当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Sub-atomic resolution crystal structure of cholesterol oxidase: what atomic resolution crystallography reveals about enzyme mechanism and the role of the FAD cofactor in redox activity.

Sub-atomic resolution crystal structure of cholesterol oxidase: what atomic resolution crystallography reveals about enzyme mechanism and the role of the FAD cofactor in redox activity.

Abstract：

:The crystal structure of cholesterol oxidase, a 56kDa flavoenzyme was anisotropically refined to 0.95A resolution. The final crystallographic R-factor and R(free) value is 11.0% and 13.2%, respectively. The quality of the electron density maps has enabled modeling of alternate conformations for 83 residues in the enzyme, many of which are located in the active site. The additional observed structural features were not apparent in the previous high-resolution structure (1.5A resolution) and have enabled the identification of a narrow tunnel leading directly to the isoalloxazine portion of the FAD prosthetic group. The hydrophobic nature of this narrow tunnel suggests it is the pathway for molecular oxygen to access the isoalloxazine group for the oxidative half reaction. Resolving the alternate conformations in the active site residues provides a model for the dynamics of substrate binding and a potential oxidation triggered gating mechanism involving access to the hydrophobic tunnel. This structure reveals that the NE2 atom of the active site histidine residue, H447, critical to the redox activity of this flavin oxidase, acts as a hydrogen bond donor rather than as hydrogen acceptor. The atomic resolution structure of cholesterol oxidase has revealed the presence of hydrogen atoms, dynamic aspects of the protein and how side-chain conformations are correlated with novel structural features such as the oxygen tunnel. This new structural information has provided us with the opportunity to re-analyze the roles played by specific residues in the mechanism of the enzyme.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Lario PI,Sampson N,Vrielink A

doi

10.1016/s0022-2836(03)00054-8

keywords:

subject

Has Abstract

pub_date

2003-03-07 00:00:00

pages

1635-50

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022283603000548

journal_volume

326

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Conservation of transition state structure in fast folding peripheral subunit-binding domains.

    abstract：:Phi-value analysis was used to characterise the structure of the transition state (TS) for folding of POB L146A Y166W, a peripheral subunit-binding domain that folds in microseconds. Helix 2 was structured in the TS with consolidating interactions from the structured loop that connects the two alpha-helices. This dist...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.06.081

    authors： Sharpe TD,Ferguson N,Johnson CM,Fersht AR

    更新日期：2008-10-31 00:00:00

  • Structural assembly of the active site in an aldo-keto reductase by NADPH cofactor.

    abstract：:A 1.9 A resolution X-ray structure of the apo-form of Corynebacterium 2,5-diketo-d-gluconic acid reductase A (2,5-DKGR A), a member of the aldo-keto reductase superfamily, has been determined by molecular replacement using the NADPH-bound form of the same enzyme as the search model. 2,5-DKGR A catalyzes the NADPH-depe...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4739

    authors： Sanli G,Blaber M

    更新日期：2001-06-22 00:00:00

  • Human cardiac myosin binding protein C: structural flexibility within an extended modular architecture.

    abstract：:New insights into the modular organization and flexibility of the N-terminal half of human cardiac myosin binding protein C (cMyBP-C) and information on the association state of the full-length protein have been deduced from a combined small-angle X-ray scattering (SAXS) and NMR study. SAXS data show that the first fi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.10.029

    authors： Jeffries CM,Lu Y,Hynson RM,Taylor JE,Ballesteros M,Kwan AH,Trewhella J

    更新日期：2011-12-16 00:00:00

  • COOH-terminal truncated cardiac myosin-binding protein C mutants resulting from familial hypertrophic cardiomyopathy mutations exhibit altered expression and/or incorporation in fetal rat cardiomyocytes.

    abstract：:Mutations in human cardiac myosin-binding protein C (cMyBP-C) gene are associated with familial hypertrophic cardiomyopathy (FHC), and most of them are predicted to produce COOH-truncated proteins. To understand the molecular mechanism(s) by which such mutations cause FHC, we analyzed (i) the accumulation of human cMy...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3276

    authors： Flavigny J,Souchet M,Sébillon P,Berrebi-Bertrand I,Hainque B,Mallet A,Bril A,Schwartz K,Carrier L

    更新日期：1999-11-26 00:00:00

  • Fibrinogen structure in projection at 18 A resolution. Electron density by co-ordinated cryo-electron microscopy and X-ray crystallography.

    abstract：:Electron microscope images of frozen-hydrated crystals of a proteolytically modified fibrinogen show excellent preservation of the structure. An electron density map of the key centric projection of the crystal at 18 A resolution has been obtained by combining the phases derived from cryo-electron microscopy with X-ra...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90739-s

    authors： Rao SP,Poojary MD,Elliott BW Jr,Melanson LA,Oriel B,Cohen C

    更新日期：1991-11-05 00:00:00

  • tRNA 3' end maturation in archaea has eukaryotic features: the RNase Z from Haloferax volcanii.

    abstract：:Here, we report the first characterization and partial purification of an archaeal tRNA 3' processing activity, the RNase Z from Haloferax volcanii. The activity identified here is an endonuclease, which cleaves tRNA precursors 3' to the discriminator. Thus tRNA 3' processing in archaea resembles the eukaryotic 3' pro...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5395

    authors： Schierling K,Rösch S,Rupprecht R,Schiffer S,Marchfelder A

    更新日期：2002-03-01 00:00:00

  • Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif.

    abstract：:Many viruses employ ATP-powered motors for genome packaging. We combined genetic, biochemical, and single-molecule techniques to confirm the predicted Walker-B ATP-binding motif in the phage λ motor and to investigate the roles of the conserved residues. Most changes of the conserved hydrophobic residues resulted in >...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2019.08.012

    authors： delToro D,Ortiz D,Ordyan M,Pajak J,Sippy J,Catala A,Oh CS,Vu A,Arya G,Smith DE,Catalano CE,Feiss M

    更新日期：2019-11-08 00:00:00

  • Structure and Function of Viral Deubiquitinating Enzymes.

    abstract：:Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including innate and adaptive immune responses. Ubiquitin-mediated control over these processes can be reversed by cellular deubiquitinating enzymes (DUBs), which remove ubiquitin from cellular targets and depolyme...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2017.06.010

    authors： Bailey-Elkin BA,Knaap RCM,Kikkert M,Mark BL

    更新日期：2017-11-10 00:00:00

  • Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation.

    abstract：:Bovine spongiform encephalopathy (BSE) is a fatal neurodegenerative prion disease affecting cattle that is transmissible to humans, manifesting as a variant of Creutzfeldt-Jakob disease (vCJD) likely following the consumption of meat contaminated with BSE prions. High-affinity antibodies are a prerequisite for the dev...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.07.027

    authors： Luginbühl B,Kanyo Z,Jones RM,Fletterick RJ,Prusiner SB,Cohen FE,Williamson RA,Burton DR,Plückthun A

    更新日期：2006-10-13 00:00:00

  • Mechanisms of Gasdermin Family Members in Inflammasome Signaling and Cell Death.

    abstract：:The Gasdermin (GSDM) family consists of Gasdermin A (GSDMA), Gasdermin B (GSDMB), Gasdermin C (GSDMC), Gasdermin D (GSDMD), Gasdermin E (GSDME) and Pejvakin (PJVK). GSDMD is activated by inflammasome-associated inflammatory caspases. Cleavage of GSDMD by human or mouse caspase-1, human caspase-4, human caspase-5, and ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2018.07.002

    authors： Feng S,Fox D,Man SM

    更新日期：2018-09-14 00:00:00

  • Cryo-electron tomography of clathrin-coated vesicles: structural implications for coat assembly.

    abstract：:Clathrin-coated vesicles mediate vesicular traffic in cells. Three-dimensional image reconstructions of homogenous populations of in vitro assembled clathrin coats have yielded a molecular model for clathrin and its interactions with some of its partners. The intrinsic averaging required for those calculations has pre...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.10.036

    authors： Cheng Y,Boll W,Kirchhausen T,Harrison SC,Walz T

    更新日期：2007-01-19 00:00:00

  • Oct-1 POU and octamer DNA co-operate to recognise the Bob-1 transcription co-activator via induced folding.

    abstract：:The expression of immunoglobulin genes is controlled in part by the DNA-binding protein Oct-1 and the B cell-specific transcription co-activator, Bob1 (also known as OCA-B or OBF-1) that together form a complex on the Igkappa promoter. We have characterised the assembly of the ternary complex using biophysical methods...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2711

    authors： Chang JF,Phillips K,Lundbäck T,Gstaiger M,Ladbury JE,Luisi B

    更新日期：1999-05-21 00:00:00

  • Conformational dynamics of Thermus aquaticus DNA polymerase I during catalysis.

    abstract：:Despite the fact that DNA polymerases have been investigated for many years and are commonly used as tools in a number of molecular biology assays, many details of the kinetic mechanism they use to catalyze DNA synthesis remain unclear. Structural and kinetic studies have characterized a rapid, pre-catalytic open-to-c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2014.06.003

    authors： Xu C,Maxwell BA,Suo Z

    更新日期：2014-08-12 00:00:00

  • Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility.

    abstract：:The worm-like chain model has often been employed to describe the average conformation of long, intrinsically straight polymer molecules, including DNA. The present study extends the applicability of the worm-like chain model to polymers containing bends or sections of different flexibility. Several cases have been ex...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.1830

    authors： Rivetti C,Walker C,Bustamante C

    更新日期：1998-07-03 00:00:00

  • Isolation and characterization of visible light-sensitive mutants of Escherichia coli K12.

    abstract：:Six mutants of Escherichia coli K12 that are sensitive to visible light have been isolated. Five of them, including an amber mutant, are defective in a gene that maps near 11 minutes on the linkage map of the chromosome, and this gene has been designated visA. The sixth mutant, which was isolated from bacteria that ca...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90180-e

    authors： Miyamoto K,Nakahigashi K,Nishimura K,Inokuchi H

    更新日期：1991-06-05 00:00:00

  • Crystal structure of rat intestinal fatty-acid-binding protein. Refinement and analysis of the Escherichia coli-derived protein with bound palmitate.

    abstract：:Rat intestinal fatty-acid-binding protein (I-FABP) is a small (15,124 Mr) cytoplasmic polypeptide that binds long-chain fatty acids in a non-covalent fashion. I-FABP is a member of a family of intracellular binding proteins that are thought to participate in the uptake, transport and/or metabolic targeting of hydropho...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90392-6

    authors： Sacchettini JC,Gordon JI,Banaszak LJ

    更新日期：1989-07-20 00:00:00

  • Biophysical characterization of structural properties and folding of interleukin-1 receptor antagonist.

    abstract：:Structural properties and folding of interleukin-1 receptor antagonist (IL-1ra), a therapeutically important cytokine with a symmetric beta-trefoil topology, are characterized using optical spectroscopy, high-resolution NMR, and size-exclusion chromatography. Spectral contributions of two tryptophan residues, Trp17 an...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.02.031

    authors： Latypov RF,Harvey TS,Liu D,Bondarenko PV,Kohno T,Fachini RA 2nd,Rosenfeld RD,Ketchem RR,Brems DN,Raibekas AA

    更新日期：2007-05-11 00:00:00

  • The major human structural IgE epitope of the Brazil nut allergen Ber e 1: a chimaeric and protein microarray approach.

    abstract：:A protein microarray system containing different dilutions of 77 related and non-related proteins was used to show that IgE from subjects allergic to Brazil nut specifically recognise the seed 2S albumin protein (Ber e 1). Further, correctly folded chimaeric 2S albumin proteins containing structural epitope replacemen...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.08.065

    authors： Alcocer MJ,Murtagh GJ,Wilson PB,Progias P,Lin J,Archer DB

    更新日期：2004-10-22 00:00:00

  • A study of four-helix bundles: investigating protein folding via similar architectural motifs in protein cores and in subunit interfaces.

    abstract：:Four-helix bundles are identified and characterized in the subunit interfaces of protein multimers. We find that this motif occurs as often in the interfaces as in the protein monomers. Common and different characteristics demonstrated by the bundles in the two environments suggest the possible stabilization mechanism...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0208

    authors： Lin SL,Tsai CJ,Nussinov R

    更新日期：1995-04-21 00:00:00

  • Isolation and characterization of a previously unrecognized myosin heavy chain gene present in the Syrian hamster.

    abstract：:A full length (25,000 base-pair) myosin heavy chain gene completely contained within a single cosmid clone was isolated from a Syrian hamster cosmid genomic library. Sequence comparison of the 3' untranslated region indicated the presence of a 75% homology with the rat embryonic myosin heavy chain gene. Extensive 5' f...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/0022-2836(91)90251-z

    authors： McCully JD,Wang RX,Kellam B,Sole MJ,Liew CC

    更新日期：1991-04-20 00:00:00

  • Structural studies on the Pseudomonas aeruginosa sialidase-like enzyme PA2794 suggest substrate and mechanistic variations.

    abstract：:Pseudomonas aeruginosa encodes an enzyme (PA2794) that is annotated as a sialidase (or neuraminidase), as it possesses three bacterial neuraminidase repeats that are a signature of nonviral sialidases. A recent report showed that when the gene encoding this sialidase is knocked out, this led to a reduction in biofilm ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.12.084

    authors： Xu G,Ryan C,Kiefel MJ,Wilson JC,Taylor GL

    更新日期：2009-02-27 00:00:00

  • Topology of the components of the DNA packaging machinery in the phage phi29 prohead.

    abstract：:Chromosome condensation inside dsDNA viral particles is a complex process requiring the coordinated action of several viral components. The similarity of the process in different viral systems has led to the suggestion that there is a common underlying mechanism for DNA packaging, in which the portal vertex or connect...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3712

    authors： Ibarra B,Castón JR,Llorca O,Valle M,Valpuesta JM,Carrascosa JL

    更新日期：2000-05-19 00:00:00

  • The 1.3 A crystal structure of a biotin-binding pseudoknot and the basis for RNA molecular recognition.

    abstract：:A pseudoknot-containing aptamer isolated from a pool of random sequence molecules has been shown previously to represent an optimal RNA solution to the problem of binding biotin. The affinity of this RNA molecule is nonetheless orders of magnitude weaker than that of its highly evolved protein analogs, avidin and stre...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3539

    authors： Nix J,Sussman D,Wilson C

    更新日期：2000-03-10 00:00:00

  • Evolution of function in protein superfamilies, from a structural perspective.

    abstract：:The recent growth in protein databases has revealed the functional diversity of many protein superfamilies. We have assessed the functional variation of homologous enzyme superfamilies containing two or more enzymes, as defined by the CATH protein structure classification, by way of the Enzyme Commission (EC) scheme. ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4513

    authors： Todd AE,Orengo CA,Thornton JM

    更新日期：2001-04-06 00:00:00

  • The first crystal structure of L-threonine dehydrogenase.

    abstract：:L-threonine dehydrogenase (TDH) is an enzyme that catalyzes the oxidation of L-threonine to 2-amino-3-ketobutyrate. We solved the first crystal structure of a medium chain L-threonine dehydrogenase from a hyperthermophilic archaeon, Pyrococcus horikoshii (PhTDH), by the single wavelength anomalous diffraction method u...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.11.060

    authors： Ishikawa K,Higashi N,Nakamura T,Matsuura T,Nakagawa A

    更新日期：2007-02-23 00:00:00

  • Molecular insights into the control of transcription initiation at the Staphylococcus aureus agr operon.

    abstract：:The accessory gene regulatory (agr) operon of the opportunistic human pathogen Staphylococcus aureus is a prime pathogenesis factor in this bacterium. The agr operon consists of two transcription units, RNAII and RNAIII, which are transcribed from divergent promoters, P2 and P3, respectively. RNAII encodes a quorum-se...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.06.018

    authors： Reynolds J,Wigneshweraraj S

    更新日期：2011-10-07 00:00:00

  • Crystallization and preliminary crystallographic investigations of the soluble glucose dehydrogenase from Acinetobacter calcoaceticus.

    abstract：:Single crystals of the soluble glucose dehydrogenase (GDH) from Acinetobacter calcoaceticus have been grown by the vapour diffusion method. These crystals diffract to beyond 2.1 A and are suitable for X-ray crystallography. The space group was determined to be P2(1) with unit cell parameters a = 55.5 A, b = 104.5 A, c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1553

    authors： Schlunegger MP,Grütter MG,Streiff MB,Olsthoorn AJ,Duine JA

    更新日期：1993-10-20 00:00:00

  • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation.

    abstract：:Residue-specific potentials between pairs of side-chains and pairs of side-chain-backbone interaction sites have been generated by collecting radial distribution data for 302 protein structures. Multiple atomic interactions have been utilized to enhance the specificity and smooth the distance-dependence of the potenti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0758

    authors： Bahar I,Jernigan RL

    更新日期：1997-02-14 00:00:00

  • A measure for the angle between projections based on the extent of correlation between corresponding central sections.

    abstract：:A pre-condition for the ab initio assignment of Euler angles to a set of projections from an asymmetric object is that at least three of the available projections correspond to rotations about different axes. For symmetric objects this condition may be relaxed. There are some applications of single-particle electron m...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.09.068

    authors： Patwardhan A,Paul D,Al-Khayat HA,Morris EP

    更新日期：2004-11-26 00:00:00

  • Conserved hydrophobic clusters on the surface of the Caf1A usher C-terminal domain are important for F1 antigen assembly.

    abstract：:The outer membrane usher protein Caf1A of the plague pathogen Yersinia pestis is responsible for the assembly of a major surface antigen, the F1 capsule. The F1 capsule is mainly formed by thin linear polymers of Caf1 (capsular antigen fraction 1) protein subunits. The Caf1A usher promotes polymerization of subunits a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.08.034

    authors： Dubnovitsky AP,Duck Z,Kersley JE,Härd T,MacIntyre S,Knight SD

    更新日期：2010-10-22 00:00:00