Genomes and Genes
Experts and Doctors on catalytic domain in New York, United States
Locale: New York, United States
Topic: catalytic domain
Publications261 found, 100 shown here
- Zoi I, Suarez J, Antoniou D, Cameron S, Schramm V, Schwartz S. Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics. J Am Chem Soc. 2016;138:3403-9 pubmed publisher..The mutagenic uncoupling of femtosecond motions between catalytic site groups and reactants decreased transition state barrier crossing by 2 orders of magnitude, an indication of the femtosecond dynamic contributions to catalysis. ..
- Vyas V, Kuchin S, Carlson M. Interaction of the repressors Nrg1 and Nrg2 with the Snf1 protein kinase in Saccharomyces cerevisiae. Genetics. 2001;158:563-72 pubmed..These results suggest that Nrg1 and Nrg2 are direct or indirect targets of the Snf1 kinase and function in glucose repression of a subset of Snf1-regulated genes. ..
- Tao X, Tong L. Crystal structure of the MAP kinase binding domain and the catalytic domain of human MKP5. Protein Sci. 2007;16:880-6 pubmed..The CD of MKP5 is observed in an active conformation, and two loops in the active site have backbone shifts of up to 5 A relative to the inactive CDs from other MKPs. ..
- Yu L, Chou C, Choi P, Tong L. Characterizing the importance of the biotin carboxylase domain dimer for Staphylococcus aureus pyruvate carboxylase catalysis. Biochemistry. 2013;52:488-96 pubmed publisher..We have also produced the isolated BC domain of SaPC. In contrast to E. coli BC, the SaPC BC domain is monomeric in solution and catalytically inactive. ..
- Huang T, Deng H, Wolkoff A, Stockert R. Phosphorylation-dependent interaction of the asialoglycoprotein receptor with molecular chaperones. J Biol Chem. 2002;277:37798-803 pubmed..The data presented provide evidence that phosphorylation of the ASGPR cytoplasmic domain is required for the binding of specific molecular chaperones with the potential to regulate receptor trafficking. ..
- Lewandowicz A, Shi W, Evans G, Tyler P, Furneaux R, Basso L, et al. Over-the-barrier transition state analogues and crystal structure with Mycobacterium tuberculosis purine nucleoside phosphorylase. Biochemistry. 2003;42:6057-66 pubmed..This approach has resulted in the highest affinity transition state analogues known for MtPNP. ..
- Pang H, Flinn R, Patsialou A, Wyckoff J, Roussos E, Wu H, et al. Differential enhancement of breast cancer cell motility and metastasis by helical and kinase domain mutations of class IA phosphoinositide 3-kinase. Cancer Res. 2009;69:8868-76 pubmed publisher..Our observations suggest that, when compared with kinase domain mutations in a genetically identical background, expression of helical domain mutants of p110alpha produce a more severe metastatic phenotype. ..
- Olsen S, Capili A, Lu X, Tan D, Lima C. Active site remodelling accompanies thioester bond formation in the SUMO E1. Nature. 2010;463:906-12 pubmed publisher..These changes displace side chains required for adenylation with side chains required for thioester bond formation. Mutational and biochemical analyses indicate these mechanisms are conserved in other E1s. ..
- Dou Y, Milne T, Ruthenburg A, Lee S, Lee J, Verdine G, et al. Regulation of MLL1 H3K4 methyltransferase activity by its core components. Nat Struct Mol Biol. 2006;13:713-9 pubmed..Mechanistic insights gained from this study can be generalized to the whole family of SET1-like histone methyltransferases in mammals. ..
- Liu X, Choudhury S, Roy R. In vitro and in vivo dimerization of human endonuclease III stimulates its activity. J Biol Chem. 2003;278:50061-9 pubmed..Therefore, it is likely that the dimerization of hNTH1 involving the N-terminal tail masks the inhibitory effect of this tail and plays a critical role in its catalytic turnover in the cell. ..
- Tan D, Marzluff W, Dominski Z, Tong L. Structure of histone mRNA stem-loop, human stem-loop binding protein, and 3'hExo ternary complex. Science. 2013;339:318-21 pubmed publisher..The 3' flanking sequence is positioned in the 3'hExo active site, but the ternary complex limits the extent of trimming. ..
- Lee E, Zhang L, Zhao S, Wei Q, Zhang J, Qi Z, et al. Phosphorylase phosphatase: new horizons for an old enzyme. Front Biosci. 1999;4:D270-85 pubmed
- Donny Clark K, Shapiro R, Broyde S. Accommodation of an N-(deoxyguanosin-8-yl)-2-acetylaminofluorene adduct in the active site of human DNA polymerase iota: Hoogsteen or Watson-Crick base pairing?. Biochemistry. 2009;48:7-18 pubmed publisher..This suggests the possibility of an expanded role for poliota in lesion bypass. ..
- Shi W, Li C, Tyler P, Furneaux R, Grubmeyer C, Schramm V, et al. The 2.0 A structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with a transition-state analog inhibitor. Nat Struct Biol. 1999;6:588-93 pubmed..The transition-state analog is shielded from bulk solvent by a catalytic loop that moves approximately 25 A to cover the active site and becomes an ordered antiparallel beta-sheet. ..
- Hadi T, Hazra S, Tanner M, Blanchard J. Structure of MurNAc 6-phosphate hydrolase (MurQ) from Haemophilus influenzae with a bound inhibitor. Biochemistry. 2013;52:9358-66 pubmed publisher..This same residue would serve to deprotonate the incoming water and reprotonate the enolate in the second half of the catalytic cycle. ..
- Huang Y, Park Y, Rich R, Segal D, Myszka D, Wu H. Structural basis of caspase inhibition by XIAP: differential roles of the linker versus the BIR domain. Cell. 2001;104:781-90 pubmed..Further biochemical characterizations clearly establish that the linker harbors the major energetic determinant, while the BIR2 domain serves as a regulatory element for caspase binding and Smac neutralization. ..
- Olsen S, Lima C. Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer. Mol Cell. 2013;49:884-96 pubmed publisher..Comparison to a Ub E1/Ub/ATP·Mg structure reveals conformational changes in the E1 that bring the E1 and E2 active sites together...
- Gandotra S, Lebron M, Ehrt S. The Mycobacterium tuberculosis proteasome active site threonine is essential for persistence yet dispensable for replication and resistance to nitric oxide. PLoS Pathog. 2010;6:e1001040 pubmed publisher..These findings suggest that proteasomal proteolysis facilitates mycobacterial persistence, that M. tuberculosis faces starvation during chronic mouse infections and that the proteasome serves a proteolysis-independent function. ..
- Farooq A, Plotnikova O, Chaturvedi G, Yan S, Zeng L, Zhang Q, et al. Solution structure of the MAPK phosphatase PAC-1 catalytic domain. Insights into substrate-induced enzymatic activation of MKP. Structure. 2003;11:155-64 pubmed
- Lu X, Zhou R, Sharma I, Li X, Kumar G, Swaminathan S, et al. Stable analogues of OSB-AMP: potent inhibitors of MenE, the o-succinylbenzoate-CoA synthetase from bacterial menaquinone biosynthesis. Chembiochem. 2012;13:129-36 pubmed publisher..A pH-dependent interconversion of the free keto acid and lactol forms of the inhibitors is also described, along with implications for inhibitor design. ..
- Wang T, Cook I, Leyh T. Design and Interpretation of Human Sulfotransferase 1A1 Assays. Drug Metab Dispos. 2016;44:481-4 pubmed publisher..This review provides an overview of the mechanistic features of SULT1A1 that are important for the design and interpretation of SULT1A1 assays. ..
- Chang J, Jiao X, Chiba K, Oh C, Martin C, Kiledjian M, et al. Dxo1 is a new type of eukaryotic enzyme with both decapping and 5'-3' exoribonuclease activity. Nat Struct Mol Biol. 2012;19:1011-7 pubmed publisher..Studies of yeast in which both Dxo1 and Rai1 are disrupted reveal that mRNAs with incomplete caps are produced even under normal growth conditions, in sharp contrast to current understanding of the capping process. ..
- Chen Y, Cann M, Litvin T, Iourgenko V, Sinclair M, Levin L, et al. Soluble adenylyl cyclase as an evolutionarily conserved bicarbonate sensor. Science. 2000;289:625-8 pubmed..sAC is also expressed in other bicarbonate-responsive tissues, which suggests that bicarbonate regulation of cAMP signaling plays a fundamental role in many biological systems. ..
- Mukai M, Mills C, Poole R, Yeh S. Flavohemoglobin, a globin with a peroxidase-like catalytic site. J Biol Chem. 2001;276:7272-7 pubmed..These data demonstrate that the active site structure of Hmp is very similar to that of peroxidases and is tailored to perform oxygen chemistry. ..
- Johnson A, O Donnell M. Ordered ATP hydrolysis in the gamma complex clamp loader AAA+ machine. J Biol Chem. 2003;278:14406-13 pubmed..Implications of these results to clamp loaders of other systems are discussed. ..
- Maianti J, McFedries A, Foda Z, Kleiner R, Du X, Leissring M, et al. Anti-diabetic activity of insulin-degrading enzyme inhibitors mediated by multiple hormones. Nature. 2014;511:94-8 pubmed publisher..These findings demonstrate the feasibility of modulating IDE activity as a new therapeutic strategy to treat type-2 diabetes and expand our understanding of the roles of IDE in glucose and hormone regulation. ..
- Lue N. A physical and functional constituent of telomerase anchor site. J Biol Chem. 2005;280:26586-91 pubmed..Coupled with previous genetic analysis, our data confirm that anchor site interaction is indeed important for telomerase function in vivo. ..
- Wang F, Shi W, Nieves E, Angeletti R, Schramm V, Grubmeyer C. A transition-state analogue reduces protein dynamics in hypoxanthine-guanine phosphoribosyltransferase. Biochemistry. 2001;40:8043-54 pubmed..Proton transfer paths, rather than dynamic motion, are required to explain exchange into a buried catalytic site peptide in the complex with the bound transition-state analogue. ..
- Jogl G, Hsiao Y, Tong L. Structure and function of carnitine acyltransferases. Ann N Y Acad Sci. 2004;1033:17-29 pubmed..In addition, our structural information suggests that the substrate carnitine may assist the catalysis by stabilizing the oxyanion in the reaction intermediate. ..
- Huang Z, Chen H, Blais S, Neubert T, Li X, Mohammadi M. Structural mimicry of a-loop tyrosine phosphorylation by a pathogenic FGF receptor 3 mutation. Structure. 2013;21:1889-96 pubmed publisher..We propose that the targeted inhibition of this pathogenic FGFR3 kinase may be achievable by small molecule kinase inhibitors that selectively bind the active-state conformation of FGFR3 kinase. ..
- Becker M, Bunikis J, Lade B, Dunn J, Barbour A, Lawson C. Structural investigation of Borrelia burgdorferi OspB, a bactericidal Fab target. J Biol Chem. 2005;280:17363-70 pubmed publisher..OspB structure, stability, and possible mechanisms of killing by H6831 and other bactericidal Fabs are discussed in light of the structural data...
- Escobar Alvarez S, Goldgur Y, Yang G, Ouerfelli O, Li Y, Scheinberg D. Structure and activity of human mitochondrial peptide deformylase, a novel cancer target. J Mol Biol. 2009;387:1211-28 pubmed publisher..Despite the lack of true S2' and S3' binding pockets, confirmed through peptide binding modeling, enzyme kinetics suggest a combined contribution from P2'and P3' positions of a formylated peptide substrate to turnover. ..
- Wang L, Smith P, Shuman S. Structure and mechanism of the 2',3' phosphatase component of the bacterial Pnkp-Hen1 RNA repair system. Nucleic Acids Res. 2013;41:5864-73 pubmed publisher..The structure illuminates a large body of mutational data regarding the metal and substrate specificity of Clostridium thermocellum Pnkp phosphatase...
- Smith P, Nair P, Das U, Zhu H, Shuman S. Structures and activities of archaeal members of the LigD 3'-phosphoesterase DNA repair enzyme superfamily. Nucleic Acids Res. 2011;39:3310-20 pubmed publisher..Our results fortify the proposal that PEs comprise a DNA repair superfamily distributed widely among taxa. ..
- Sampoli Benitez B, Arora K, Balistreri L, Schlick T. Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation. J Mol Biol. 2008;384:1086-97 pubmed publisher..The possibility of syn conformers resonates with other low-fidelity enzymes such as Dpo4 (from the Y family), which readily accommodate oxidative lesions. ..
- Zito E, Melo E, Yang Y, Wahlander Ã, Neubert T, Ron D. Oxidative protein folding by an endoplasmic reticulum-localized peroxiredoxin. Mol Cell. 2010;40:787-97 pubmed publisher..These observations implicate ER-localized PRDX4 in a previously unanticipated, parallel, ERO1-independent pathway that couples hydroperoxide production to oxidative protein folding in mammalian cells. ..
- Rechkoblit O, Delaney J, Essigmann J, Patel D. Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions. Structure. 2011;19:821-32 pubmed publisher..Our studies provide insights into mechanisms related to hindered and mutagenic bypass of methylated lesions and models associated with damage recognition by repair demethylases. ..
- Hsu H, Tong S, Zhou Y, Elmes M, Yan S, Kaczocha M, et al. The Antinociceptive Agent SBFI-26 Binds to Anandamide Transporters FABP5 and FABP7 at Two Different Sites. Biochemistry. 2017;56:3454-3462 pubmed publisher..Our work reveals two binding poses of SBFI-26 in its target transporters. This knowledge will guide the development of more potent FABP inhibitors based upon the SBFI-26 scaffold. ..
- Forouhar F, Lew S, Seetharaman J, Xiao R, Acton T, Montelione G, et al. Structures of bacterial biosynthetic arginine decarboxylases. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1562-6 pubmed publisher..The PLP cofactor is recognized by hydrogen-bonding, ?-stacking and van der Waals interactions. ..
- Feldman T, Kabaleeswaran V, Jang S, Antczak C, Djaballah H, Wu H, et al. A class of allosteric caspase inhibitors identified by high-throughput screening. Mol Cell. 2012;47:585-95 pubmed publisher..Based on these kinetic, biochemical, and structural analyses, we suggest that these compounds are allosteric caspase inhibitors that function through binding to the dimerization interface of caspases. ..
- Cao J, Kozarekar P, Pavlaki M, Chiarelli C, Bahou W, Zucker S. Distinct roles for the catalytic and hemopexin domains of membrane type 1-matrix metalloproteinase in substrate degradation and cell migration. J Biol Chem. 2004;279:14129-39 pubmed..These data demonstrated that each domain of MT1-MMP plays a distinct role in substrate degradation and cell migration. ..
- Glekas A, Pillarsetty N, Punzalan B, Khan N, Smith Jones P, Larson S. In vivo imaging of Bcr-Abl overexpressing tumors with a radiolabeled imatinib analog as an imaging surrogate for imatinib. J Nucl Med. 2011;52:1301-7 pubmed publisher..Because (18)F-SKI696 has been taken up in vivo by tumors that overexpress Bcr-Abl, we are exploring a possible role for identifying tumors that will respond to imatinib before therapy. ..
- Mandel C, Tweel B, Tong L. Crystal structure of human mitochondrial acyl-CoA thioesterase (ACOT2). Biochem Biophys Res Commun. 2009;385:630-3 pubmed publisher..The active site is located in a large pocket at the interface between the two domains. The structural information has significant relevance for other type I ACOTs and related enzymes. ..
- Liu Y, Xu X, Carlson M. Interaction of SNF1 protein kinase with its activating kinase Sak1. Eukaryot Cell. 2011;10:313-9 pubmed publisher..These findings indicate that the C terminus of Sak1 confers its function as the primary Snf1-activating kinase and suggest that the physical association of Sak1 with SNF1 facilitates responses to environmental change. ..
- Caplan A, Mandal A, Theodoraki M. Molecular chaperones and protein kinase quality control. Trends Cell Biol. 2007;17:87-92 pubmed..This requirement might relate to conformational changes that take place during the protein kinase activity cycle. ..
- Sciorra V, Hammond S, Morris A. Potent direct inhibition of mammalian phospholipase D isoenzymes by calphostin-c. Biochemistry. 2001;40:2640-6 pubmed..Our results suggest that inhibition of PLD1 and PLD2 may explain some of the PKC-independent effects of calphostin-c observed when the compound is applied to intact cells. ..
- Agarwal R, Burley S, Swaminathan S. Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase. Proteins. 2012;80:261-8 pubmed publisher..Comparison of our structure to that of the structures of other sugar kinases revealed conformational variations that suggest domain-domain closure movements are responsible for establishing the observed active site environment. ..
- Momcilovic M, Iram S, Liu Y, Carlson M. Roles of the glycogen-binding domain and Snf4 in glucose inhibition of SNF1 protein kinase. J Biol Chem. 2008;283:19521-9 pubmed publisher..Analysis of mutant cells lacking glycogen synthase showed that regulation of SNF1 is normal in the absence of glycogen. These findings reveal novel roles for Snf4 and the GBD in regulation of SNF1. ..
- Nakanishi K, Weinberg D, Bartel D, Patel D. Structure of yeast Argonaute with guide RNA. Nature. 2012;486:368-74 pubmed publisher..Mutation analyses and analogies to ribonuclease H indicate that insertion of this glutamate finger completes a universally conserved catalytic tetrad, thereby activating Argonaute for RNA cleavage. ..
- Serganov A, Patel D. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat Rev Genet. 2007;8:776-90 pubmed..These findings have implications for understanding how cellular functions might have evolved from RNA-based origins. ..
- Chen Y, Jakoncic J, Carpino N, Nassar N. Structural and functional characterization of the 2H-phosphatase domain of Sts-2 reveals an acid-dependent phosphatase activity. Biochemistry. 2009;48:1681-90 pubmed publisher..They also demonstrate that nonconserved active site residues are responsible for the difference in activity between the two isoforms. These differences reflect possible distinct physiological substrates. ..
- Cook I, Wang T, Almo S, Kim J, Falany C, Leyh T. The gate that governs sulfotransferase selectivity. Biochemistry. 2013;52:415-24 pubmed publisher..Equilibrium and pre-steady-state binding studies confirm that SULT1A1 undergoes a nucleotide-induced isomerzation that controls substrate selection. ..
- Wang L, Shuman S. Structure-function analysis of yeast tRNA ligase. RNA. 2005;11:966-75 pubmed..We identify yeastlike tRNA ligases in the proteomes of Leishmania and Trypanosoma. These findings recommend tRNA ligase as a target for antifungal and antiprotozoal drug discovery. ..
- Ghanem M, Zhadin N, Callender R, Schramm V. Loop-tryptophan human purine nucleoside phosphorylase reveals submillisecond protein dynamics. Biochemistry. 2009;48:3658-68 pubmed publisher..F159W-Leuko-PNP provides a novel protein platform to investigate the protein conformational dynamics occurring prior to transition state formation. ..
- Saito T, Stopkova P, Diaz L, Papolos D, Boussemart L, Lachman H. Polymorphism screening of PIK4CA: possible candidate gene for chromosome 22q11-linked psychiatric disorders. Am J Med Genet B Neuropsychiatr Genet. 2003;116B:77-83 pubmed
- Sun J, Wu L, Fedorov A, Almo S, Zhang Z. Crystal structure of the Yersinia protein-tyrosine phosphatase YopH complexed with a specific small molecule inhibitor. J Biol Chem. 2003;278:33392-9 pubmed
- Chi Y, Zhou B, Wang W, Chung S, Kwon Y, Ahn Y, et al. Comparative mechanistic and substrate specificity study of inositol polyphosphate 5-phosphatase Schizosaccharomyces pombe Synaptojanin and SHIP2. J Biol Chem. 2004;279:44987-95 pubmed
- Budhwar R, Lu A, Hirsch J. Nutrient control of yeast PKA activity involves opposing effects on phosphorylation of the Bcy1 regulatory subunit. Mol Biol Cell. 2010;21:3749-58 pubmed publisher..Stimulation of Bcy1 phosphorylation by Gpb1 and Gpb2 produces a form of Bcy1 that is more stable and is a more effective PKA inhibitor. ..
- Kim D, Zheng H, Huang Y, Montelione G, Hunt J. ATPase active-site electrostatic interactions control the global conformation of the 100 kDa SecA translocase. J Am Chem Soc. 2013;135:2999-3010 pubmed publisher..This network forms the foundation of the allosteric mechanochemistry that efficiently harnesses the chemical energy stored in ATP to drive complex mechanical processes. ..
- Samai P, Shuman S. Structure-function analysis of the OB and latch domains of chlorella virus DNA ligase. J Biol Chem. 2011;286:22642-52 pubmed publisher..Arg-285 is a key component of the OB-NTase interface, where it forms a salt bridge to the essential Asp-29 side chain, which is imputed to coordinate divalent metal catalysts during the nick sealing steps. ..
- Finnin M, Donigian J, Cohen A, Richon V, Rifkind R, Marks P, et al. Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature. 1999;401:188-93 pubmed publisher..These structures also suggest a mechanism for the deacetylation reaction and provide a framework for the further development of HDAC inhibitors as antitumour agents...
- Chen H, Xu C, Ma J, Eliseenkova A, Li W, Pollock P, et al. A crystallographic snapshot of tyrosine trans-phosphorylation in action. Proc Natl Acad Sci U S A. 2008;105:19660-5 pubmed publisher..We propose that the salient mechanistic features of Y769 trans-phosphorylation are applicable to trans-phosphorylation of the equivalent major phosphorylation sites in many other RTKs. ..
- McGinty R, Kim J, Chatterjee C, Roeder R, Muir T. Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation. Nature. 2008;453:812-6 pubmed publisher..This work demonstrates a direct biochemical crosstalk between two modifications on separate histone proteins within a nucleosome. ..
- Bhuiya M, Liu C. Engineering monolignol 4-O-methyltransferases to modulate lignin biosynthesis. J Biol Chem. 2010;285:277-85 pubmed publisher..The 4-O-methoxylation of monolignol efficiently impairs oxidative radical coupling in vitro, highlighting the potential for applying this novel enzyme in managing lignin polymerization in planta...
- Gu M, Rice C. Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism. Proc Natl Acad Sci U S A. 2010;107:521-8 pubmed publisher..These findings suggest feasible strategies for developing specific inhibitors to block the action of this attractive, yet largely unexplored drug target. ..
- Vasquez Del Carpio R, Silverstein T, Lone S, Swan M, Choudhury J, Johnson R, et al. Structure of human DNA polymerase kappa inserting dATP opposite an 8-OxoG DNA lesion. PLoS ONE. 2009;4:e5766 pubmed publisher..The structure also provides a basis for why Polkappa is more efficient at inserting an A opposite the lesion than other Y-family DNA polymerases. ..
- Mok K, Lie P, Mruk D, Mannu J, Mathur P, Silvestrini B, et al. The apical ectoplasmic specialization-blood-testis barrier functional axis is a novel target for male contraception. Adv Exp Med Biol. 2012;763:334-355 pubmed
- Lehman K, Schwer B, Ho C, Rouzankina I, Shuman S. A conserved domain of yeast RNA triphosphatase flanking the catalytic core regulates self-association and interaction with the guanylyltransferase component of the mRNA capping apparatus. J Biol Chem. 1999;274:22668-78 pubmed
- Barton W, Biggins J, Jiang J, Thorson J, Nikolov D. Expanding pyrimidine diphosphosugar libraries via structure-based nucleotidylyltransferase engineering. Proc Natl Acad Sci U S A. 2002;99:13397-402 pubmed..In aggregate, our results provide valuable blueprints for altering nucleotidylyltransferase specificity by design, which is the first step toward in vitro glycorandomization. ..
- Chu C, Alapat D, Wen X, Timo K, Burstein D, Lisanti M, et al. Ectopic expression of murine diphosphoinositol polyphosphate phosphohydrolase 1 attenuates signaling through the ERK1/2 pathway. Cell Signal. 2004;16:1045-59 pubmed..This result suggests that inhibition of signaling through the ERK1/2 pathway is a distinct function of muDIPP1 that is not dependent on, but may be regulated by, its activity as a phosphohydrolase. ..
- Yin Q, Park H, Chung J, Lin S, Lo Y, da Graca L, et al. Caspase-9 holoenzyme is a specific and optimal procaspase-3 processing machine. Mol Cell. 2006;22:259-68 pubmed..Therefore, in addition to dimerization, the apoptosome activates caspase-9 by enhancing its affinity for procaspase-3, which is important for procaspase-3 activation at the physiological concentration. ..
- Tremblay L, Xu H, Blanchard J. Structures of the Michaelis complex (1.2 Å) and the covalent acyl intermediate (2.0 Å) of cefamandole bound in the active sites of the Mycobacterium tuberculosis ?-lactamase K73A and E166A mutants. Biochemistry. 2010;49:9685-7 pubmed publisher..2 and 2.0 Å, respectively. These structures provide insight into the details of the catalytic mechanism. ..
- Reverter D, Lima C. A basis for SUMO protease specificity provided by analysis of human Senp2 and a Senp2-SUMO complex. Structure. 2004;12:1519-31 pubmed
- Benarroch D, Jankowska Anyszka M, Stepinski J, Darzynkiewicz E, Shuman S. Cap analog substrates reveal three clades of cap guanine-N2 methyltransferases with distinct methyl acceptor specificities. RNA. 2010;16:211-20 pubmed publisher..The relaxed cap specificity of MimiTgs is revealed at alkaline pH. Our findings highlight both stark and subtle differences in acceptor specificity and reaction outcomes among Tgs family members. ..
- Bochevarov A, Li J, Song W, Friesner R, Lippard S. Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases. J Am Chem Soc. 2011;133:7384-97 pubmed publisher..Finally, similarities between the oxygen activation mechanisms of the monooxygenases and cytochrome P450 are discussed. ..
- Mzhavia N, Pan H, Che F, Fricker L, Devi L. Characterization of endothelin-converting enzyme-2. Implication for a role in the nonclassical processing of regulatory peptides. J Biol Chem. 2003;278:14704-11 pubmed..Taken together, these results are consistent with an important role for ECE-2 in the processing of regulatory peptides at nonclassical sites. ..
- Yunus A, Lima C. Structure of the Siz/PIAS SUMO E3 ligase Siz1 and determinants required for SUMO modification of PCNA. Mol Cell. 2009;35:669-82 pubmed publisher..Mutational analysis of Siz1 and PCNA revealed surfaces on both proteins that are required for efficient SUMO modification of PCNA in vitro and in vivo. ..
- Rajagopalan S, Wang C, Yu K, Kuzin A, Richter F, Lew S, et al. Design of activated serine-containing catalytic triads with atomic-level accuracy. Nat Chem Biol. 2014;10:386-91 pubmed publisher..Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents. ..
- Shekhtman A, Ghose R, Wang D, Cole P, Cowburn D. Novel mechanism of regulation of the non-receptor protein tyrosine kinase Csk: insights from NMR mapping studies and site-directed mutagenesis. J Mol Biol. 2001;314:129-38 pubmed..We conclude that the SH3-SH2 linker plays a major role in the activation of the Csk catalytic domain. ..
- Mitra S, Laederach A, Golden B, Altman R, Brenowitz M. RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. RNA. 2011;17:1589-603 pubmed publisher..Our results also suggest a potential role of naturally selected peripheral A-minor interactions in balancing RNA structural stability with folding efficiency. ..
- Faehnle C, Walleshauser J, Joshua Tor L. Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis. Nat Struct Mol Biol. 2017;24:658-665 pubmed publisher..Finally, ZK2 of TUT4(7) aids oligoU addition by engaging the growing oligoU tail through uracil-specific interactions. ..