Structures of DegQ from Legionella pneumophila Define Distinct ON and OFF States.

Abstract:

:HtrA (high-temperature requirement A) family proteins play important roles in protein-quality control processes in the bacterial periplasm. A common feature of all members of this family is their modular organization comprising a chymotrypsin-like protease domain and at least one PDZ (postsynaptic density of 95 kDa, disks large homolog 1 and zonula occludens 1) domain. All characterized HtrA proteins assemble into complex oligomers consisting of typically 3-24 monomers, which allow a tight regulation of proteolytic activity. Here, we provide evidence that the assembly of proteolytically active, higher-order complexes of DegQ from Legionella pneumophila is triggered by the binding of substrate-derived peptides. Crystal structures of inactive 3-mers and active 12-mers of DegQ reveal molecular details of elements of a conserved allosteric activation cascade that defines distinct protease ON and OFF states. Results from DegQ(Lp) variants harboring structure-based amino acid substitutions indicate that peptide binding to the PDZ1 domain is critical for proteolytic activity but not for the formation of higher-order oligomers. Combining structural, mutagenesis and biochemical data, we show that, in contrast to the proteolytic activity, the chaperone function of DegQ is not affected by the state of the activation cascade.

journal_name

J Mol Biol

authors

Schubert A,Wrase R,Hilgenfeld R,Hansen G

doi

10.1016/j.jmb.2015.06.023

subject

Has Abstract

pub_date

2015-08-28 00:00:00

pages

2840-51

issue

17

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(15)00388-5

journal_volume

427

pub_type

杂志文章
  • A short DNA sequence from lambda phage inhibits protein synthesis in Escherichia coli rap.

    abstract::The Escherichia coli rap mutant inhibits vegetative growth of bacteriophage lambda. Phage mutations termed bar, which overcome the rap defect, have been mapped to three genetic loci in the pL operon. Plasmids with a lambda wild-type bar DNA segment cloned downstream from an active promoter cannot be maintained in rap ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(05)80316-x

    authors: Pérez-Morga D,Guarneros G

    更新日期:1990-11-20 00:00:00

  • Headful packaging revisited: the packaging of more than one DNA molecule into a bacteriophage P1 head.

    abstract::Like a variety of other bacteriophages, such as T4 and P22, bacteriophage P1 packages DNA by a "headful" mechanism in which the capacity of the viral capsid determines the size of the single DNA molecule that is packaged. Because of the long-standing and general acceptance of this packaging mechanism, we were surprise...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0287

    authors: Coren JS,Pierce JC,Sternberg N

    更新日期:1995-05-26 00:00:00

  • High-resolution crystal structures of trimeric and rod phycocyanin.

    abstract::The phycobilisome light-harvesting antenna in cyanobacteria and red algae is assembled from two substructures: a central core composed of allophycocyanin surrounded by rods that always contain phycocyanin (PC). Unpigmented proteins called linkers are also found within the rods and core. We present here two new structu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.10.036

    authors: David L,Marx A,Adir N

    更新日期:2011-01-07 00:00:00

  • Amyloid beta (1-42) folding multiplicity and single-molecule binding behavior studied with STM.

    abstract::The fine folding and assembling characteristics of amyloid beta (Abeta) peptides are important to pharmaceutical studies of drug molecules and to the pathological analysis of neurodegenerative disorders such as Alzheimer's disease at the molecular level. Here we present observations of the multiple folding characteris...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.03.054

    authors: Ma X,Liu L,Mao X,Niu L,Deng K,Wu W,Li Y,Yang Y,Wang C

    更新日期:2009-05-15 00:00:00

  • The human telomeric protein TRF1 specifically recognizes nucleosomal binding sites and alters nucleosome structure.

    abstract::Telomeres are dynamic nucleoprotein structures that cap the ends of eukaryotic chromosomes. In humans, the long (TTAGGG)(n) double-stranded telomeric DNA repeats are bound specifically by the two related proteins TRF1 and TRF2, and are organized in nucleosomes. Whereas the role of TRF1 and TRF2 in telomeric function h...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.04.071

    authors: Galati A,Rossetti L,Pisano S,Chapman L,Rhodes D,Savino M,Cacchione S

    更新日期:2006-07-07 00:00:00

  • Crystal structure of the dog lipocalin allergen Can f 2: implications for cross-reactivity to the cat allergen Fel d 4.

    abstract::The dog lipocalin allergen Can f 2 is an important cause of allergic sensitization in humans worldwide. Here, the first crystal structure of recombinant rCan f 2 at 1.45 A resolution displays a classical lipocalin fold with a conserved Gly-Xaa-Trp motif, in which Trp19 stabilizes the overall topology of the monomeric ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.043

    authors: Madhurantakam C,Nilsson OB,Uchtenhagen H,Konradsen J,Saarne T,Högbom E,Sandalova T,Grönlund H,Achour A

    更新日期:2010-08-06 00:00:00

  • Conserved structural features are found upstream from the three co-ordinately regulated discoidin I genes of Dictyostelium discoideum.

    abstract::The discoidin I genes of Dictyostelium form a small, co-ordinately regulated multigene family. We have sequenced and compared the upstream regions of the DiscI-alpha, -beta and -gamma genes. For the most part the upstream regions of the three genes are non-homologous. The upstream sequences of the beta and gamma genes...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(84)80038-8

    authors: Poole SJ,Firtel RA

    更新日期:1984-01-15 00:00:00

  • Interactions between activating region 3 of the Escherichia coli cyclic AMP receptor protein and region 4 of the RNA polymerase sigma(70) subunit: application of suppression genetics.

    abstract::The Escherichia coli cyclic AMP receptor protein, CRP, induces transcription at Class II CRP-dependent promoters by making three different activatory contacts with different surfaces of holo RNA polymerase. One contact surface of CRP, known as Activating Region 3 (AR3), is functional in the downstream subunit of the C...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3737

    authors: Rhodius VA,Busby SJ

    更新日期:2000-06-02 00:00:00

  • Bile acid interactions with rabbit ileal lipid binding protein and an engineered helixless variant reveal novel ligand binding properties of a versatile beta-clam shell protein scaffold.

    abstract::The intracellular ileal lipid binding proteins (ILBPs) are involved in the transport and enterohepatic circulation of bile acids. ILBPs from different species show high sequence and structural homology and have been shown to bind multiple bile acid ligands with differing degrees of selectivity and positive co-operativ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.06.024

    authors: Kouvatsos N,Thurston V,Ball K,Oldham NJ,Thomas NR,Searle MS

    更新日期:2007-08-31 00:00:00

  • Transcriptional and post-transcriptional control of specific messenger RNAs in adult and embryonic liver.

    abstract::The rate of synthesis and the concentrations of a variety of messenger RNA sequences have been compared between adult mouse liver cells and cells in other adult tissues, and between cells in fetal and neonatal liver. The sequences were distinguished as "liver-specific" or "common" in a previous report, where liver was...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90304-8

    authors: Powell DJ,Friedman JM,Oulette AJ,Krauter KS,Darnell JE Jr

    更新日期:1984-10-15 00:00:00

  • Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.

    abstract::Ground-state dynamics in RNA is a critical precursor for structural adaptation observed ubiquitously in protein-RNA recognition. A tertiary conformational analysis of the stem-loop structural element in the transactivation response element (TAR) from human immunodeficiency virus type 1 (HIV-I) RNA is presented using r...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5235

    authors: Al-Hashimi HM,Gosser Y,Gorin A,Hu W,Majumdar A,Patel DJ

    更新日期:2002-01-11 00:00:00

  • Optogenetic Control of Ca2+ and Voltage-Dependent Large Conductance (BK) Potassium Channels.

    abstract::Ca2+ concentration jumps for the activation of Ca2+-dependent ion channels or transporters can be obtained either by fast solution exchange or by the use of caged Ca2+. Here, we report on an alternate optogenetic method for the activation of Ca2+ and voltage-dependent large conductance (BK) potassium channels. This wa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2017.02.004

    authors: Mager T,Wood PG,Bamberg E

    更新日期:2017-03-24 00:00:00

  • Molecular Insights into the Architecture of the Human SMC5/6 Complex.

    abstract::A family of Structural Maintenance of Chromosome (SMC) complexes is essential for key cellular processes ensuring proper cohesion, condensation and replication. They share a common SMC-kleisin architecture allowing them to embrace DNA. In SMC5/6, the NSE1 and NSE3 KITE and NSE4 kleisin subunits form a stable subcomple...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.04.024

    authors: Adamus M,Lelkes E,Potesil D,Ganji SR,Kolesar P,Zabrady K,Zdrahal Z,Palecek JJ

    更新日期:2020-06-12 00:00:00

  • Folding pattern of the alpha-crystallin domain in alphaA-crystallin determined by site-directed spin labeling.

    abstract::The folding pattern of the alpha-crystallin domain, a conserved protein module encoding the molecular determinants of structure and function in the small heat-shock protein superfamily, was determined in the context of the lens protein alphaA-crystallin by systematic application of site-directed spin labeling. The seq...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3242

    authors: Koteiche HA,Mchaourab HS

    更新日期:1999-11-26 00:00:00

  • Amino acid sequence, crystallization and structure determination of reduced and oxidized cytochrome c6 from the green alga Scenedesmus obliquus.

    abstract::Cytochrome c6from the unicellular green alga Scenedesmus obliquus was sequenced, crystallized in its reduced and oxidized state and the three-dimensional structure of the protein in both redox states was determined by X-ray crystallography. Reduced cytochrome c6crystallized as a monomer in the space group P 21212, whe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2944

    authors: Schnackenberg J,Than ME,Mann K,Wiegand G,Huber R,Reuter W

    更新日期:1999-07-30 00:00:00

  • Solution structure of GDP-tubulin double rings to 3 nm resolution and comparison with microtubules.

    abstract::GDP liganded tubulin, which is inactive in microtubule assembly, polymerizes into rings more readily than the active GTP liganded protein. The structure of double rings made of highly purified GDP-tubulin has been characterized to 3 nm resolution with synchrotron X-ray solution scattering. The scattering profile has c...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1282

    authors: Díaz JF,Pantos E,Bordas J,Andreu JM

    更新日期:1994-04-29 00:00:00

  • Characterization of the electrostatic perturbation of a catalytic site (Cys)-S-/(His)-Im+H ion-pair in one type of serine proteinase architecture by kinetic and computational studies on chemically mutated subtilisin variants.

    abstract::We have used two structurally well-characterized serine proteinase variants, subtilisins Carlsberg and BPN', to produce (Cys)-S-/(His)-Im+H ion-pairs by chemical mutation in well defined, different, electrostatic microenvironments. These ion-pairs have been characterized by pH-dependent rapid reaction kinetics using, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0225

    authors: Plou FJ,Kowlessur D,Malthouse JP,Mellor GW,Hartshorn MJ,Pinitglang S,Patel H,Topham CM,Thomas EW,Verma C,Brocklehurst K

    更新日期:1996-04-19 00:00:00

  • Predictive QM/MM Modeling of Modulations in Protein-Protein Binding by Lysine Methylation.

    abstract::Lysine methylation is a key regulator of protein-protein binding. The amine group of lysine can accept up to three methyl groups, and experiments show that protein-protein binding free energies are sensitive to the extent of methylation. These sensitivities have been rationalized in terms of chemical and structural fe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.166745

    authors: Rahman S,Wineman-Fisher V,Al-Hamdani Y,Tkatchenko A,Varma S

    更新日期:2021-02-05 00:00:00

  • P. aeruginosa PilT structures with and without nucleotide reveal a dynamic type IV pilus retraction motor.

    abstract::Type IV pili are bacterial extracellular filaments that can be retracted to create force and motility. Retraction is accomplished by the motor protein PilT. Crystal structures of Pseudomonas aeruginosa PilT with and without bound beta,gamma-methyleneadenosine-5'-triphosphate have been solved at 2.6 A and 3.1 A resolut...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.066

    authors: Misic AM,Satyshur KA,Forest KT

    更新日期:2010-07-30 00:00:00

  • Conformational changes in phosphoglucose isomerase induced by ligand binding.

    abstract::Phosphoglucose isomerase (PGI; EC 5.3.1.9) is the second enzyme in glycolysis, where it catalyzes the isomerization of D-glucose-6-phosphate to D-fructose-6-phosphate. It is the same protein as autocrine motility factor, differentiation and maturation mediator, and neuroleukin. Here, we report a new X-ray crystal stru...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00892-6

    authors: Arsenieva D,Jeffery CJ

    更新日期:2002-10-11 00:00:00

  • Crystallization and subunit structure of canine myeloperoxidase.

    abstract::Three crystal forms of canine myeloperoxidase are described. An orthorhombic form in space group P2(1)2(1)2(1) has unit cell dimensions: a = 108.3 A (1 A = 0.1 nm) b = 205.9 A and c = 139.9 A. A trigonal form in space group P3(1)21 or P3(2)21 has unit cell dimensions: a = b = 138.9 A and c = 145.2 A. A monoclinic form...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90413-x

    authors: Fenna RE

    更新日期:1987-08-20 00:00:00

  • Multiple sequence threading: an analysis of alignment quality and stability.

    abstract::Methods that compare a protein sequence directly to a structure can be divided into those that construct a molecular model (threading methods) and those that perform a sequence alignment with the structure encoded as a sequence of structural states (one-dimensional/three-dimensional (1D/3D) matching). The former take ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1008

    authors: Taylor WR

    更新日期:1997-06-27 00:00:00

  • Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis.

    abstract::In a previous paper, 2'-deoxy-N(6)-methoxyadenosine (mo(6)A) was shown to form a mismatch base-pair with 2'-deoxycytidine with a Watson-Crick-type geometry. To fully understand the structural basis of genetic mutations with damaged DNA, it is necessary to examine whether the methoxylated adenine residue still has the ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3304

    authors: Chatake T,Hikima T,Ono A,Ueno Y,Matsuda A,Takénaka A

    更新日期:1999-12-17 00:00:00

  • Crystallization of a chymotrypsin inhibitor from Erythrina caffra seeds.

    abstract::Crystals of a chymotrypsin inhibitor from Erythrina caffra seeds have been grown out of lithium sulfate, by the hanging drop method of vapor diffusion. The crystals belong to the rhombohedral space group R32, with a = 67.2 A and alpha = 99.4 degrees, and diffract to 3 A resolution. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90300-B

    authors: Shieh HS,Leimgruber NK,Palmier MO,Wun TC,Leimgruber RM,Abdel-Meguid SS

    更新日期:1990-03-05 00:00:00

  • Genetic dissection of the consensus sequence for the class 2 and class 3 flagellar promoters.

    abstract::Computational searches for DNA binding sites often utilize consensus sequences. These search models make assumptions that the frequency of a base pair in an alignment relates to the base pair's importance in binding and presume that base pairs contribute independently to the overall interaction with the DNA-binding pr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.04.043

    authors: Wozniak CE,Hughes KT

    更新日期:2008-06-20 00:00:00

  • Single-cell analysis of lambda immunity regulation.

    abstract::We have examined expression of the lambdacI operon in single cells via a rex Colon, two colons gfp substitution. Although average fluorescence agreed with expectations for expression of lambda-repressor, fluorescence fluctuated greatly from cell-to-cell. Fluctuations in repressor concentration are not predicted by pre...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.09.037

    authors: Baek K,Svenningsen S,Eisen H,Sneppen K,Brown S

    更新日期:2003-11-28 00:00:00

  • Archaeal N-terminal protein maturation commonly involves N-terminal acetylation: a large-scale proteomics survey.

    abstract::We present the first large-scale survey of N-terminal protein maturation in archaea based on 873 proteomically identified N-terminal peptides from the two haloarchaea Halobacterium salinarum and Natronomonas pharaonis. The observed protein maturation pattern can be attributed to the combined action of methionine amino...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.07.086

    authors: Falb M,Aivaliotis M,Garcia-Rizo C,Bisle B,Tebbe A,Klein C,Konstantinidis K,Siedler F,Pfeiffer F,Oesterhelt D

    更新日期:2006-10-06 00:00:00

  • Effect of organic co-solvents on the dimer/tetramer equilibrium of human haemoglobin.

    abstract::We have studied the effect of organic co-solvents (monohydric alcohols and formamide) on the dimer-tetramer equilibrium of human haemoglobin by measuring the dependence of oxygen affinity upon haemoglobin concentration over a 100-fold concentration range and analysing the data with a modified Monod-Wyman-Changeux mode...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90514-0

    authors: Cupane A,Vitrano E,Cordone L

    更新日期:1986-05-20 00:00:00

  • The reverse transcriptase encoded by the non-LTR retrotransposon R2 is as error-prone as that encoded by HIV-1.

    abstract::Reverse transcriptases (RTs) encoded by a wide range of mobile retroelements have had a major impact on the structure and function of genomes. Among the most abundant elements in eukaryotes are the non long terminal repeat (LTR) retrotransposons. Here we compare the dNTP concentration requirements and error rates of t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.02.015

    authors: Jamburuthugoda VK,Eickbush TH

    更新日期:2011-04-15 00:00:00

  • Supercoiling-dependent site-specific binding of HU to naked Mu DNA.

    abstract::Using HU chemical nucleases to probe HU-DNA interactions, we report here for the first time site-specific binding of HU to naked DNA. An unique feature of this interaction is the absolute requirement for negative DNA supercoiling for detectable levels of site-specific DNA binding. The HU binding site is the Mu spacer ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2805

    authors: Kobryn K,Lavoie BD,Chaconas G

    更新日期:1999-06-18 00:00:00