylinositol transfer protein (Sec14p) is essential for Golgi secretory function. It is widely accepted, though unproven, that phosphatidylinositol transfer between membranes represents the physiological activity of phosphatidylinositol transfer proteins (PITPs). We report that Sec14pK66,239A is inactivated for phosphatidylinositol, but not phosphatidylcholine (PC), transfer activity. As expected, Sec14pK66,239A fails to meet established criteria for a PITP in vitro and fails to stimulate phosphoinositide production in vivo. However, its expression efficiently rescues the lethality and Golgi secretory defects associated with sec14-1ts and sec14 null mutations. This complementation requires neither phospholipase D activation nor the involvement of a novel class of minor yeast PITPs. These findings indicate that PI binding/transfer is remarkably dispensable for Sec14p function in vivo.

The active site base controls cofactor reactivity in Escherichia coli amine oxidase: x-ray crystallographic studies with mutational variants

Amine oxidases utilize a proton abstraction mechanism following binding of the amine substrate to the C5 position of the cofactor, the quinone form of trihydroxyphenylalanine (TPQ). Previous work [Wilmot, C. M., et al. (1997) Biochemistry 36, 1608-1620] has shown that Asp383 in Escherichia coliamine oxidase (ECAO) is the catalytic base which performs the key step of proton abstraction. This paper explores in more depth this and other roles of Asp383. The crystal structures of three mutational variants are presented together with their catalytic properties, visible spectra, and binding properties for a substrate-like inhibitor, 2-hydrazinopyridine (2-HP), in comparison to those of the wild type enzyme. In wild type ECAO, the TPQ is located in a wedge-shaped pocket which allows more freedom of movement at the substrate binding position (C5) than for TPQ ring carbons C1-C4. A role of Asp383, whose carboxylate is located close to O5, is to stabilize the TPQ in its major conformation in the pocket. Replacement of Asp383 with the isostructural, but chemically distinct, Asn383 does not affect the location or dynamics of the TPQ cofactor significantly, but eliminates catalytic activity and drastically reduces the affinity for 2-HP. Removal of the side chain carboxyl moiety, as in Ala383, additionally allows the TPQ the greater conformational flexibility to coordinate to the copper, which demonstrates that Asp383 helps maintain the active site structure by preventing TPQ from migrating to the copper. Glu383 has a greatly decreased catalytic activity, as well as a decreased affinity for 2-HP relative to that of wild type ECAO. The electron density reveals that the longer side chain of Glu prevents the pivotal motion of the TPQ by hindering its movement within the wedge-shaped active site pocket. The results show that Asp383 performs multiple roles in the catalytic mechanism of ECAO, not only in acting as the active site base at different stages of the catalytic cycle but also in regulating the mobility of the TPQ that is essential to catalysis.

Polyanionic inhibitors of phosphoglycerate mutase: combined structural and biochemical analysis

The effects that the inhibitors inositol hexakisphosphate and benzene tri-, tetra- and hexacarboxylates have on the phosphoglycerate mutases from Saccharomyces cerevisiae and Schizosaccharomyces pombe have been determined. Their Kivalues have been calculated, and the ability of the inhibitors to protect the enzymes against limited proteolysis investigated. These biochemical data have been placed in a structural context by the solution of the crystal structures of S. cerevisiae phosphoglycerate mutase soaked with inositol hexakisphosphate or benzene hexacarboxylate. These large polyanionic compounds bind to the enzyme so as to block the entrance to the active-site cleft. They form multiple interactions with the enzyme, consistent with their low Kivalues, and afford good protection against limited proteolysis of the C-terminal region by thermolysin. The inositol compound is more efficacious because of its greater number of negative charges. The S. pombe phosphoglycerate mutase that is inherently lacking a comparable C-terminal region has higher Kivalues for the compounds tested. Moreover, the S. pombe enzyme is less sensititive to proteolysis, and the presence or absence of the inhibitor molecules has little effect on susceptibility to proteolysis.

Crystallization and preliminary X-ray crystallographic studies of RepDC, a hybrid rolling-circle plasmid replication initiator protein

The hybrid plasmid-replication initiator protein RepDC, which is a fusion of the catalytic fragment of the RepD protein and the DNA-binding fragment of the RepC protein from Staphylococcus aureus, has been successfully crystallized and X-ray data to 3.5 A have been collected on a synchrotron radiation source. Crystals belong to space group I4132 with unit-cell dimensions a = b = c = 165.1 A. The crystals are estimated to contain one protein monomer per asymmetric unit, with 55% solvent content.

Plasmid replication initiator protein RepD increases the processivity of PcrA DNA helicase

The replication initiator protein RepD encoded by the Staphylococcus chloramphenicol resistance plasmid pC221 stimulates the helicase activity of the Bacillus stearothermophilus PcrA DNA helicase in vitro. This stimulatory effect seems to be specific for PcrA and differs from the stimulatory effect of the Escherichia coli ribosomal protein L3. Whereas L3 stimulates the PcrA helicase activity by promoting co-operative PcrA binding onto its DNA substrate, RepD stimulates the PcrA helicase activity by increasing the processivity of the enzyme and enables PcrA to displace DNA from a nicked substrate. The implication of these results is that PcrA is the helicase recruited into the replisome by RepD during rolling circle replication of plasmids of the pT181 family.

Sulphate ions observed in the 2.12 A structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism

The structure of a new crystal form of Saccharomyces cerevisiae phosphoglycerate mutase has been solved and refined to 2.12 A with working and free R-factors of 19.7 and 22.9 %, respectively. Higher-resolution data and greater non-crystallographic symmetry have produced a more accurate protein structure than previously. Prominent among the differences from the previous structure is the presence of two sulphate ions within each active site cleft. The separation of the sulphates suggests that they may occupy the same sites as phospho groups of the bisphosphate ligands of the enzyme. Plausible binding modes for 2,3-bisphosphoglycerate and 1, 3-bisphosphoglycerate are thereby suggested. These results support previous conclusions from mutant studies, highlight interesting new targets for mutagenesis and suggest a possible mechanism of enzyme phosphorylation.

Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 A resolution

The crystal structure of intact elongation factor Tu (EF-Tu) from Escherichia coli in GDP-bound conformation has been determined using a combination of multiple isomorphous replacement (MIR) and multiwavelength anomalous diffraction (MAD) methods. The current atomic model has been refined to a crystallographic R factor of 20.3 % and free R-factor of 26.8 % in the resolution range of 10-2.05 A. The protein consists of three domains: domain 1 has an alpha/beta structure; while domain 2 and domain 3 are beta-barrel structures. Although the global fold of the current model is similar to those of published structures, the secondary structural assignment has been improved due to the high quality of the current model. The switch I region (residues 40-62) is well ordered in this structure. Comparison with the structure of EF-Tu in GDP-bound form from Thermus aquaticus shows that although the individual domain structures are similar in these two structures, the orientation of domains changes significantly. Interactions between domains 1 and 3 in our E. coli EF-Tu-GDP complex are quite different from those of EF-Tu with bound GTP from T. aquaticus, due to the domain rearrangement upon GTP binding. The binding sites of the Mg2+ and guanine nucleotide are revealed in detail. Two water molecules that co-ordinate the Mg2+ have been identified to be well conserved in the GDP and GTP-bound forms of EF-Tu structures, as well as in the structure of Ras p21 with bound GDP. Comparisons of the Mg2+ binding site with other guanine nucleotide binding proteins in GDP-bound forms show that the Mg2+ co-ordination patterns are well preserved among these structures.

A proposal for the reliable culture of Borrelia burgdorferi from patients with chronic Lyme disease, even from those previously aggressively treated

Since culture of Borrelia burgdorferi from patients with chronic Lyme disease has been an extraordinarily rare event, clarification of the nature of the illness and proving its etiology as infectious have been difficult. A method for reliably and reproducibly culturing B. burgdorferi from the blood of patients with chronic Lyme disease was therefore sought by making a controlled blood culture trial studying 47 patients with chronic Lyme disease. All had relapsed after long-term oral and intravenous antibiotics. 23 patients with other chronic illness formed the control group. Positive cultures were confirmed by fluorescent antibody immuno-electron microscopy using monoclonal antibody directed against Osp A, and Osp A PCR. 43/47 patients (91%) cultured positive. 23/23 controls (100%) cultured negative. Although persistent infection has been, to date, strongly suggested in chronic Lyme disease by positive PCR and antigen capture, there are major problems with these tests. This new method for culturing B. burgdorferi from patients with chronic Lyme disease certainly defines the nature of the illness and establishes that it is of chronic infectious etiology. This discovery should help to reestablish the gold standard in laboratory diagnosis of Lyme disease.

Crystal structures of a series of RNA aptamers complexed to the same protein target

We have determined the crystal structures, at 2.8 A resolution, of two different RNA aptamers, each bound to MS2 coat protein. One of the aptamers contains a non-Watson-Crick base pair, while the other is missing one of the unpaired adenines that make sequence-specific contacts in the wild-type complex. Despite these differences, the RNA aptamers bind in the same location on the protein as the wild-type translational operator. Comparison of these new structures with other MS2-RNA complexes allows us to refine further the definition of the minimal recognition elements and suggests a possible application of the MS2 system for routine structure determination of small nucleic acid motifs.

Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence

The crystal structure of the type II restriction endonuclease BglI bound to DNA containing its specific recognition sequence has been determined at 2.2 A resolution. This is the first structure of a restriction endonuclease that recognizes and cleaves an interrupted DNA sequence, producing 3' overhanging ends. BglI is a homodimer that binds its specific DNA sequence with the minor groove facing the protein. Parts of the enzyme reach into both the major and minor grooves to contact the edges of the bases within the recognition half-sites. The arrangement of active site residues is strikingly similar to other restriction endonucleases, but the co-ordination of two calcium ions at the active site gives new insight into the catalytic mechanism. Surprisingly, the core of a BglI subunit displays a striking similarity to subunits of EcoRV and PvuII, but the dimer structure is dramatically different. The BglI-DNA complex demonstrates, for the first time, that a conserved subunit fold can dimerize in more than one way, resulting in different DNA cleavage patterns.

A phosphatidylinositol 3-kinase and phosphatidylinositol transfer protein act synergistically in formation of constitutive transport vesicles from the trans-Golgi network

Current evidence suggests that phosphatidylinositol (PI) kinases and phosphatidylinositol transfer protein (PITP) are involved in driving vesicular traffic from yeast and mammalian trans-Golgi network (TGN). We have tested the interaction between these cytosolic proteins in an assay that measures the formation of constitutive transport vesicles from the TGN in a hepatocyte cell-free system. This reaction is dependent on a novel PI 3-kinase, and we now report that, under conditions of limiting cytosol, purified PI 3-kinase and PITP functionally cooperate to drive exocytic vesicle formation. This synergy was observed with both yeast and mammalian PITPs, and it also extended to the formation of PI 3-phosphate. These collective findings indicate that the PI 3-kinase and PITP synergize to form a pool of PI 3-phosphate that is essential for formation of exocytic vesicles from the hepatocyte TGN.

Low-resolution structural characterization of the arginine repressor/activator from Bacillus subtilis: a combined X-ray crystallographic and electron microscopical approach

Attempts to determine the X-ray crystal structure of the intact homohexameric arginine repressor/activator from B. subtilis have so far been unsuccessful. The major problem appears to be the lack of an isomorphous heavy-atom derivative with a manageable number of substitution sites. Here it is shown how electron microscopy of thin three-dimensional crystals, the same as those used for the X-ray crystallographic studies, made it possible (i) to obtain experimental support for some conclusions drawn on the basis of X-ray data alone, (ii) to determine the low-resolution distribution of electron density in several different crystallographic projections, and (iii) to obtain a tentative low-resolution model of the whole hexamer.

Type I posterior laryngeal clefts

Posterior laryngeal clefts (PLCs) are described in the literature as rare laryngeal abnormalities. The authors believe type I clefts are much more common than previously reported. In two busy pediatric tertiary care centers, such clefts are the second most common congenital laryngeal finding at rigid endoscopy, second only to laryngomalacia. PLCs frequently present with symptomatology that can be attributed to other common disease processes and are often undiagnosed unless the surgeon maintains a high index of suspicion and specifically examines the posterior glottis by palpation during microlaryngoscopy. This report presents a series of 41 patients with type I PLCs, reviews their subtle and often confusing presenting signs and symptoms, and describes a simple yet reliable method of diagnosis.

The 2.3 A X-ray crystal structure of S. cerevisiae phosphoglycerate mutase

The high resolution crystal structure of Saccharomyces cerevisiae phosphoglycerate mutase has been determined. This structure shows important differences from the lower resolution structure deposited in 1982. The crystal used to determine the new structure was of a different form, having spacegroup P2(1). The model was refined to a crystallographic R-factor of 18.9% and a free R-factor of 28.4% using all data between 25 and 2.3 A and employing a bulk solvent correction. The enzyme is a tetramer of identical, 246 amino acid subunits, whose structure is revealed to be a dimer of dimers, with four independent active sites located well away from the subunit contacts. Each subunit contains two domains, the larger with a typical nucleotide binding fold, although phosphoglycerate mutase has no physiological requirement to bind nucleotides. The catalytic-site histidine residues are no longer in a "clapping-hands" conformation, but more resemble the conformation seen in the distantly related enzymes prostatic acid phosphatase and fructose-2,6-bisphosphatase. However, the catalytic histidine residues in the mutase are found to be much closer to each other than in the phosphatase structures, perhaps due to the absence of bound ligands in the mutase crystal. An intricate web of H-bonds is found around the catalytic histidine residues, high-lighting residues probably important for maintaining their correct orientation and charge. The positions of certain other residues, including some found near the catalytic site and some lining the catalytic-site cleft, have been changed by the correction of registration errors between sequence and electron density in the original structure. Electron density was apparent for a portion of the functionally important C-terminal tail, which was absent from the earlier structure, showing it to adopt a mainly helical conformation.

Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution

The crystal structure, at 2.8 A resolution, of an RNA aptamer bound to bacteriophage MS2 coat protein has been determined. It provides an opportunity to compare the interactions of MS2 coat protein and wild type operator with those of an aptamer, whose secondary structure differs from the wild type RNA in having a three-base loop (compared to a tetraloop) and an additional base pair between this loop and the sequence-specific recognition element in the stem. The RNA binds in the same location on the coat protein as the wild type operator and maintains many of the same RNA-protein interactions. In order to achieve this, the RNA stem loop undergoes a concerted rearrangement of the 3' side while leaving the 5' side and the loop interactions largely unchanged, illustrating the ability of RNA to present similar molecular recognition surfaces from distinct primary and secondary structures.

Crystal structure of the Saccharomyces cerevisiae phosphatidylinositol-transfer protein

The yeast phosphatidylinositol-transfer protein (Sec14) catalyses exchange of phosphatidylinositol and phosphatidylcholine between membrane bilayers in vitro. In vivo, Sec14 activity is essential for vesicle budding from the Golgi complex. Here we report a three-dimensional structure for Sec14 at 2.5 A resolution. Sec14 consists of twelve alpha-helices, six beta-strands, eight 3(10)-helices and has two distinct domains. The carboxy-terminal domain forms a hydrophobic pocket which, in the crystal structure, is occupied by two molecules of n-octyl-beta-D-glucopyranoside and represents the phospholipid-binding domain. This pocket is reinforced by a string motif whose disruption in a sec14 temperature-sensitive mutant results in destabilization of the phospholipid-binding domain. Finally, we have identified an unusual surface helix that may play a critical role in driving Sec14-mediated phospholipid exchange. From this structure, we derive the first molecular clues into how a phosphatidylinositol-transfer protein functions.

Molecular cloning and characterization of a nitrobenzylthioinosine-insensitive (ei) equilibrative nucleoside transporter from human placenta

Mammalian equilibrative nucleoside transporters are typically divided into two classes, es and ei, based on their sensitivity or resistance respectively to inhibition by nitrobenzylthioinosine (NBMPR). Previously, we have reported the isolation of a cDNA clone encoding a prototypic es-type transporter, hENT1 (human equilibrative nucleoside transporter 1), from human placenta. We now report the molecular cloning and functional expression in Xenopus oocytes of a cDNA from the same tissue encoding a homologous ei-type transporter, which we designate hENT2. This 456-residue protein is 46% identical in amino acid sequence with hENT1 and corresponds to a full-length form of the delayed-early proliferative response gene product HNP36, a protein of unknown function previously cloned in a form bearing a sequence deletion. In addition to placenta, hENT2 is found in brain, heart and ovarian tissue. Like hENT1, hENT2 mediates saturable transport of the pyrimidine nucleoside uridine (Km 0.2+/-0.03 mM) and also transports the purine nucleoside adenosine. However, in contrast with hENT1, which is potently inhibited by NBMPR (Ki 2 nM), hENT2 is NBMPR-insensitive (IC50<1 microM). It is also much less sensitive to inhibition by the coronary vasoactive drugs dipyridamole and dilazep and to the lidoflazine analogue draflazine, properties that closely resemble those reported for classical ei-type transport in studies with intact cells.

Antibody fragment Fv4155 bound to two closely related steroid hormones: the structural basis of fine specificity

BACKGROUND

The concentration of steroid glucuronides in serial samples of early morning urine (EMU) can be used to predict the fertile period in the female menstrual cycle. The monoclonal antibody 4155 has been used as a convenient means of measuring the concentration of steroid glucuronides in EMU, as it specifically recognises the steroid hormone estrone beta-D-glucuronide (E3G), with very high affinity, and the closely related hormone estriol 3-(beta-d-glucuronide) (EI3G), with reduced affinity. Although 4115 binds these hormones with different affinities, EI3G differs from E3G only in the addition of a hydroxyl group and reduction of an adjacent carbonyl. To investigate the structural basis of this fine binding specificity, we have determined the crystal structures of the variable fragment (Fv) of 4155 in complex with each of these hormones.

RESULTS

Two crystal forms of the Fv4155-EI3G complex, at resolutions of 2.1 A and 2.5 A, and one form of the Fv4155-E3G complex, at 2.1 A resolution were solved and refined. The crystal structures show the E3G or EI3G antigen lying in an extended cleft, running form the centre of the antibody combining site down one side of the variable domain interface, and formed almost entirely from residues in the heavy chain. The binding cleft lies primarily between the heavy chain complementarity determining regions (CDRs), rather than in the interface between the heavy and light chains. In both complexes the binding of the glucuronic sugar, and rings A and B of the steroid, is specified by the shape of the narrow cleft. Analysis of the Fv structure reveals that five of the six CDR regions can be assigned to one of the predefined canonical structural classes.

CONCLUSIONS

The difference in the binding affinity of Fv4155 for the two steroid hormones is accounted for by a subtle combination of a less favoured hydrogen-bond geometry, and a minor rearrangement of the water molecule network around the binding site. The rearrangement of water molecules results from the burial of the additional hydroxyl group of the EI3G in a hydrophobic environment.

Essential role for diacylglycerol in protein transport from the yeast Golgi complex

Yeast phosphatidylinositol transfer protein (Sec14p) is required for the production of secretory vesicles from the Golgi. This requirement can be relieved by inactivation of the cytosine 5'-diphosphate (CDP)-choline pathway for phosphatidylcholine biosynthesis, indicating that Sec14p is an essential component of a regulatory pathway linking phospholipid metabolism with vesicle trafficking (the Sec14p pathway). Sac1p (refs 7 and 8) is an integral membrane protein related to inositol-5-phosphatases such as synaptojanin, a protein found in rat brain. Here we show that defects in Sac1p also relieve the requirement for Sec14p by altering phospholipid metabolism so as to expand the pool of diacylglycerol (DAG) in the Golgi. Moreover, although short-chain DAG improves secretory function in strains with a temperature-sensitive Sec14p, expression of diacylglycerol kinase from Escherichia coli further impairs it. The essential function of Sec14p may therefore be to maintain a sufficient pool of DAG in the Golgi to support the production of secretory vesicles.

Mapping the minimal domain of hMSH-2 sufficient for binding mismatched oligonucleotides

The human MSH-2 gene product is a member of a highly conserved family of proteins involved in post-replication mismatch repair. Germline mutations in this gene have been implicated in hereditary non-polyposis colorectal cancer (HNPCC). Alterations in the coding region of the hMSH-2 gene result in a mutator phenotype with marked instability of microsatellite sequences, indicative of a deficiency in DNA repair. We have previously shown that a region of high homology between MutS proteins of different species containing a nucleotide binding domain, is sufficient to bind DNA containing specific mismatched residues. In order to determine the minimal domain of hMSH-2 necessary for binding mismatch-containing oligonucleotides, deletion analysis of the C-terminal region was performed. We have constructed a 5' and 3' deletion series, expressed each deletion as a bacterial fusion protein and assessed it for ATPase activity and its ability to identify mismatch containing DNA. Here we demonstrate that a 585 bp fragment encoding 195 amino acids within the C-terminal domain of hMSH-2 is sufficient to bind to DNA containing mismatches.

Catalytic mechanism of the quinoenzyme amine oxidase from Escherichia coli: exploring the reductive half-reaction

The crystal structure of the complex between the copper amine oxidase from Escherichia coli (ECAO) and a covalently bound inhibitor, 2-hydrazinopyridine, has been determined to a resolution of 2.0 A. The inhibitor covalently binds at the 5 position of the quinone ring of the cofactor, 2,4,5-trihydroxyphenylalaninequinone (TPQ). The inhibitor complex is analogous to the substrate Schiff base formed during the reaction with natural monoamine substrate. A proton is abstracted from a methylene group adjacent to the amine group by a catalytic base during the reaction. The inhibitor, however, has a nitrogen at this position, preventing proton abstraction and trapping the enzyme in a covalent complex. The electron density shows this nitrogen is hydrogen bonded to the side chain of Asp383, a totally conserved residue, identifying it as the probable catalytic base. The positioning of Asp383 is such that the pro-S proton of a substrate would be abstracted, consistent with the stereospecificity of the enzyme determined by 1H NMR spectroscopy. Site-directed mutagenesis and in vivo suppression have been used to substitute Asp383 for 12 other residues. The resulting proteins either lack or, in the case of glutamic acid, have very low enzyme activity consistent with an essential catalytic role for Asp383. The O4 position on the quinone ring is involved in a short hydrogen bond with the hydroxyl of conserved residue Tyr369. The distance between the oxygens is less than 2.5 A, consistent with a shared proton, and suggesting ionization at the O4 position of the quinone ring. The Tyr369 residue appears to play an important role in stabilizing the position of the quinone/inhibitor complex. The O2 position on the quinone ring is hydrogen bonded to the apical water ligand of the copper. The basal water ligand, which lies 2.0 A from the copper in the native structure, is at a distance of 3.0 A in the complex. In the native structure, the active site is completely buried, with no obvious route for entry of substrate. In the complex, the tip of the pyridine ring of the bound inhibitor is on the surface of the protein at the edge of the interface between domains 3 and 4, suggesting this as the entry point for the amine substrate.

Mutational analysis of the nucleotide binding domain of the mismatch repair enzyme hMSH-2

The genes involved in postreplicative DNA mismatch repair are a highly conserved family of proteins. In humans, germline mutations in these genes (hMSH-2, hMLH-1, hPMS-1, and hPMS-2) have been implicated in hereditary nonpolyposis colorectal cancer (HNPCC). We have previously shown that a region of high homology between the members of this class of proteins in different species contains a type A nucleotide binding site consensus sequence which has ATPase activity and is sufficient to bind DNA containing specific mismatched residues (1). To identify residues which are necessary for this activity, we have created a range of mutants containing amino acid substitutions within the nucleotide binding domain of hMSH-2. These mutants have been expressed and assessed for ATPase activity and their ability to identify mismatch-containing DNA. Here we demonstrate that a variant protein which has the conserved residue Lys 675 within the nucleotide binding consensus sequence altered to an alanine has severely impaired ATPase activity and is unable to bind DNA containing specific mismatched residues.

Effects of systematic variation of the minimal Escherichia coli met consensus operator site: in vivo and in vitro met repressor binding

We have produced a set of sequence variants based upon the idealized, minimal Escherichia coli met operator in which each position within the basic recognition unit, the 8 bp met box (dAGACGTCT), has been changed to all other possible sequences containing single symmetrical base substitutions. The effects of these sequence variations have been assayed in vivo by monitoring the production of beta-galactosidase from a standard promoter regulated by the operator variants, and in vitro by gel-retardation assay. The two sets of data are consistent and correlate well with expectations based on the three-dimensional structure of the holorepressor bound to a minimal idealized operator and the results of in vitro evolution experiments. Comparison with two natural operators, metA and metC, suggests that in vivo, with non-consensus operators, the repressor binds to at least four consecutive met boxes.

A carboxy terminal domain of the hMSH-2 gene product is sufficient for binding specific mismatched oligonucleotides

The human MSH-2 gene product is a member of a highly conserved family of proteins which are involved in post-replication mismatch repair. hMSH-2 is homologous to Escherichia coli (E. coli) MutS and Sacchromyces cerevisiae MSH-1 and MSH-2 proteins, which recognise heteroduplex DNA at the sites of all single base mismatches and deletions or insertions up to 4 base pairs. hMSH-2 is one of the hereditary non-polyposis colorectal cancer (HNPCC) tumor suppressor genes, and maps to human chromosome 2p16. Alterations in the coding region of the hMSH-2 gene result in a mutator phenotype with marked instability of microsatellite sequences, indicative of a deficiency in DNA repair. It has been shown that purified hMSH-2 binds specifically to nucleotide mismatches in double-stranded DNA. Here we demonstrate that a region of high homology between the members of this class of proteins contains a type A nucleotide binding site consensus sequence which has ATPase activity and is sufficient to bind DNA containing specific mismatched residues.

Crystallization and preliminary crystallographic analysis of RepA1, a replication control protein of the RepFIC replicon of enterotoxin plasmid EntP307

RepA1 protein is essential for replication of the RepFIC replicon of enterotoxin plasmid EntP307 and is thought to interact directly with the origin of replication. We have purified RepA1 from an over-producing expression system and have prepared single crystals using a macroseeding technique. The crystals belong to space group P2(1)2(1)2(1) or P2(1)2(1)2, with cell dimensions a = 61 A, b = 67 A, and c = 243 A. They diffract X-rays to 3.3 A resolution and probably contain two 40,000 molecular weight RepA1 molecules per asymmetric unit.

Structure and function of Escherichia coli met repressor: similarities and contrasts with trp repressor

Transcription of genes encoding enzymes for the biosynthesis of methionine and trytophan in Escherichia coli is regulated by the ligand-activated met and trp repressors. X-ray crystallographic studies show how these two small proteins, although similar in size and function, have totally different three-dimensional structures and specifically recognize their respective DNA operator sequences in different ways. A common feature is that both repressors bind as cooperative arrays to tandem repeats of 8 base-pair 'Met' or 'Trp boxes' respectively, and the consensus sequences share the rare tetranucleotide CTAG. A series of structural and functional studies have shown how the two repressors discriminate between their operators, using a combination of direct contacts between side chains and bases, and indirect sensing of conformational properties of the DNA.

Crystal structure of a quinoenzyme: copper amine oxidase of Escherichia coli at 2 A resolution

BACKGROUND

Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).

RESULTS

The crystal structure of amine oxidase from Escherichia coli has been determined in both an active and an inactive form. The only structural differences are in the active site, where differences in copper coordination geometry and in the position and interactions of the redox cofactor, TPQ, are observed. Each subunit of the mushroom-shaped dimer comprises four domains: a 440 amino acid C-terminal beta sandwich domain, which contains the active site and provides the dimer interface, and three smaller peripheral alpha/beta domains (D1-D3), each of about 100 amino acids. D2 and D3 show remarkable structural and sequence similarity to each other and are conserved throughout the quinoenzyme family. In contrast, D1 is absent from some amine oxidases. The active sites are well buried from solvent and lie some 35 A apart, connected by a pair of beta hairpin arms.

CONCLUSIONS

The crystal structure of E. coli copper amine oxidase reveals a number of unexpected features and provides a basis for investigating the intriguing similarities and differences in catalytic mechanism of members of this enzyme family. In addition to the three conserved histidines that bind the copper, our studies identify a number of other conserved residues close to the active site, including a candidate for the catalytic base and a fourth conserved histidine which is involved in an interesting intersubunit interaction.