Crystallographic data deposition.
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Archives↗
Biomedical subjects
G Dodson
Publications and source records attributed to G Dodson.
A protein catalytic framework with an N-terminal nucleophile is capable of self-activation.
The crystal structures of three amidohydrolases have been determined recently: glutamine PRPP amidotransferase (GAT), penicillin acylase, and the proteasome. These enzymes use the side chain of the amino-terminal residue, incorporated in a beta-sheet, as the nucleophile in the catalytic attack at the carbonyl carbon. The nucleophile is cysteine in GAT, serine in penicillin acylase, and threonine in the proteasome. Here we show that all three enzymes share an unusual fold in which the nucleophile and other catalytic groups occupy equivalent sites. This fold provides both the capacity for nucleophilic attack and the possibility of autocatalytic processing. We suggest the name Ntn (N-terminal nucleophile) hydrolases for this structural superfamily of enzymes which appear to be evolutionarily related but which have diverged beyond any recognizable sequence similarity.
Amidophosphoribosyltransferase↗
Penicillin acylase has a single-amino-acid catalytic centre.
Penicillin acylase (penicillin amidohydrolase, EC 3.5.1.11) is widely distributed among microorganisms, including bacteria, yeast and filamentous fungi. It is used on an industrial scale for the production of 6-aminopenicillanic acid, the starting material for the synthesis of semi-synthetic penicillins. Its in vivo role remains unclear, however, and the observation that expression of the Escherichia coli enzyme in vivo is regulated by both temperature and phenylacetic acid has prompted speculation that the enzyme could be involved in the assimilation of aromatic compounds as carbon sources in the organism's free-living mode. The mature E. coli enzyme is a periplasmic 80K heterodimer of A and B chains (209 and 566 amino acids, respectively) synthesized as a single cytoplasmic precursor containing a 26-amino-acid signal sequence to direct export to the cytoplasm and a 54-amino-acid spacer between the A and B chains which may influence the final folding of the chains. The N-terminal serine of the B chain reacts with phenylmethylsulphonyl fluoride, which is consistent with a catalytic role for the serine hydroxyl group. Modifying this serine to a cysteine inactivates the enzyme, whereas threonine, arginine or glycine substitution prevents in vivo processing of the enzyme, indicating that this must be an important recognition site for cleavage. Here we report the crystal structure of penicillin acylase at 1.9 A resolution. Our analysis shows that the environment of the catalytically active N-terminal serine of the B chain contains no adjacent histidine equivalent to that found in the serine proteases. The nearest base to the hydroxyl of this serine is its own alpha-amino group, which may act by a new mechanism to endow the enzyme with its catalytic properties.
Amino Acid Sequence↗
Dorothy Hodgkin 1910-1994.
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Crystallography, X-Ray↗
Drug design. Reflections on a peptide.
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Amino Acid Sequence↗
Crystallization and preliminary X-ray analysis of a fungal endoglucanase I.
An endoglucanase I (EG1) from a fungal source (Humicola insolens) has been crystallized in a number of forms suitable for X-ray diffraction analysis. Four crystal forms have been grown from various precipitants using vapour phase diffusion methods in hanging drops. Three of these crystal forms diffract to beyond 2.5 A resolution. Two forms, obtained from ammonium sulphate at pH 5.4, or 8.0, grow as tetragonal bipyramids in space group P4(1)22 or P4(3)22, with approximate cell dimensions a = b = 102 A, c = 282 A. The other crystal forms were grown from polyethylene glycol 8000 at pH 8.0. One grows as monoclinic plates, space group P2(1), with cell dimensions a = 66.9 A, b = 75.2 A, c = 86.9 A and beta = 102.9 degrees and the other as long hexagonal rods in space group P6(1)22 or P6(5)22, with cell dimensions a = b = 119 A, c = 83 A.
Cellulose 1,4-beta-Cellobiosidase↗
High resolution crystal structures and comparisons of T-state deoxyhaemoglobin and two liganded T-state haemoglobins: T(alpha-oxy)haemoglobin and T(met)haemoglobin.
The origin of co-operativity in haemoglobin (Hb) resides in the reduced affinity of the T-state. T-state Hb crystals grown from polyethyleneglycol can be liganded without the molecule switching to the R high affinity state. X-ray analysis of T-state alpha-oxy Hb and T-state met Hb has identified the structural basis for reduced affinity. The nature of the chemical tension at the haem environment is different in the alpha and beta haems. There are small but definite structural changes associated with ligation in the T-state: these prove to be mostly in the same direction as the larger changes that occur in the T-->R transition.
Computer Simulation↗
Crystal structure of an N-terminal fragment of the DNA gyrase B protein.
The crystal structure of an N-terminal fragment of the Escherichia coli DNA gyrase B protein, complexed with a nonhydrolysable ATP analogue, has been solved at 2.5 A resolution. It consists of two domains, both containing novel protein folds. The protein fragment forms a dimer, whose N-terminal domains are responsible for ATP binding and hydrolysis. The C-terminal domains form the sides of a 20 A hole through the protein dimer which may play a role in DNA strand passage during the supercoiling reaction.
Adenosine Triphosphate↗
A serine protease triad forms the catalytic centre of a triacylglycerol lipase.
True lipases attach triacylglycerols and act at an oil-water interface; they constitute a ubiquitous group of enzymes catalysing a wide variety of reactions, many with industrial potential. But so far the three-dimensional structure has not been reported for any lipase. Here we report the X-ray structure of the Mucor miehei triglyceride lipase and describe the atomic model obtained at 3.1 A resolution and refined to 1.9 A resolution. It reveals a Ser..His..Asp trypsin-like catalytic triad with an active serine buried under a short helical fragment of a long surface loop.
Amino Acid Sequence↗
Stereochemistry of carbon monoxide binding to normal human adult and Cowtown haemoglobins.
The structures of carbonmonoxyhaemoglobins A and Cowtown (His146 beta----Leu) have been refined at 2.2 A (1 A = 0.1 nm) and 2.3 A resolution, respectively. The least squares fit to the Fe-C-O line makes an angle to the haem normal of about 6 degrees. The Fe-C-O group is bent from linearity by about 7 degrees. The porphyrins in the CO liganded haemoglobins are ruffled. This deformation of the haem and the distortion of the Fe-C-O group may explain the low CO affinity of haemoglobin. The electron density for the C-terminal residues is low but sufficient to distinguish the histidyl and leucyl residues clearly. The similarity between these two structures, apart from 146 beta, means that the reduced alkaline Bohr effect is due solely to the replacement of histidine by a leucine.
Carbon Monoxide↗
Structure of insulin: results of joint neutron and X-ray refinement.
Neutron diffraction data for porcine 2Zn insulin were collected to 2.2 A resolution from a single crystal deuterated by slow exchange of mother liquor. A joint neutron/X-ray restrained-least-squares refinement was undertaken using the neutron data, as well as the 1.5 A resolution X-ray data collected previously. The final R factors were 0.182 for the X-ray data and 0.191 for the neutron data. Resulting atomic coordinates were compared with the initial X-ray model, showing a total r.m.s. shift of 0.36 A for the protein and 0.6 A for the solvent. Protonation of a number of individual amino acids was investigated by analysis of the neutron maps. No D atoms were found between the carboxylates of Glu B13 which make an intermolecular contact, suggesting nonbonded interaction rather than the predicted hydrogen bond. Amide hydrogen exchange was investigated in a refinement of their atomic occupancies. Regions of unexchanged amide groups were found in the center of the B helices. The results of this study emphasize the limited amount of information available in neutron diffraction studies of proteins at resolution lower than 2 A.
Animals↗
Monomeric insulins obtained by protein engineering and their medical implications.
The use of insulin as an injected therapeutic agent for the treatment of diabetes has been one of the outstanding successes of modern medicine. The therapy has, however, had its associated problems, not least because injection of insulin does not lead to normal diurnal concentrations of insulin in the blood. This is especially true at meal times when absorption from subcutaneous tissue is too slow to mimic the normal rapid increments of insulin in the blood. In the neutral solutions used for therapy, insulin is mostly assembled as zinc-containing hexamers and this self-association, which under normal physiological circumstances functions to facilitate proinsulin transport, conversion and intracellular storage, may limit the rate of absorption. We now report that it is possible, by single amino-acid substitutions, to make insulins which are essentially monomeric at pharmaceutical concentrations (0.6 mM) and which have largely preserved their biological activity. These monomeric insulins are absorbed two to three times faster after subcutaneous injection than the present rapid-acting insulins. They are therefore capable of giving diabetic patients a more physiological plasma insulin profile at the time of meal consumption.
Animals↗
Structure of the liganded T state of haemoglobin identifies the origin of cooperative oxygen binding.
A molecular description of haemoglobin's cooperative oxygen binding and release was founded on the X-ray crystal structures of the deoxy-T and oxy-R states. Since the R state's oxygen affinity is close to that of an isolated subunit, the crucial allosteric phenomena are (1) the reduced affinity of the T state and (2) the kinetic pathway between the two quaternary structures. To investigate these phenomena directly, we have determined at high resolution (dmin = 2.1 A) the crystal structures of two liganded T-state haemoglobins. In the liganded T-state alpha subunit, both the tight packing of the haem and the intersubunit contacts inhibit a conformational change between the F helix and FG corner which would allow the haem to become planar and the iron to assume symmetrical R-like coordination. In the beta subunit, by contrast, we find no strain on the proximal side, but the intersubunit contacts prevent the haem from tilting about an axis parallel to the F helix which would open up the binding site to oxygen. In both subunits, ligand binding in the T state induces structural changes towards the tertiary conformation of the R state.
Heme↗
Apomyoglobin as a molecular recognition surface: expression, reconstitution and crystallization of recombinant porcine myoglobin in Escherichia coli.
Recombinant porcine myoglobin has been produced in Escherichia coli using the lambda cII fusion expression system of Nagai and Thøgersen [Nature, 309, 810-812 (1984)]. After processing and reconstitution with haem, the protein is gel-electrophoretically and spectrophotometrically indistinguishable from native pig myoglobin. Large crystals of both native and recombinant porcine myoglobin were grown from 50 mM sodium phosphate, pH 7.1, 80% ammonium sulphate. The crystals belong to space group C2 (a = 156.9 A, b = 42.0 A, c = 92.2 A, beta = 127.9 degrees) and diffract to a nominal 2.5 A resolution. We plan to explore apomyoglobin as a binding surface in studies combining site-directed mutagenesis and X-ray analysis. These experiments will be extended by studying the binding of haem analogues to the mutant apoproteins.
Animals↗
An examination of the role of insulin dimerisation and negative cooperativity using the biological properties of the despentapeptide and deshexapeptide insulins.
The C-terminus of the insulin B chain is essential for dimerisation and expression of negative cooperativity. In order to evaluate the possible physiological role of these phenomena, we have studied the properties in vivo and in vitro of despentapeptide insulin (B26-30 deleted), derived from beef insulin, and deshexapeptide insulin (B25-30 deleted), derived from pork insulin. These materials do not dimerise and have 15% and 0% retention of negative cooperativity respective. Lipogenesis potencies in rat adipocytes were: despentapeptide insulin 19.9 +/- 0.3%; deshexapeptide insulin 19.9 +/- 1.5%. Binding potencies in adipocytes were: despentapeptide insulin 22.6 +/- 7.8%; deshexapeptide insulin 13.2 +/- 3.3%. Metabolic clearance rates were reduced compared to insulin (insulin = 19.1 +/- 0.9; despentapeptide insulin = 9.7 +/- 0.8; deshexapeptide insulin = 6.4 +/- 0.6 ml . min-1 . kg-1 at plasma concentration 0.5 nmol/l). Hypoglycaemic potencies were reduced for both analogues (40% and 30%) when calculated on the basis of plasma concentration although both analogues and insulin were equally effective at lowering plasma glucose concentration in equimolar doses. Plasma half-disappearance time was prolonged (despentapeptide insulin = 7.3 +/- 0.5; deshexapeptide insulin = 9.1 +/- 0.2 min). Both analogues were full agonists and conformed to the general relationship between in vitro and in vivo properties seen with a wide range of modified insulins. They resemble other analogues with modifications which reduce receptor affinity without impairing dimerisation or negative cooperativity. The results do not support a physiological role for dimerisation or negative cooperativity.
Adipose Tissue↗
Resistance of the insulin crystal to lysosomal proteases: implications for pancreatic B-cell crinophagy.
Insulin is thought to be chemically stabilized within beta-granules in the crystal form. The other major products of the beta-granule, proinsulin and C-peptide, by contrast, are not thought able to crystallize. The physico-chemical properties of peptides in soluble or crystalline form are dramatically different. The ability of insulin to crystallize in the beta-granule might thus explain why this peptide, but not proinsulin/C-peptide, remains stable even after its introduction into lysosomes as occurs during granulolysis (crinophagy). We have now studied this by exposing proinsulin or insulin to lysosomal proteases in vitro. 125I-insulin in soluble form was found to be degraded at the same rate as 125I-proinsulin. Strikingly, however, when the labelled insulin was crystallized, its rate of degradation was decreased from 1.9 to 0.2 pmol/min. We take these data as confirmation that the insulin crystal is resistant to degradation, thereby possibly accounting for (a) the presence of insulin immunoreactivity within multigranular bodies, and (b) the unusually slow rate of degradation of insulin within B cells compared with that of other hormones in their cells of origin.
Animals↗
Structure-function relationships of shortened [LeuB25]insulins, semisynthetic analogues of a mutant human insulin.
Replacement of B25-phenylalanine by leucine in the insulin sequence causes marked inactivation. The effect of this sequence variation was studied here in des-(B26-30)-insulin. [LeuB25]des-(B26-30)-insulin and its B25-amide were prepared by trypsin-mediated semisynthesis from N-terminally protected des-(B23-30)-insulin and synthetic tripeptides. The relative lipogenic potency in isolated rat adipocytes was 8.0% for the truncated analogue with a free B25-carboxyl function, and 18.1% for the amidated analogue. Binding to cultured human IM-9 lymphocytes was 4% and 9%, respectively. Thus, both shortened insulins are markedly more active than [LeuB25]insulin. The PheB25----LeuB25 substitution in both the shortened and the full sequence has a moderate effect on the CD spectrum, indicating that the gross main chain conformation is largely retained in both molecules. Independent of the substitution an absolute increase of the circular dichroism is observed upon amidation of the B25-carboxyl group.
Adipose Tissue↗