A structural limitation on enzyme activity: the case of HMG-CoA synthase.

Abstract:

:Recent structural studies of the HMG-CoA synthase members of the thiolase superfamily have shown that the catalytic loop containing the nucleophilic cysteine follows the phi and psi angle pattern of a II' beta turn. However, the i + 1 residue is conserved as an alanine, which is quite unusual in this position as it must adopt a strained positive phi angle to accommodate the geometry of the turn. To assess the effect of the conserved strain in the catalytic loop, alanine 110 of Enterococcus faecalis 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase was mutated to a glycine. Subsequent enzymatic studies showed that the overall reaction rate of the enzyme was increased 140-fold. An X-ray crystallographic study of the Ala110Gly mutant enzyme demonstrated unanticipated adjustments in the active site that resulted in additional stabilization of all three steps of the reaction pathway. The rates of acetylation and hydrolysis of the mutant enzyme increased because the amide nitrogen of Ser308 shifts 0.4 A toward the catalytic cysteine residue. This motion positions the nitrogen to better stabilize the intermediate negative charge that develops on the carbonyl oxygen of the acetyl group during both the formation of the acyl-enzyme intermediate and its hydrolysis. In addition, the hydroxyl of Ser308 rotates 120 degrees to a position where it is able to stabilize the carbanion intermediate formed by the methyl group of the acetyl-S-enzyme during its condensation with acetoacetyl-CoA.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Steussy CN,Robison AD,Tetrick AM,Knight JT,Rodwell VW,Stauffacher CV,Sutherlin AL

doi

10.1021/bi061505q

subject

Has Abstract

pub_date

2006-12-05 00:00:00

pages

14407-14

issue

48

eissn

0006-2960

issn

1520-4995

journal_volume

45

pub_type

杂志文章
  • Aromatic C-methyltransferases with antipodal stereoselectivity for structurally diverse phenolic amino acids catalyze the methylation step in the biosynthesis of the actinomycin chromophore.

    abstract::The actinomycin biosynthetic gene cluster of Streptomyces chrysomallus harbors two paralogous genes, acmI and acmL, encoding methyltransferases. To unveil their suspected role in the formation of 3-hydroxy-4-methyl-anthranilic acid (4-MHA), the building block of the actinomycin chromophore, each gene was expressed in ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi101422r

    authors: Crnovcić I,Süssmuth R,Keller U

    更新日期:2010-11-16 00:00:00

  • The metastasis-promoting phosphatase PRL-3 shows activity toward phosphoinositides.

    abstract::Phosphatase of regenerating liver 3 (PRL-3) is suggested as a biomarker and therapeutic target in several cancers. It has a well-established causative role in cancer metastasis. However, little is known about its natural substrates, pathways, and biological functions, and only a few protein substrates have been sugges...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi201095z

    authors: McParland V,Varsano G,Li X,Thornton J,Baby J,Aravind A,Meyer C,Pavic K,Rios P,Köhn M

    更新日期:2011-09-06 00:00:00

  • Position-dependent local motions in spin-labeled analogues of a short alpha-helical peptide determined by electron spin resonance.

    abstract::We have used electron spin resonance and circular dichroism to examine and compare the dynamics in two analogues of the Ala-based 3K(I) peptide [Marqusee, S., Robbins, V.H., & Baldwin, R. L. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 5286-5290], labeled at positions 4 and 8, throughout the alpha-helix----coil transition...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00103a016

    authors: Miick SM,Todd AP,Millhauser GL

    更新日期:1991-10-01 00:00:00

  • Surface salt bridges, double-mutant cycles, and protein stability: an experimental and computational analysis of the interaction of the Asp 23 side chain with the N-terminus of the N-terminal domain of the ribosomal protein l9.

    abstract::Experimental and theoretical double-mutant cycles have been used to investigate a salt bridge in the N-terminal domain of the protein L9. Aspartic acid 23 is the only acidic residue involved in a well-defined pairwise interaction, namely, a partially solvent-exposed salt bridge with the protonated N-terminus of the pr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi027202n

    authors: Luisi DL,Snow CD,Lin JJ,Hendsch ZS,Tidor B,Raleigh DP

    更新日期:2003-06-17 00:00:00

  • Role of zinc binding in type A botulinum neurotoxin light chain's toxic structure.

    abstract::Clostridial neurotoxins are zinc endopeptidases, and each contains one Zn(2+)/molecule. To investigate the structural/functional role of Zn(2+) in botulinum neurotoxin light chain (the enzymatic subunit of the neurotoxin), the effect of the removal of zinc on protein folding and enzyme kinetics was investigated. The a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0007472

    authors: Li L,Singh BR

    更新日期:2000-08-29 00:00:00

  • Fluorescence study of conformational flexibility of RNase S-peptide: distance-distribution, end-to-end diffusion, and anisotropy decays.

    abstract::Frequency-domain fluorescence resonance energy transfer and anisotropy measurements were performed to characterize conformational dynamics of an analog of the RNase S-peptide (residues 1-20). Trp was used as a donor by replacing Phe 8, and a dansyl acceptor group was introduced at position 1 or 18. The distance-distri...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00097a009

    authors: Maliwal BP,Lakowicz JR,Kupryszewski G,Rekowski P

    更新日期:1993-11-23 00:00:00

  • Characterization of the lysyl adducts of prostaglandin H-synthases that are derived from oxygenation of arachidonic acid.

    abstract::These investigations characterize the covalent binding of reactive products of prostaglandin H-synthases (PGHSs) to the enzyme and to other molecules. The intermediate product of oxygenation of arachidonic acid by the PGHSs, prostaglandin (PG) H2, undergoes rearrangement to the highly reactive gamma-keto aldehydes, le...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi002629k

    authors: Boutaud O,Brame CJ,Chaurand P,Li J,Rowlinson SW,Crews BC,Ji C,Marnett LJ,Caprioli RM,Roberts LJ 2nd,Oates JA

    更新日期:2001-06-12 00:00:00

  • Aminoacyl thioester chemistry of class II aminoacyl-tRNA synthetases.

    abstract::Lysyl-tRNA synthetase, a class II enzyme, edits homocysteine by converting it into homocysteine thiolactone. In a similar reaction, the enzyme converts homoserine into homoserine lactone. Other class II enzymes, aspartyl-tRNA synthetase and seryl-tRNA synthetase, do not edit any of the amino acids tested. However, all...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi970589n

    authors: Jakubowski H

    更新日期:1997-09-16 00:00:00

  • Oxygen equilibria of Octopus dofleini hemocyanin.

    abstract::Oxygen binding by Octopus dofleini hemocyanin was examined under very nearly physiological conditions. The effects of pH, ionic composition, temperature, and aggregation were controlled so that the role each plays in modulating oxygen binding can be isolated. There is a very large effect of pH on affinity, the Bohr ef...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00338a015

    authors: Miller KI

    更新日期:1985-08-13 00:00:00

  • Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange.

    abstract::The backbone dynamics of the liganded (holo) and unliganded (apo) forms of Escherichia coli-derived rat intestinal fatty acid-binding protein (I-FABP) have been characterized and compared using amide 15N relaxation and 1H exchange NMR measurements. The amide 1H/15N resonances for apo and holo I-FABP were assigned at 2...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi962018l

    authors: Hodsdon ME,Cistola DP

    更新日期:1997-02-25 00:00:00

  • Effects of metal ligation and oxygen on the reversibility of the thermal denaturation of Pseudomonas aeruginosa azurin.

    abstract::Thermodynamic equilibrium transition models in DSC are only applicable to reversible processes, but reversibility of the thermal transitions of proteins is comparatively rare because of intermolecular aggregation of denatured proteins and the degradation that occurs at high temperatures. The cupredoxin azurin from Pse...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0157621

    authors: Sandberg A,Leckner J,Shi Y,Schwarz FP,Karlsson BG

    更新日期:2002-01-22 00:00:00

  • Subunit affinities and stoichiometries of the human papillomavirus type 11 E1:E2:DNA complex.

    abstract::The association between the papillomavirus E1 and E2 proteins is an important regulatory interaction, imparting coordinated control of viral transcription and replication. Using fluorescence polarization, we have characterized the interactions between HPV-11 E1, HPV-11 E2, and DNA in solution at equilibrium. For these...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi982616v

    authors: Chao SF,Rocque WJ,Daniel S,Czyzyk LE,Phelps WC,Alexander KA

    更新日期:1999-04-06 00:00:00

  • Multiple replacements of glutamine 143 in human manganese superoxide dismutase: effects on structure, stability, and catalysis.

    abstract::Glutamine 143 in human manganese superoxide dismutase (MnSOD) forms a hydrogen bond with the manganese-bound solvent molecule and is investigated by replacement using site-specific mutagenesis. Crystal structures showed that the replacement of Gln 143 with Ala made no significant change in the overall structure of the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9929958

    authors: Lévêque VJ,Stroupe ME,Lepock JR,Cabelli DE,Tainer JA,Nick HS,Silverman DN

    更新日期:2000-06-20 00:00:00

  • Evolutionary coadaptation of the motif 2--acceptor stem interaction in the class II prolyl-tRNA synthetase system.

    abstract::Known crystal structures of class II aminoacyl-tRNA synthetases complexed to their cognate tRNAs reveal that critical acceptor stem contacts are made by the variable loop connecting the beta-strands of motif 2 located within the catalytic core of class II synthetases. To identify potential acceptor stem contacts made ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi001835p

    authors: Burke B,Yang F,Chen F,Stehlin C,Chan B,Musier-Forsyth K

    更新日期:2000-12-19 00:00:00

  • Kinetic analysis of product inhibition in human manganese superoxide dismutase.

    abstract::Manganese superoxide dismutase (MnSOD) cycles between the Mn(II) and Mn(III) states during the catalyzed disproportionation of O(2)(*-), a catalysis that is limited at micromolar levels of superoxide by a peroxide-inhibited complex with the metal. We have investigated the role in catalysis and inhibition of the conser...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi011047f

    authors: Hearn AS,Stroupe ME,Cabelli DE,Lepock JR,Tainer JA,Nick HS,Silverman DN

    更新日期:2001-10-09 00:00:00

  • Photogenerated reagents for membrane labeling. 2. Phenylcarbene and adamantylidene formed within the lipid bilayer.

    abstract::Phenylcarbene and adamantylidene have been generated photochemically from the corresponding diazirines within lipid bilayers. Reasonable yields of labeled fatty acid side chains have been observed. The products have been characterized by gas chromatography-mass spectrometry and derive both from the insertion of the c...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00605a026

    authors: Bayley H,Knowles JR

    更新日期:1978-06-13 00:00:00

  • A molecular ruler for chain elongation catalyzed by octaprenyl pyrophosphate synthase and its structure-based engineering to produce unprecedented long chain trans-prenyl products.

    abstract::Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of farnesyl pyrophosphate (FPP) with five molecules of isopentenyl pyrophosphate (IPP) to generate C(40) octaprenyl pyrophosphate (OPP) which constitutes the side chain of menaquinone. We have previously reported the X-ray structure ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi036336d

    authors: Guo RT,Kuo CJ,Ko TP,Chou CC,Liang PH,Wang AH

    更新日期:2004-06-22 00:00:00

  • Potent bifunctional anticoagulants: Kunitz domain-tissue factor fusion proteins.

    abstract::A strategy to design potent antagonists of human coagulation factor VIIa (FVIIa) by linking two proteins that independently inhibit activity and bind at separate, nonoverlapping sites is presented. A bifunctional inhibitor (KDTF5), comprising a Kunitz-type domain engineered to inhibit the FVIIa active site and a solub...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi970388j

    authors: Lee GF,Lazarus RA,Kelley RF

    更新日期:1997-05-13 00:00:00

  • Proteolytic activation of protein C from bovine plasma.

    abstract::Protein C is a vitamin K dependent protein present in bovine plasma (Stenflo, J. (1976), J. Biol. Chem. 251, 355). It is a glycoprotein (mol wt approximately 62 000) composed of a heavy chain (mol wt 41 000) and a light chain (mol wt 21 000). The heavy chain has an amino-terminal sequence of Asp-Thr-Asn-Gln and contai...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00667a022

    authors: Kisiel W,Ericsson LH,Davie EW

    更新日期:1976-11-02 00:00:00

  • Anomalous electrophoresis of deoxyribonucleic acid restriction fragments on polyacrylamide gels.

    abstract::A detailed study has been made of the polyacrylamide gel electrophoresis of DNA restriction fragments obtained from two plasmids, pBR322 and p82-6B. Variables studied were molecular weight, gel concentration, temperature, and electric field strength. The retardation coefficients of the larger fragments (greater than 8...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00295a023

    authors: Stellwagen NC

    更新日期:1983-12-20 00:00:00

  • Inhibition mechanism of rat α₃β₄ nicotinic acetylcholine receptor by the Alzheimer therapeutic tacrine.

    abstract::Nicotinic acetylcholine receptors (nAChRs) were studied in detail in the past regarding their interaction with therapeutic and drug addiction related compounds. Using fast kinetic whole-cell recording, we have now studied effects of tacrine, an agent used clinically to treat Alzheimer's disease, on currents elicited b...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi101789y

    authors: Cheffer A,Ulrich H

    更新日期:2011-03-22 00:00:00

  • Equilibrium folding studies of tetrameric R67 dihydrofolate reductase.

    abstract::R67 dihydrofolate reductase (DHFR) is an R-plasmid encoded enzyme that confers resistance to the antibacterial drug trimethoprim. This enzyme is not homologous in sequence or structure to chromosomal DHFRs. Equilibrium folding of tetrameric R67 DHFR was studied and found to be fully reversible. Formation of an inactiv...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00180a018

    authors: Zhuang P,Eisenstein E,Howell EE

    更新日期:1994-04-12 00:00:00

  • Synthesis and characterization of fluorescently labeled bovine brain G protein subunits.

    abstract::G proteins play an important role in transmitting hormonal signals, and fluorescence techniques would be useful to study their cellular distribution and mechanisms. To prepare active fluorescent G protein Go/Gi or beta gamma subunits were reacted with fluorescein isothiocyanate (FITC) to label the alpha (F-alpha) and ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00060a035

    authors: Kwon G,Remmers AE,Datta S,Neubig RR

    更新日期:1993-03-09 00:00:00

  • Probing receptor binding activity of interleukin-8 dimer using a disulfide trap.

    abstract::Interleukin-8 (IL-8), a member of the chemokine superfamily, exists as both monomers and dimers, and mediates its function by binding to neutrophil CXCR1 and CXCR2 receptors that belong to the G protein-coupled receptor class. It is now well established that the monomer functions as a high-affinity ligand, but the bin...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0605944

    authors: Rajarathnam K,Prado GN,Fernando H,Clark-Lewis I,Navarro J

    更新日期:2006-06-27 00:00:00

  • Equilibrium and stop-flow kinetic studies of fluorescently labeled DNA substrates with DNA repair proteins XPA and replication protein A.

    abstract::Nucleotide excision repair (NER) is a crucial pathway in the maintenance of genome stability requiring at least two dozen proteins. XPA and RPA have essential roles in the damage recognition step of NER. To better understand the mechanism of their interactions with DNA, we utilized equilibrium and stop-flow kinetic ap...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi011041q

    authors: Iakoucheva LM,Walker RK,van Houten B,Ackerman EJ

    更新日期:2002-01-08 00:00:00

  • Tyrosine kinase-mediated serine phosphorylation of adenylyl cyclase.

    abstract::Receptor tyrosine kinase (RTK) activation is associated with modulation of heptahelical receptor-stimulated adenylyl cyclase responses. The mechanisms underlying the RTK-mediated enhancement of adenylyl cyclase function remain unclear. In the present studies, we show that the tyrosine kinase-dependent enhancement of a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0015818

    authors: Tan CM,Kelvin DJ,Litchfield DW,Ferguson SS,Feldman RD

    更新日期:2001-02-13 00:00:00

  • N-ethylmaleimide inhibits Ncd motor function by modification of a cysteine in the stalk domain.

    abstract::N-Ethylmaleimide (NEM), which reacts readily with exposed sulfhydryl groups, has been shown to inhibit the activity of the microtubule (MT) motors kinesin, Ncd, and dynein. Currently, the mechanism of inhibition is not known for any of these proteins. To investigate the mechanism by which NEM inhibits Ncd, the recombi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi990706+

    authors: Phelps KK,Walker RA

    更新日期:1999-08-17 00:00:00

  • Redesign of the proton-pumping machinery of cytochrome c oxidase: proton pumping does not require Glu(I-286).

    abstract::One of the putative proton-transfer pathways leading from solution toward the binuclear center in many cytochrome c oxidases is the D-pathway, so-called because it starts with a highly conserved aspartate [D(I-132)] residue. Another highly conserved amino acid residue in this pathway, glutamate(I-286), has been indica...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0012641

    authors: Aagaard A,Gilderson G,Mills DA,Ferguson-Miller S,Brzezinski P

    更新日期:2000-12-26 00:00:00

  • An unusually low pK(a) for Cys282 in the active site of human muscle creatine kinase.

    abstract::All phosphagen kinases contain a conserved cysteine residue which has been shown by crystallographic studies, on both creatine kinase and arginine kinase, to be located in the active site. There are conflicting reports as to whether this cysteine is essential for catalysis. In this study we have used site-directed mut...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi011208f

    authors: Wang PF,McLeish MJ,Kneen MM,Lee G,Kenyon GL

    更新日期:2001-10-02 00:00:00

  • Molecular characterization of limulin, a sialic acid binding lectin from the hemolymph of the horseshoe crab, Limulus polyphemus.

    abstract::The sialic acid binding lectin, limulin, was isolated by gel filtration and ion-exchange chromatography from the hemolymph of Limulus polyphemus. When the purified protein was characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the presence of beta-mercaptoethanol, two major protein bands wer...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00638a026

    authors: Kaplan R,Li SS,Kehoe JM

    更新日期:1977-09-20 00:00:00