Genomes and Genes
Summary: A class of enzymes that catalyze geometric or structural changes within a molecule to form a single product. The reactions do not involve a net change in the concentrations of compounds other than the substrate and the product.(from Dorland, 28th ed) EC 5.
- Teplyakov A, Obmolova G, Badet Denisot M, Badet B. The mechanism of sugar phosphate isomerization by glucosamine 6-phosphate synthase. Protein Sci. 1999;8:596-602 pubmed..The enediol intermediate is stabilized by a helix dipole and the epsilon-amino group of Lys603. Lys485 may play a role in deprotonating the hydroxyl O1 of the intermediate. ..
- van der Wal F, Oliver J, High S. The transient association of ERp57 with N-glycosylated proteins is regulated by glucose trimming. Eur J Biochem. 1998;256:51-9 pubmed..These data are combined to present a unified model for the role of ERp57/ER lectin complexes during glycoprotein folding in vivo. ..
- Marsh E, Drennan C. Adenosylcobalamin-dependent isomerases: new insights into structure and mechanism. Curr Opin Chem Biol. 2001;5:499-505 pubmedAdenosylcobalamin-dependent isomerases catalyze a variety of chemically difficult 1,2-rearrangements that proceed through a mechanism involving free radical intermediates...
- Lindquist J, Jensen O, Mann M, Hammerling G. ER-60, a chaperone with thiol-dependent reductase activity involved in MHC class I assembly. EMBO J. 1998;17:2186-95 pubmed..In a beta2-microglobulin (beta2m)-negative mouse cell line, S3, ER-60-calnexin-heavy chain complexes are shown to bind to TAP, suggesting that beta2m is not required for the association of MHC class I heavy chains with TAP...
- Lesburg C, Zhai G, Cane D, Christianson D. Crystal structure of pentalenene synthase: mechanistic insights on terpenoid cyclization reactions in biology. Science. 1997;277:1820-4 pubmed
- High S, Lecomte F, Russell S, Abell B, Oliver J. Glycoprotein folding in the endoplasmic reticulum: a tale of three chaperones?. FEBS Lett. 2000;476:38-41 pubmed..These components are calnexin, calreticulin and ERp57, and this review focuses on the molecular basis for their capacity to influence glycoprotein folding. ..
- Teplyakov A, Obmolova G, Badet B, Badet Denisot M. Channeling of ammonia in glucosamine-6-phosphate synthase. J Mol Biol. 2001;313:1093-102 pubmed..Based on the structure, a mechanism of enzyme action and self-regulation is proposed. It involves large domain movements triggered by substrate binding that lead to the formation of the channel. ..
- Peters R, Ravn M, Coates R, Croteau R. Bifunctional abietadiene synthase: free diffusive transfer of the (+)-copalyl diphosphate intermediate between two distinct active sites. J Am Chem Soc. 2001;123:8974-8 pubmed..In addition, both mutant enzymes enhance the activity of wild-type abietadiene synthase with geranylgeranyl diphosphate as substrate. The implications of these results for the kinetic mechanism of abietadiene synthase are discussed. ..
- Köksal M, Jin Y, Coates R, Croteau R, Christianson D. Taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis. Nature. 2011;469:116-20 pubmed publisher..A class?II cyclase activates the isoprenoid substrate by protonation instead of ionization, and the TXS structure reveals a definitive connection between the two distinct cyclase classes in the evolution of terpenoid biosynthesis. ..
- Frickel E, Riek R, Jelesarov I, Helenius A, Wuthrich K, Ellgaard L. TROSY-NMR reveals interaction between ERp57 and the tip of the calreticulin P-domain. Proc Natl Acad Sci U S A. 2002;99:1954-9 pubmed..These results are analyzed with regard to the functional mechanism of the CRT/ERp57 chaperone system. ..
- Jin Y, Williams D, Croteau R, Coates R. Taxadiene synthase-catalyzed cyclization of 6-fluorogeranylgeranyl diphosphate to 7-fluoroverticillenes. J Am Chem Soc. 2005;127:7834-42 pubmed
- Prisic S, Xu J, Coates R, Peters R. Probing the role of the DXDD motif in Class II diterpene cyclases. Chembiochem. 2007;8:869-74 pubmed
- Dick T, Bangia N, Peaper D, Cresswell P. Disulfide bond isomerization and the assembly of MHC class I-peptide complexes. Immunity. 2002;16:87-98 pubmed..These findings suggest a role for disulfide bond isomerization in tapasin-mediated peptide loading. ..
- Antoniou A, Ford S, Alphey M, Osborne A, Elliott T, Powis S. The oxidoreductase ERp57 efficiently reduces partially folded in preference to fully folded MHC class I molecules. EMBO J. 2002;21:2655-63 pubmed..Our data suggest that the reductase activity of ERp57 may be involved during the unfolding of MHC class I molecules, leading to targeting for degradation. ..
- Mata N, Radu R, Clemmons R, Travis G. Isomerization and oxidation of vitamin a in cone-dominant retinas: a novel pathway for visual-pigment regeneration in daylight. Neuron. 2002;36:69-80 pubmed..Together these activities comprise a novel pathway that regenerates opsin photopigments at a rate 20-fold faster than the known visual cycle. We suggest that this pathway is responsible for sustained daylight vision in vertebrates. ..
- Bouvier M. Accessory proteins and the assembly of human class I MHC molecules: a molecular and structural perspective. Mol Immunol. 2003;39:697-706 pubmed
- Lappi A, Lensink M, Alanen H, Salo K, Lobell M, Juffer A, et al. A conserved arginine plays a role in the catalytic cycle of the protein disulphide isomerases. J Mol Biol. 2004;335:283-95 pubmed..This intra-domain motion resolves the apparent dichotomy of the pK(a) requirements for the C-terminal active-site cysteine. ..
- Karala A, Psarrakos P, Ruddock L, Klappa P. Protein disulfide isomerases from C. elegans are equally efficient at thiol-disulfide exchange in simple peptide-based systems but show differences in reactivity towards protein substrates. Antioxid Redox Signal. 2007;9:1815-23 pubmed
- Sureshkumar S, Todesco M, Schneeberger K, Harilal R, Balasubramanian S, Weigel D. A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana. Science. 2009;323:1060-3 pubmed publisher..The Bur-0 IIL1 defect thus presents a genetically tractable model for triplet repeat expansions and their variability in natural populations. ..
- Lorence M, Murry B, Trant J, Mason J. Human 3 beta-hydroxysteroid dehydrogenase/delta 5----4isomerase from placenta: expression in nonsteroidogenic cells of a protein that catalyzes the dehydrogenation/isomerization of C21 and C19 steroids. Endocrinology. 1990;126:2493-8 pubmed..Thus, the dehydrogenation/isomerization steps of steroid biosynthesis can be catalyzed by a single polypeptide chain, which can metabolize all of the major physiological substrates. ..
- Zapun A, Bardwell J, Creighton T. The reactive and destabilizing disulfide bond of DsbA, a protein required for protein disulfide bond formation in vivo. Biochemistry. 1993;32:5083-92 pubmed..This implies that the disulfide bond destabilizes the folded conformation of DsbA. This was confirmed by demonstrating that the reduced protein was 3.6 +/- 1.4 kcal.mol-1 more stable than that with the disulfide bond. ..
- Zhang H, Donnenberg M. DsbA is required for stability of the type IV pilin of enteropathogenic escherichia coli. Mol Microbiol. 1996;21:787-97 pubmed..These data illuminate the early steps in the biogenesis of type IV fimbriae by demonstrating that newly synthesized prepilin is a transmembrane protein accessible to periplasmic and cytoplasmic processing enzymes. ..
- Edman J, Ellis L, Blacher R, Roth R, Rutter W. Sequence of protein disulphide isomerase and implications of its relationship to thioredoxin. Nature. 1985;317:267-70 pubmed..The cDNA predicts a signal peptide consistent with the view that PDI is a luminal endoplasmic reticulum protein. PDI messenger RNA, although ubiquitous, is more highly concentrated in secretory cells. ..
- Kemmink J, Darby N, Dijkstra K, Nilges M, Creighton T. Structure determination of the N-terminal thioredoxin-like domain of protein disulfide isomerase using multidimensional heteronuclear 13C/15N NMR spectroscopy. Biochemistry. 1996;35:7684-91 pubmed..The results confirm that PDI has a modular, multidomain structure, which will facilitate its structural and functional characterization. ..
- Bouchard B, del Marmol V, Jackson I, Cherif D, Dubertret L. Molecular characterization of a human tyrosinase-related-protein-2 cDNA. Patterns of expression in melanocytic cells. Eur J Biochem. 1994;219:127-34 pubmed..TYRP2 has been mapped to the chromosomal region 13q32, thus extending a region of synteny with mouse-chromosome 14. ..
- Subramanya H, Roper D, Dauter Z, Dodson E, Davies G, Wilson K, et al. Enzymatic ketonization of 2-hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomerases. Biochemistry. 1996;35:792-802 pubmed..Finally, the molecular basis for substrate specificity in the two enzymes is discussed. ..
- Orlow S, Hearing V, Sakai C, Urabe K, Zhou B, Silvers W, et al. Changes in expression of putative antigens encoded by pigment genes in mouse melanomas at different stages of malignant progression. Proc Natl Acad Sci U S A. 1995;92:10152-6 pubmed
- Bourdi M, Demady D, Martin J, Jabbour S, Martin B, George J, et al. cDNA cloning and baculovirus expression of the human liver endoplasmic reticulum P58: characterization as a protein disulfide isomerase isoform, but not as a protease or a carnitine acyltransferase. Arch Biochem Biophys. 1995;323:397-403 pubmed..However, it did have protein disulfide isomerase activity, indicating that the physiological activity of human liver P58 may be attributed, at least in part, to this activity. ..
- Tachikawa H, Takeuchi Y, Funahashi W, Miura T, Gao X, Fujimoto D, et al. Isolation and characterization of a yeast gene, MPD1, the overexpression of which suppresses inviability caused by protein disulfide isomerase depletion. FEBS Lett. 1995;369:212-6 pubmed..MPD1 was not essential for growth, but overexpression of the gene suppressed the maturation defect of carboxypeptidase Y caused by PDI1 deletion, indicative of the related function to PDI in the yeast ER. ..
- Yokoyama K, Suzuki H, Yasumoto K, Tomita Y, Shibahara S. Molecular cloning and functional analysis of a cDNA coding for human DOPAchrome tautomerase/tyrosinase-related protein-2. Biochim Biophys Acta. 1994;1217:317-21 pubmed..Human TRP-2/DOPAchrome tautomerase is composed of 519 amino acids with a molecular weight of 59,000 and has about 84% identity with the mouse counterpart. ..
- Chivers P, Laboissiere M, Raines R. The CXXC motif: imperatives for the formation of native disulfide bonds in the cell. EMBO J. 1996;15:2659-67 pubmed..Thus, an enzymic thiolate is both necessary and sufficient for the formation of native disulfide bonds in the cell. ..
- Grauschopf U, Winther J, Korber P, Zander T, Dallinger P, Bardwell J. Why is DsbA such an oxidizing disulfide catalyst?. Cell. 1995;83:947-55 pubmed..The pKa of Cys-30 varied dramatically from mutant to mutant and could accurately predict the oxidizing power of each DsbA mutant protein. ..
- Hirano N, Shibasaki F, Sakai R, Tanaka T, Nishida J, Yazaki Y, et al. Molecular cloning of the human glucose-regulated protein ERp57/GRP58, a thiol-dependent reductase. Identification of its secretory form and inducible expression by the oncogenic transformation. Eur J Biochem. 1995;234:336-42 pubmed..Moreover, it is likely that ERp57/GRP58 is involved in the oncogenic transformation. ..
- Martin J, Bardwell J, Kuriyan J. Crystal structure of the DsbA protein required for disulphide bond formation in vivo. Nature. 1993;365:464-8 pubmed..These features suggest that DsbA might act by binding to partially folded polypeptide chains before oxidation of cysteine residues. ..
- Oliver J, van der Wal F, Bulleid N, High S. Interaction of the thiol-dependent reductase ERp57 with nascent glycoproteins. Science. 1997;275:86-8 pubmed..Thus, it is likely that ERp57 functions as part of the glycoprotein-specific quality control machinery operating in the lumen of the ER. ..
- Bardwell J, McGovern K, Beckwith J. Identification of a protein required for disulfide bond formation in vivo. Cell. 1991;67:581-9 pubmed..The purified DsbA protein is capable of reducing the disulfide bonds of insulin, an activity that it shares with these disulfide oxidoreductases. Our results suggest that disulfide bond formation is facilitated by DsbA in vivo. ..
- Tan H, Lim K, Yang Q, Fan J, Sayed A, Low L, et al. Prolyl isomerization of the CENP-A N-terminus regulates centromeric integrity in fission yeast. Nucleic Acids Res. 2017;: pubmed publisher..fidelity, which appears to be carried out by two FK506-binding protein (FKBP) family prolyl cis-trans isomerases. Using proteomics analysis, we further identified the SpCENP-A-localizing chaperone Sim3 as a SpCENP-A NTD ..
- Martin T, Lou Y, Aryal S, Tai J, Chen C. 1H, 13C and 15N resonance assignments and secondary structures of cyclophilin 2 from Trichomonas vaginalis. Biomol NMR Assign. 2018;12:27-30 pubmed publisherCyclophilins are peptidyl prolyl isomerases that play an important role in a wide variety of biological functions like protein folding and trafficking, intracellular and extracellular signaling pathways, nuclear translocation and in pre-..
- Upham J, Acott P, O regan P, Sinal C, Crocker J, Geldenhuys L, et al. The pesticide adjuvant, Toximul, alters hepatic metabolism through effects on downstream targets of PPARalpha. Biochim Biophys Acta. 2007;1772:1057-64 pubmed
- Marks A. Cellular functions of immunophilins. Physiol Rev. 1996;76:631-49 pubmedImmunophilins are members of a highly conserved family of proteins all of which are cis-trans peptidyl-prolyl isomerases. The prototypic members of the immunophilin family, cyclophilin A and FKPB12, were discovered on the basis of their ..
- Balali Mood K, Bond P, Sansom M. Interaction of monotopic membrane enzymes with a lipid bilayer: a coarse-grained MD simulation study. Biochemistry. 2009;48:2135-45 pubmed publisher..Deeper insertion seems to correlate with a greater number of basic residues in the "foot" whereby a monotopic protein interacts with the membrane. ..
- Thomloudi E, Skagia A, Venieraki A, Katinakis P, Dimou M. Functional analysis of the two cyclophilin isoforms of Sinorhizobium meliloti. World J Microbiol Biotechnol. 2017;33:28 pubmed publisher..ppiA and ppiB, encoding two cyclophilin isoforms which belong to the superfamily of peptidyl prolyl cis/trans isomerases (PPIase, EC: 18.104.22.168)...
- Kim S, Choi H, Ahn S. Pin1 induces the ADP-induced migration of human dental pulp cells through P2Y1 stabilization. Oncotarget. 2016;7:85381-85392 pubmed publisherPIN1, which belongs to a family of prolyl isomerases, specifically binds to phosphorylated Ser/Thr-pro motifs to catalytically regulate the post-phosphorylation conformation of its substrates...
- Schumann M, Ihling C, Prell E, Schierhorn A, Sinz A, Fischer G, et al. Identification of low abundance cyclophilins in human plasma. Proteomics. 2016;16:2815-2826 pubmed publisherCylophilins (Cyps) belong to the ubiquitously distributed enzyme class of peptidyl prolyl cis/trans isomerases (EC22.214.171.124), which are foldases capable of accelerating slow steps in the refolding of denatured proteins...
- Sui X, Kiser P, Che T, Carey P, Golczak M, Shi W, et al. Analysis of carotenoid isomerase activity in a prototypical carotenoid cleavage enzyme, apocarotenoid oxygenase (ACO). J Biol Chem. 2014;289:12286-99 pubmed publisher..These results indicate that careful selection of detergent is critical for the success of structural studies aimed at elucidating structures of CCE-carotenoid/retinoid complexes. ..
- Poelarends G, Almrud J, Serrano H, Darty J, Johnson W, Hackert M, et al. Evolution of enzymatic activity in the tautomerase superfamily: mechanistic and structural consequences of the L8R mutation in 4-oxalocrotonate tautomerase. Biochemistry. 2006;45:7700-8 pubmed..The results also suggest that the evolution of new functions within the tautomerase superfamily could be quite facile, requiring only a few strategically placed active-site mutations. ..
- Jiang B, Pei D. A Selective, Cell-Permeable Nonphosphorylated Bicyclic Peptidyl Inhibitor against Peptidyl-Prolyl Isomerase Pin1. J Med Chem. 2015;58:6306-12 pubmed publisher..nonphosphorylated bicyclic peptide as a potent and selective Pin1 inhibitor, which inhibited the intracellular Pin1 activity in cultured mammalian cells but had little effect on other isomerases such as Pin4, FKBP12, or cyclophilin A.
- Powell K, Wales T, Fitzgerald M. Thermodynamic stability measurements on multimeric proteins using a new H/D exchange- and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry-based method. Protein Sci. 2002;11:841-51 pubmed..Our results on the model proteins in this study indicate that this new method can be used to determine folding free energies for proteins with the accuracy and precision of conventional spectroscopy-based methods. ..
- Ferreira Camargo L, Tran M, Beld J, Burkart M, Mayfield S. Selenocystamine improves protein accumulation in chloroplasts of eukaryotic green algae. AMB Express. 2015;5:126 pubmed publisher..While it has been shown that chloroplasts contain chaperones, peptidyl prolylisomerases and protein disulfide isomerases that facilitate these complex proteins folding and assembly, little has been done to determine which processes ..
- Kasaragod P, Schmitz W, Hiltunen J, Wierenga R. The isomerase and hydratase reaction mechanism of the crotonase active site of the multifunctional enzyme (type-1), as deduced from structures of complexes with 3S-hydroxy-acyl-CoA. FEBS J. 2013;280:3160-75 pubmed publisher..The structural variability of loop-2 between MFE1 and its monofunctional homologues correlates with differences in the respective substrate preferences and catalytic rates. ..
- Skagia A, Zografou C, Vezyri E, Venieraki A, Katinakis P, Dimou M. Cyclophilin PpiB is involved in motility and biofilm formation via its functional association with certain proteins. Genes Cells. 2016;21:833-51 pubmed publisherPpiB belongs to the superfamily of peptidyl-prolyl cis/trans isomerases (PPIases, EC: 126.96.36.199), which catalyze the rate-limiting protein folding step at peptidyl-prolyl bonds and control several biological processes...
- Lapsekili E, Mentes O, Balkan M, Gunal A, Yaman H, Kozak O, et al. Role of alkaline phosphatase intestine-isomerase in acute mesenteric ischemia diagnosis. Ulus Travma Acil Cerrahi Derg. 2016;22:115-20 pubmed publisher..However, ALP intestine-isomerase enzyme and D-dimer plasma levels were not found to contribute to the diagnosis. ..
- Rahier A, Karst F. Plant cyclopropylsterol-cycloisomerase: key amino acids affecting activity and substrate specificity. Biochem J. 2014;459:289-99 pubmed publisher..The mutated isomerases were assayed both in vivo by quantification of cycloeucalenol conversion into ergosterol in erg7 cells, and in ..
- Lindquist J, Hammerling G, Trowsdale J. ER60/ERp57 forms disulfide-bonded intermediates with MHC class I heavy chain. FASEB J. 2001;15:1448-50 pubmed
- Kuhn D, Bühler B, Schmid A. Production host selection for asymmetric styrene epoxidation: Escherichia coli vs. solvent-tolerant Pseudomonas. J Ind Microbiol Biotechnol. 2012;39:1125-33 pubmed publisher..Finding the optimal strain engineering strategy requires profound understanding of bioprocess and biocatalyst operation. In this respect, a possible negative influence of solvent tolerance on yield and activity is discussed. ..
- Mayer M, Frey S, Koivunen P, Myllyharju J, Buchner J. Influence of the oxidoreductase ER57 on the folding of an antibody fab fragment. J Mol Biol. 2004;341:1077-84 pubmed..These results indicate that the cooperation of the two oxidoreductases with different partner proteins may explain their different roles in the folding of proteins in the ER. ..
- Gao B, Adhikari R, Howarth M, Nakamura K, Gold M, Hill A, et al. Assembly and antigen-presenting function of MHC class I molecules in cells lacking the ER chaperone calreticulin. Immunity. 2002;16:99-109 pubmed..The peptide-loading function was specific to calreticulin, since the defect in K42 could be rectified by transfection with calreticulin but not a soluble form of calnexin, which shares its lectin-like activity. ..
- Nagashima H, Zulkharnain A, Maeda R, Fuse H, Iwata K, Omori T. Cloning and nucleotide sequences of carbazole degradation genes from marine bacterium Neptuniibacter sp. strain CAR-SF. Curr Microbiol. 2010;61:50-6 pubmed publisher..This is the first report of genes involved in carbazole degradation isolated from a marine bacterium...
- Marrakchi H, Choi K, Rock C. A new mechanism for anaerobic unsaturated fatty acid formation in Streptococcus pneumoniae. J Biol Chem. 2002;277:44809-16 pubmed..pneumoniae occurs following the formation of trans-2-decenoyl-ACP, in contrast to E. coli where the branch point takes place after the formation of beta-hydroxydecanoyl-ACP. ..
- Chang Y, Kim B, Kim S. Metabolic flux analysis of diterpene biosynthesis pathway in rice. Biotechnol Lett. 2005;27:1375-80 pubmed..In comparison, light-illumination used almost all geranylgeranyl pyrophosphate (96%) for gibberellin biosynthesis to stimulate the plant growth and strongly repressed the metabolic flux for phytoalexins biosynthesis. ..
- Ellgaard L, Frickel E. Calnexin, calreticulin, and ERp57: teammates in glycoprotein folding. Cell Biochem Biophys. 2003;39:223-47 pubmed..However, recent structural and biochemical data have provided important new insights into this chaperone system and present a solid basis for further mechanistic studies. ..
- Oelschlägel M, Gröning J, Tischler D, Kaschabek S, Schlömann M. Styrene oxide isomerase of Rhodococcus opacus 1CP, a highly stable and considerably active enzyme. Appl Environ Microbiol. 2012;78:4330-7 pubmed publisher..A half-life of 15 min was determined at a phenylacetaldehyde concentration of about 55 mM, indicating substantial limitations of applicability and the need to modify the process. ..
- Brodelius M, Lundgren A, Mercke P, Brodelius P. Fusion of farnesyldiphosphate synthase and epi-aristolochene synthase, a sesquiterpene cyclase involved in capsidiol biosynthesis in Nicotiana tabacum. Eur J Biochem. 2002;269:3570-7 pubmed..The bifunctional enzymes showed a more efficient conversion of isopentenyl diphosphate to epi-aristolochene than the corresponding amount of single enzymes. ..
- Brik A, Dawson P, Keinan E. The product of the natural reaction catalyzed by 4-oxalocrotonate tautomerase becomes an affinity label of its mutant. Bioorg Med Chem. 2002;10:3891-7 pubmed
- Coirini H, Gouézou M, Delespierre B, Liere P, Pianos A, Eychenne B, et al. Characterization and regulation of the 3beta-hydroxysteroid dehydrogenase isomerase enzyme in the rat sciatic nerve. J Neurochem. 2003;84:119-26 pubmed..06 +/- 2.58 microm). When the effects of different steroids were tested, both oestradiol and PROG significantly inhibited the conversion of PREG to PROG. ..
- Raffalli Mathieu F, Persson D, Mannervik B. Differences between bovine and human steroid double-bond isomerase activities of Alpha-class glutathione transferases selectively expressed in steroidogenic tissues. Biochim Biophys Acta. 2007;1770:130-6 pubmed..We discuss likely reasons for the contrasting steroid isomerase activities of bGST A1-1 and hGST A3-3, and alternative roles of bGST A1-1. ..