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At least 1,279 records · Page 71Linked to original sources
PubMed1999

Rapid structural characterisation of a murine monoclonal IgA alpha chain: heterogeneity in the oligosaccharide structures at a specific site in samples produced in different bioreactor systems.

A murine hybridoma cell line which secretes a monoclonal IgA antibody, directed against the LPS antigen of Vibrio cholerae, was grown in either a continuous stirred tank reactor, a fluidised bed reactor or a hollow fibre reactor. Different methods were used for the structural characterisation of the IgA alpha chains. A classical approach consisted of Edman sequencing and mass determination of peptides separated by reversed phase HPLC. Alternatively, peptides and glycopeptides from a tryptic digest of each alpha chain were identified directly by MALDI-TOF mass spectrometry. A detailed analysis of the oligosaccharide structures at an unique site on the alpha chain was made by labelling the oligosaccharides released by N-glycosidase F with 1-(p-methoxy)phenyl-3-methyl-5-pyrazolone. After separation by HPLC, mass measurements were made using matrix-assisted laser desorption time of flight mass spectrometry before and after digestion with specific exoglycosidases. The primary structure of the alpha chain of IgA was not affected by different cell culture conditions; in contrast, significant variations could be detected in the pattern of N-linked oligosaccharide structures, most prominently in the degree of sialylation. The efficiency of the analytical techniques in providing quality control of the identity, integrity and consistency of the glycoprotein is shown and discussed.

Amino Acid Sequence↗
PubMed2000

Deoxyribonuclease II: structure and chromosomal localization of the murine gene, and comparison with the genomic structure of the human and three C. elegans homologs.

Deoxyribonuclease II (DNase II) has been implicated in diverse functions including degradation of foreign DNA, genomic instability, and in mediating the DNA digestion associated with apoptosis. The production of a mouse deleted for DNase II would clearly help to discriminate these functions. We have cloned and sequenced the mouse gene encoding DNase II. It was found to have a similar intron/exon structure to the human gene, although introns 3 and 5 are considerably shorter. The gene is located on mouse chromosome 8. The order of genes at this locus is mGCDH, mEKLF, mDNase II, mSAST, which is the same order that these genes are found on human chromosome 19. The GenBank database contains incorrect expressed sequence tags (ESTs) for the 3' end of the mouse mRNA. Furthermore, the gene structure of two of the three homologs in C. elegans is also incorrectly predicted in the database. We have established the correct intron/exon structure for these genes and show the conserved sequence and structure of the C. elegans, murine and human genes.

Amino Acid Sequence↗
PubMed1997

RNA structures and folding: from conventional to new issues in structure predictions.

Prediction and modeling of RNA structures has become an indispensable tool of biological research disciplines. Currently, reliable predictions require massive input of experimental data. Structure-forming elements are conventional base pairs, as well as a rapidly increasing repertoire of novel structural motifs. New developments extend structural analysis beyond the one-sequence/one-structure paradigm and allow questions that are relevant to molecular evolution to be answered.

Algorithms↗
PubMed2002

Structure of the cathelicidin motif of protegrin-3 precursor: structural insights into the activation mechanism of an antimicrobial protein.

Cathelicidins are a family of antimicrobial proteins isolated from leucocytes and epithelia cells that contribute to the innate host defense mechanisms in mammalians. Located in the C-terminal part of the holoprotein, the cathelicidin-derived antimicrobial peptide is liberated by a specific protease cleavage. Here, we report the X-ray structure of the cathelicidin motif of protegrin-3 solved by MAD phasing using the selenocysteine-labeled protein. Its overall structure represents a fold homologous to the cystatin family and adopts two native states, a monomer, and a domain-swapped dimer. This crystal structure is the first example of a structural characterization of the highly conserved cathelicidin motif and thus provides insights into the possible mechanism of activation of the antimicrobial protegrin peptide.

Amino Acid Motifs↗
PubMed1996

The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of stable RNA structures and the diversity of recognition sites.

BACKGROUND: Non-canonical base pairs are fundamental building blocks of RNA structures. They can adopt geometries quite different from those of canonical base pairs and are common in RNA molecules that do not transfer sequence information. Tandem U-U base pairs occur frequently, and can stabilize duplex formation despite the fact that a single U-U base pair is destabilizing. RESULTS: We determined the crystal structure of the RNA dodecamer GGCGCUUGCGUC at 2.4 A resolution. The molecule forms a duplex containing tandem U-U base pairs, which introduce an overall bend of 11-12 degrees in the duplex resulting from conformational changes at each interface between the tandem U-U base pairs and a flanking duplex sequence. The formation of the U-U base pairs cause small changes in several backbone torsion angles; base stacking is preserved and two hydrogen bonds are formed per base pair, explaining the stability of the structure. CONCLUSIONS: Tandem U-U base pairs can produce stable structures not accessible to normal A-form RNA, which may allow the formation of specific interfaces for RNA-RNA or RNA-protein recognition. These base-pairs show an unusual pattern of hydrogen-bond donors and acceptors in the major and minor grooves, which could also act as a recognition site.

Base Composition↗
PubMed1996

Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site.

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.

Carboxylic Acids↗
PubMed1997

Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis.

BACKGROUND: The hydrogenase of Desulfovibrio sp. catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. The Ni-Fe active center of Desulfovibrio hydrogenase has an unusual ligand structure with non-protein ligands. An atomic model at high resolution is required to make concrete assignment of the ligands which coordinate the Ni-Fe center. These in turn will provide insight into the mechanism of electron transfer, during the reaction catalysed by hydrogenase. RESULTS: The X-ray structure of the hydrogenase from Desulfovibrio vulgaris Miyazaki has been solved at 1.8 A resolution and refined to a crystallographic R factor of 0.229. The overall folding pattern and the spatial arrangement of the metal centers are very similar to those found in Desulfovibrio gigas hydrogenase. This high resolution crystal structure enabled us to assign the non-protein ligands to the Fe atom in the Ni-Fe site and revealed the presence of a Mg center, located approximately 13 A from the Ni-Fe active center. CONCLUSIONS: From the nature of the electron-density map, stereochemical geometry and atomic parameters of the refined structure, the most probable candidates for the four ligands, coordinating the Ni-Fe center, have been proposed to be diatomic S=O, C triple bond O and C triple bond N molecules and one sulfur atom. The assignment was supported by pyrolysis mass spectrometry measurements. These ligands may have a role as an electron sink during the electron transfer reaction between the hydrogenase and its biological counterparts, and they could stabilize the redox state of Fe(II), which may not change during the catalytic cycle and is independent of the redox transition of the Ni. The hydrogen-bonding system between the Ni-Fe and the Mg centers suggests the possible.

Binding Sites↗
PubMed1998

The crystal structure of the novel snake venom plasminogen activator TSV-PA: a prototype structure for snake venom serine proteinases.

BACKGROUND: Trimeresurus stejnejeri venom plasminogen activator (TSV-PA) is a snake venom serine proteinase that specifically activates plasminogen. Snake venom serine proteinases form a subfamily of trypsin-like proteinases that are characterised by a high substrate specificity and resistance to inhibition. Many of these venom enzymes specifically interfere with haemostatic mechanisms and display a long circulating half-life. For these reasons several of them have commercial applications and are potentially attractive pharmacological tools. RESULTS: The crystal structure of TSV-PA has been determined to 2.5 A resolution and refined to an R factor of 17.8 (R free, 24.4). The enzyme, showing the overall polypeptide fold of trypsin-like serine proteinases, displays unique structural elements such as the presence of a phenylalanine at position 193, a C-terminal tail clamped via a disulphide bridge to the 99-loop, and a structurally conserved Asp97 residue. The presence of a cis proline at position 218 is in agreement with evolutionary relationships to glandular kallikrein. CONCLUSIONS: We postulate that Phe 193 accounts for the high substrate specificity of TSV-PA and renders it incapable of forming a stable complex with bovine pancreatic trypsin inhibitor and other extended substrates and inhibitors. Mutational studies previously showed that Asp97 is crucial for the plasminogenolytic activity of TSV-PA, here we identify the conservation of Asp97 in both types of mammalian plasminogen activator - tissue-type (tPA) and urokinase-type (uPA). It seems likely that Asp97 of tPA and uPA will have a similar role in plasminogen recognition. The C-terminal extension of TSV-PA is conserved among snake venom serine proteinases, although its function is unknown. The three-dimensional structure presented here is the first of a snake venom serine proteinase and provides an excellent template for modelling other homologous family members.

Amino Acid Chloromethyl Ketones↗
PubMed1999

The 2.7 A crystal structure of deoxygenated hemoglobin from the sea lamprey (Petromyzon marinus): structural basis for a lowered oxygen affinity and Bohr effect.

BACKGROUND: The hemoglobins of the sea lamprey are unusual in that cooperativity and sensitivity to pH arise from an equilibrium between a high-affinity monomer and a low-affinity oligomer. Although the crystal structure of the monomeric cyanide derivative has previously been determined, the manner by which oligomerization acts to lower the oxygen affinity and confer a strong Bohr effect has, until now, been speculative. RESULTS: We have determined the crystal structure of deoxygenated lamprey hemoglobin V by molecular replacement to 2.7 A resolution, in a crystal form with twelve protomers in the asymmetric unit. The subunits are arranged as six essentially identical dimers, with a novel subunit interface formed by the E helices and the AB corner using the standard hemoglobin helical designations. In addition to nonpolar interactions, the interface includes a striking cluster of four glutamate residues. The proximity of the interface to ligand-binding sites implicates a direct effect on ligand affinity. CONCLUSIONS: Comparison of the deoxy structure with that of the cyanide derivative revealed conformational changes that appear to be linked to the functional behavior. Oligomerization is coupled with a movement of the first half of the E helix by up to 1.0 A towards the heme, resulting in steric interference of ligand binding to the deoxy structure. The Bohr effect seems to result from proton uptake by glutamate residues as they are buried in the interface. Unlike human and mollusc hemoglobins, in which modulation of function is due to primarily proximal effects, regulation of oxygen affinity in lamprey hemoglobin V seems to depend on changes at the distal (ligand-binding) side of the heme group.

Animals↗
PubMed2003

The Southeast Collaboratory for Structural Genomics: a high-throughput gene to structure factory.

The Southeast Collaboratory for Structural Genomics consists of four working groups. The protein production group supplies/develops high-output production of Pyrococcus furiosus, Caenorhabditis elegans, and selected human proteins. The X-ray crystallography group conducts high-throughput structure production in parallel with production-related research/development in nanocrystallization robotics, capillary crystallization cassette, synchrotron/home X-ray instrumentation, sample mounting robotics, data processing and pipelined structure analysis, combined refinement/validation protocols, and direct use of unlabeled native crystals (Direct Crystallography). The NMR group emphasizes/develops sample screening and backbone structure determination from residual dipolar coupling data. The bioinformatics group implements/develops local database interfaces, pipelined sequence/structure information search/updates, and database/bioinformatics toolkits.

Animals↗
PubMed1995

Structural basis for the sequence-specific DNA strand cleavage by the enediyne neocarzinostatin chromophore. Structure of the post-activated chromophore-DNA complex.

Neocarzinostatin chromophore (NCS chrom) belongs to a family of highly potent enediyne antitumor antibiotics which bind to specific DNA sequences and cause single- and/or double-strand lesions. NCS chrom-DNA complexes have eluded structural studies since the native form of the drug is extremely labile in aqueous conditions. We report the three-dimensional structure of the stable glutathione post-activated NCS chrom (NCSi-glu)-DNA complex [NCSi-glu-d(GGAGCGC).d(GCGCTCC)] using NMR and distance geometry-molecular dynamics simulation methods. NCSi-glu interacts with the GCTC tetranucleotide on one strand and with the AGC trinucleotide on the other strand through the unique intercalation at the 5'-CT/5'-AG step and minor groove binding. The DNA-drug complex exhibits an extended, unwound V-shaped intercalation site and wider and shallower grooves than the free DNA duplex. The structure of the complex manifests specific van der Waals interactions and H-bond formation between the carbohydrate moiety and a specific DNA sugar/phosphate. Prominent among those are the contacts of the NCSi-glu residues with the functional groups in the minor groove that are characteristic of individual DNA bases. These results provide a structural model for understanding the sequence specificity of the single- and double-strand cleavage at the AGC and related sites by the enediyne NCS chrom.

Base Sequence↗
PubMed2000

Crystal structures of spin labeled T4 lysozyme mutants: implications for the interpretation of EPR spectra in terms of structure.

High resolution (1.43-1.8 A) crystal structures and the corresponding electron paramagnetic resonance (EPR) spectra were determined for T4 lysozyme derivatives with a disulfide-linked nitroxide side chain [-CH(2)-S-S-CH(2)-(3-[2,2,5,5-tetramethyl pyrroline-1-oxyl]) identical with R1] substituted at solvent-exposed helix surface sites (Lys65, Arg80, Arg119) or a tertiary contact site (Val75). In each case, electron density is clearly resolved for the disulfide group, revealing distinct rotamers of the side chain, defined by the dihedral angles X(1) and X(2). The electron density associated with the nitroxide ring in the different mutants is inversely correlated with its mobility determined from the EPR spectrum. Residue 80R1 assumes a single g(+)()g(+)() conformation (Chi(1) = 286, X(2) = 294). Residue 119R1 has two EPR spectral components, apparently corresponding to two rotamers, one similar to that for 80R1 and the other in a tg(-)() conformation (Chi(1) = 175, X(2) = 54). The latter state is apparently stabilized by interaction of the disulfide with a Gln at i + 4, a situation also observed at 65R1. R1 residues at helix surface site 65 and tertiary contact site 75 make intra- as well as intermolecular contacts in the crystal and serve to identify the kind of molecular interactions possible for the R1 side chain. A single conformation of the entire 75R1 side chain is stabilized by a variety of interactions with the nitroxide ring, including hydrophobic contacts and two unconventional C-H.O hydrogen bonds, one in which the nitroxide acts as a donor (with tyrosine) and the other in which it acts as an acceptor (with phenylalanine). The interactions revealed in these structures provide an important link between the dynamics of the R1 side chain, reflected in the EPR spectrum, and local protein structure. A library of such interactions will provide a basis for the quantitative interpretation of EPR spectra in terms of protein structure and dynamics.

Bacteriophage T4↗
PubMed1984

Primary structure of wheat germ agglutinin isolectin 2. Peptide order deduced from X-ray structure.

The complete amino acid sequence of wheat germ agglutinin isolectin 2 has been determined by the method of sequential Edman degradation and with the aid of the three-dimensional structure known from X-ray crystallography. Peptides ranging from 2 to 18 residues in length were obtained by thermolysin digestion of the S-carboxymethylated protein and purified by gel filtration and high-performance liquid chromatography. The peptide order was established primarily by matching (carboxymethyl)cysteines with the clearly defined half-cystine positions in the X-ray structure, thereby satisfying the disulfide repeat pattern observed in all four isostructural domains (A, B, C, and D) of wheat germ agglutinin, and by examination of amino acid compositions and terminal sequences of ten tryptic peptides. The unique assignment of peptides to these domains was consistent with all invariant half-cystines and glycines, as well as the single tryptophan, the two closely spaced histidines, and a number of other residues clearly identified in the X-ray structure analysis. Discrepancies between the chemical and X-ray sequences lie exclusively in poorly defined regions of the electron density map, at the N- and C-termini, and at the first intercystine loop of each domain. The latter loop was found to be eight instead of six residues in length, thus extending the size of domains A, B, and C from 41 to 43 residues and that of domain D to 42 residues. Regions of extensive interdomain homology, in addition to that of the half-cystines, are clustered at the central portion of each domain fold and are likely to be important for the integrity of the three-dimensional structure of the dimer molecule.

Amino Acid Sequence↗
PubMed1984

5S RNA structure and interaction with transcription factor A. 1. Ribonuclease probe of the structure of 5S RNA from Xenopus laevis oocytes.

The structure of Xenopus laevis oocyte (Xlo) 5S ribosomal RNA has been probed with single-strand-specific ribonucleases T1, T2, and A with double-strand-specific ribonuclease V1 from cobra venom. The digestion of 5'- or 3'-labeled renatured 5S RNA samples followed by gel purification of the digested samples allowed the determination of primary cleavage sites. Results of these ribonuclease digestions provide support for the generalized 5S RNA secondary structural model derived from comparative sequence analysis. However, three putative single-stranded regions of the molecule exhibited unexpected V1 cuts, found at C36, U73, U76, and U102. These V1 cuts reflect additional secondary structural features of the RNA including A.G base pairs and support the extended base pairing in the stem containing helices IV and V which was proposed by Stahl et al. [Stahl, D. A., Luehrsen, K. R., Woese, C. R., & Pace, N. R. (1981) Nucleic Acids Res. 9, 6129-6137]. A conserved structure for helix V having a common unpaired uracil residue at Xlo position 84 is proposed for all eukaryotic 5S RNAs. Our results are compared with nuclease probes of other 5S RNAs.

Animals↗
PubMed1987

Solution structure of [d(GGTATACC)]2: wrinkled D structure of the TATA moiety.

Phase-sensitive two-dimensional nuclear Overhauser effect spectra of [d(GGTATACC)]2 in aqueous deuterium oxide solution at four mixing times were quantified to give all nonoverlapping cross-peak intensities. A structural model for [d(GGTATACC)]2 was built in which the GG- and -CC moieties were in the B-DNA form, while the middle -TATA- moiety was in the wrinkled-D form (BDB model). This model was subjected to energy refinement by molecular mechanics calculations with the program AMBER. Counterions (Na+) were added to neutralize the charges, and water molecules were placed bridging across the minor groove. A complete relaxation matrix analysis was used to calculate two-dimensional nuclear Overhauser effect spectra of [d(GGTATACC)]2 from the above models (before and after energy refinement) and from four other [d(GGTATACC)]2 structural models: regular A, crystalline A, regular B, and energy-minimized B. Among them, the energy-minimized BDB model yielded a set of theoretical spectra that gave the best fit to the experimental spectra. It was also the energetically most stable. Therefore, it is a good representation of the ensemble- and time-averaged structure of the octamer in solution. This model has backbone torsion angles similar to those of B-form DNA in the GG- and -CC moieties and torsion angles similar to those of wrinkled D form DNA in the -TATA- moiety. The base stacking and base pairing are not interrupted at the junctions between the two structural moieties. Its minor groove is narrower than that of B DNA, and the solvent-accessible surface of the minor groove forms a closed hydration tunnel in the middle -TATA- segment.

Adenine↗
PubMed1980

Stability and reversibility of higher ordered structure of interphase chromatin: continuity of deoxyribonucleic acid is not required for maintenance of folded structure.

The organization of the higher order structure of chromatin has been examined in chicken erythrocyte. Chromatin solubilized during the time course of a gentle micrococcal nuclease digestion of nuclei shows a continuous variation in the distribution of molecular weights. Electron microscopy studies of large chromatin fragments solubilized at physiological ionic strength (0.14 M NaCl or KCl) suggest that the polynucleosome chain is folded in continuous compact structures of an average diameter of 23 nm in which the individual nucleosomes are difficult to distinguish. This compact structure is destabilized even at intermediate ionic strengths (e.g., 40 mM NaCl), resulting in looser fibers of similar diameter. At 5 mM NaCl the fiber is unraveled into a continuous filament of 10-nm diameter. These conformational changes are reversible as determined by hydrodynamic and biochemical parameters. The 10-nm leads to 23-nm transition of chromatin appears to be a cooperative process requiring the full complement of histones H1 and H5. Micrococcal nuclease cleaves the DNA in the compact chromatin structure to an apparent limit of digestion corresponding to an average of eight to nine nucleosomes with little effect on the size of the fiber. Thus, the continuity of the DNA is not required for the stability of the folded chromatin fiber. Histones H1 and H5 exhibit a binding preference to larger chromatin fragments regardless of the length of the DNA. This behavior is not observed with relaxed chromatin, suggesting that multiple stabilizing interactions involving H1 (H5) are possible only in the compact configuration.

Animals↗
PubMed2004

X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures.

The X-ray crystal structure of recombinant Desulfovibrio vulgaris rubrerythrin (Rbr) that was subjected to metal constitution first with zinc and then iron, yielding ZnS(4)Rbr, is reported. A [Zn(SCys)(4)] site with no iron and a diiron site with no appreciable zinc in ZnS(4)Rbr were confirmed by analysis of the anomalous scattering data. Partial reduction of the diiron site occurred during the synchrotron X-ray irradiation at 95 K, resulting in two different diiron site structures in the ZnS(4)Rbr crystal. These two structures can be classified as containing mixed-valent Fe1(III)(mu-OH(-))(mu-GluCO(2)(-))(2)Fe2(II) and Fe1(II)(mu-GluCO(2)(-))(2)Fe2(III)-OH(-) cores. The data do not show any evidence for alternative positions of the protein or solvent ligands. The iron and ligand positions of the solvent-bridged site are close to those of the diferric site in all-iron Rbr. The diiron site with only the two carboxylato bridges differs by an approximately 2 A shift in the position of Fe1, which changes from six- to four-coordination. The Fe1- - -Fe2 distance (3.6 A) in this latter site is significantly longer than that of the site with the additional solvent bridge (3.4 A) but significantly shorter than that previously reported for the diferrous site (4.0 A) in all-iron Rbr. The apparent redox-induced movement of Fe1 at 95 K in the ZnS(4)Rbr crystal implies an extremely low activation barrier, which is consistent with the rapid (approximately 30 s(-1)) room temperature turnover of the all-iron Rbr during its catalysis of two-electron reduction of hydrogen peroxide. ZnS(4)Rbr does not show peroxidase activity, presumably because the [Zn(SCys)(4)] site, unlike the [Fe(SCys)(4)] site, cannot mediate electron transfer to the diiron site. One or both of the diiron site structures in the cryoreduced ZnS(4)Rbr crystal are likely to represent that (those) of transient mixed-valent diiron site(s) that must occur upon return of the diferric to the diferrous oxidation level during peroxidase turnover.

Bacterial Proteins↗
PubMed1997

Structure of hexadienoyl-CoA bound to enoyl-CoA hydratase determined by transferred nuclear Overhauser effect measurements: mechanistic predictions based on the X-ray structure of 4-(chlorobenzoyl)-CoA dehalogenase.

The structure of the substrate analog 2,4-hexadienoyl-coenzyme A (HD-CoA) bound to the enzyme enoyl-CoA hydratase has been determined using transferred nuclear Overhauser enhancement (TRNOE) spectroscopy. NOEs between the adenine H8 proton and several pantetheine protons in the bound form of HD-CoA indicate that the overall structure of the CoA molecule is bent, while NOEs between adenine and ribose protons indicate that the conformation about the glycosidic bond is anti. The absence of long range NOEs along the pantetheine moiety is consistent with this region of the molecule being bound in an extended conformation. In addition, NOEs between the vinylic protons indicate that the HD moiety is s-trans about C3-C4. The conformation of the CoA portion of bound HD-CoA is strikingly similar to that of the CoA portion of 4-(hydroxybenzoyl)-CoA bound to the active site of 4-(chlorobenzoyl)-CoA dehalogenase [Benning, M. M., et al. (1996) Biochemistry 35, 8103-8109]. The structural similarity of the ligands along with the primary sequence homology validates the modeling of the enoyl-CoA hydratase structure with the 4-(chlorobenzoyl)-CoA dehalogenase backbone. The homology modeling allows the prediction that the enoyl-CoA substrates are bound in an s-cis conformation about C1-C2 and that Glu 144 is present at the active site and can function as a general acid/base.

Alkadienes↗