The archaeal XPB protein is a ssDNA-dependent ATPase with a novel partner.


:XPB is a superfamily 2 helicase with a 3'-5' polarity. In eukaryotes, XPB is an integral subunit of the transcription factor TFIIH, which plays a dual role in DNA opening at RNA polymerase II promoters and in establishing the repair bubble around a DNA lesion in nucleotide excision repair. Eukaryotic XPB has only very limited helicase activity in vitro and may function as a DNA-dependent molecular switch to catalyse local distortion of DNA in transcription and repair. Most archaea have one or two homologues of the XPB protein with a presumed role in DNA repair, but only one other subunit of the TFIIH complex, the 5'-3' helicase XPD, has been identified in archaea. Here we report the biochemical characterisation of the two homologous XPB proteins from the crenarchaeon Sulfolobus solfataricus. Although both proteins are single-stranded-DNA-stimulated ATPases, neither displays any helicase activity in vitro, consistent with recent studies of eukaryotic XPB. In almost all archaeal genomes, the xpb gene lies adjacent to a conserved partner gene, and we demonstrate that these two gene products form a physical interaction in vitro. We propose the name Bax1 (Binds archaeal XPB) for this protein, which has a predicted endonuclease domain. XPB and Bax1 may collaborate in processing nucleic acid in an archaeal-specific DNA repair pathway.


J Mol Biol


Richards JD,Cubeddu L,Roberts J,Liu H,White MF




Has Abstract


2008-02-22 00:00:00














  • Myosin isoform determines the conformational dynamics and cooperativity of actin filaments in the strongly bound actomyosin complex.

    abstract::We used transient phosphorescence anisotropy to detect the microsecond rotational dynamics of erythrosin-iodoacetamide-labeled actin strongly bound to single-headed fragments of muscle myosin subfragment 1 (S1) and non-muscle myosin V (MV). The conformational dynamics of actin filaments in solution are markedly influe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Prochniewicz E,Chin HF,Henn A,Hannemann DE,Olivares AO,Thomas DD,De La Cruz EM

    更新日期:2010-02-26 00:00:00

  • Structure of alpha-chymotrypsin refined at 1.68 A resolution.

    abstract::Diffraction data for alpha-chymotrypsin crystals at -10 degrees C were measured at 1.68 A resolution and refined by restrained structure-factor least-squares refinement. The two independent chymotrypsin molecules in the crystallographic asymmetric unit were refined independently. The overall structure of alpha-chymotr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Tsukada H,Blow DM

    更新日期:1985-08-20 00:00:00

  • The type I restriction endonuclease EcoR124I, couples ATP hydrolysis to bidirectional DNA translocation.

    abstract::Type I restriction endonuclease holoenzymes contain methylase (M), restriction (R) and specificity (S) subunits, present in an M2:R2:S1 stoichiometry. These enzymes bind to specific DNA sequences and translocate dsDNA in an ATP-dependent manner toward the holoenzyme anchored at the recognition sequence. Once transloca...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Bianco PR,Hurley EM

    更新日期:2005-09-30 00:00:00

  • RecA protein assisted selection reveals a low fidelity of recognition of homology in a duplex DNA by an oligonucleotide.

    abstract::We have developed an in vitro selection procedure to elucidate the specificity of RecA assisted oligonucleotide recognition of double stranded DNA. The procedure was based on formation of a synaptic complex between an oligonucleotide-RecA filament and a supercoiled plasmid bearing a homologous partially degenerate reg...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Malkov VA,Sastry L,Camerini-Otero RD

    更新日期:1997-08-15 00:00:00

  • The relationship between conservation, thermodynamic stability, and function in the SH3 domain hydrophobic core.

    abstract::To investigate the relationships between sequence conservation, protein stability, and protein function, we have measured the thermodynamic stability, folding kinetics, and in vitro peptide-binding activity of a large number of single-site substitutions in the hydrophobic core of the Fyn SH3 domain. Comparison of thes...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Di Nardo AA,Larson SM,Davidson AR

    更新日期:2003-10-24 00:00:00

  • Crystal structure of metastasis-associated protein S100A4 in the active calcium-bound form.

    abstract::S100A4 (metastasin) is a member of the S100 family of calcium-binding proteins that is directly involved in tumorigenesis. Until recently, the only structural information available was the solution NMR structure of the inactive calcium-free form of the protein. Here we report the crystal structure of human S100A4 in t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Pathuri P,Vogeley L,Luecke H

    更新日期:2008-10-31 00:00:00

  • Structural and functional analysis of a human 7 S K RNA gene.

    abstract::Using purified RNA from HeLa cells, we have synthesized and cloned a cDNA encoding an almost entire 7 S K RNA. This cDNA probe was used to isolate 7 S K RNA gene sequences from a human genomic library by high-stringency colony hybridization. In order to differentiate between functional genes and related sequences, we ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Krüger W,Benecke BJ

    更新日期:1987-05-05 00:00:00

  • Characterization of oligomeric intermediates in alpha-synuclein fibrillation: FRET studies of Y125W/Y133F/Y136F alpha-synuclein.

    abstract::The aggregation of alpha-synuclein is believed to be a critical step in the etiology of Parkinson's disease. A variety of biophysical techniques were used to investigate the aggregation and fibrillation of alpha-synuclein in which one of the four intrinsic Tyr residues was replaced by Trp, and two others by Phe, in or...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kaylor J,Bodner N,Edridge S,Yamin G,Hong DP,Fink AL

    更新日期:2005-10-21 00:00:00

  • The IL-10R2 binding hot spot on IL-22 is located on the N-terminal helix and is dependent on N-linked glycosylation.

    abstract::IL-22 is a class 2 alpha-helical cytokine involved in the generation of inflammatory responses. These activities require IL-22 to engage the cell surface receptors IL-22R1 and the low-affinity signaling molecule IL-10R2. IL-10R2 also interacts with five other class 2 cytokines: IL-10, IL-26, and the interferon-like cy...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Logsdon NJ,Jones BC,Allman JC,Izotova L,Schwartz B,Pestka S,Walter MR

    更新日期:2004-09-10 00:00:00

  • Reversible and irreversible changes in nucleosome structure along the c-fos and c-myc oncogenes following inhibition of transcription.

    abstract::A new affinity chromatographic procedure for the separation of transcriptionally active nucleosomes has been used to study the changes that take place in chromatin structure along the c-fos and c-myc genes when RNA synthesis is inhibited. Mercury-affinity chromatography separates the sulfhydryl-reactive nucleosomes of...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Chen TA,Sterner R,Cozzolino A,Allfrey VG

    更新日期:1990-04-05 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


    authors: Wozniak CE,Hughes KT

    更新日期:2008-06-20 00:00:00

  • Unique base-pair breathing dynamics in PNA-DNA hybrids.

    abstract::Kinetic and thermodynamic parameters, derived from 1H-NMR measurements of the imino proton exchange rates upon titration with the exchange catalyst ammonia, are reported for two mixed-sequence peptide nucleic acid (PNA)-DNA hybrids and their counterpart DNA duplex. The exchange times of the imino protons in the PNA st...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Leijon M,Sehlstedt U,Nielsen PE,Gräslund A

    更新日期:1997-08-22 00:00:00

  • Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases.

    abstract::The position of the tertiary Levitt pair between nucleotides 15 and 48 in the transfer RNA core region suggests a key role in stabilizing the joining of the two helical domains, and in maintaining the relative orientations of the D and variable loops. E. coli tRNA(Gln) possesses the canonical Pu15-Py48 trans pairing a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Sherlin LD,Bullock TL,Newberry KJ,Lipman RS,Hou YM,Beijer B,Sproat BS,Perona JJ

    更新日期:2000-06-02 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


    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

  • Three-dimensional structure of a cloning vector. X-ray diffraction studies of filamentous bacteriophage M13 at 7 A resolution.

    abstract::Filamentous bacteriophage M13 is a single-stranded DNA phage about 65 A in diameter and 9300 A long. X-ray diffraction studies of magnetically oriented fibers of native, mercury and iodine-labeled phage particles have been used to determine the arrangement of the major coat protein, the gene 8 product, in the virion. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Glucksman MJ,Bhattacharjee S,Makowski L

    更新日期:1992-07-20 00:00:00

  • Comparative thermodynamics for monomer and dimer sequence-dependent binding of a heterocyclic dication in the DNA minor groove.

    abstract::Phenylamidine cationic groups linked by a furan ring (furamidine) and related symmetric diamidine compounds bind as monomers in the minor groove of AT sequences of DNA. DB293, an unsymmetric derivative with one of the phenyl rings of furamidine replaced with a benzimidazole, can bind to AT sequences as a monomer but b...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Wang L,Kumar A,Boykin DW,Bailly C,Wilson WD

    更新日期:2002-03-29 00:00:00

  • Structural characterization of the Yersinia pestis type III secretion system needle protein YscF in complex with its heterodimeric chaperone YscE/YscG.

    abstract::The plague-causing bacterium Yersinia pestis utilizes a type III secretion system to deliver effector proteins into mammalian cells where they interfere with signal transduction pathways that mediate phagocytosis and the inflammatory response. Effector proteins are injected through a hollow needle structure composed o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Sun P,Tropea JE,Austin BP,Cherry S,Waugh DS

    更新日期:2008-03-28 00:00:00

  • Alternative splicing of an amino-terminal PEVK-like region generates multiple isoforms of Drosophila projectin.

    abstract::Drosophila projectin is an extremely large protein found within the muscle sarcomeric unit, parallel with the actin and myosin filaments. Projectin has been suggested as the elastic component of C-filaments in insect indirect flight muscles, which is consistent with its localization from the Z band to the tip of the A...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Southgate R,Ayme-Southgate A

    更新日期:2001-11-09 00:00:00

  • Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis.

    abstract::Catalytic antibodies 6D9 and 9C10, which were induced by immunization with a haptenic transition-state analog (TSA), catalyze the hydrolysis of a nonbioactive chloramphenicol monoester derivative to generate a bioactive chloramphenicol. These antibodies stabilize the transition state to catalyze the hydrolysis reactio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Oda M,Ito N,Tsumuraya T,Suzuki K,Sakakura M,Fujii I

    更新日期:2007-05-25 00:00:00

  • Mutant alleles of the MRS2 gene of yeast nuclear DNA suppress mutations in the catalytic core of a mitochondrial group II intron.

    abstract::Previous studies show that some yeast strains carrying point mutations of domain 5 that block splicing of a mitochondrial group II intron yield spontaneous revertants in which splicing is partially restored by dominant mutations of nuclear genes. Here we cloned and sequenced the suppressor allele of one such gene, and...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Schmidt U,Maue I,Lehmann K,Belcher SM,Stahl U,Perlman PS

    更新日期:1998-09-25 00:00:00

  • Crystal structure of zebrafish hatching enzyme 1 from the zebrafish Danio rerio.

    abstract::Fish hatching enzymes are zinc metalloproteases that digest the egg envelope (chorion) at the time of hatching. The crystal structure of zebrafish hatching enzyme 1 (ZHE1) has been solved at 1.10 Å resolution. ZHE1 is monomeric, is mitten shaped, and has a cleft at the center of the molecule. ZHE1 consists of three 3(...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Okada A,Sano K,Nagata K,Yasumasu S,Ohtsuka J,Yamamura A,Kubota K,Iuchi I,Tanokura M

    更新日期:2010-10-08 00:00:00

  • Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures.

    abstract::Structural analysis of delta131delta, a fragment model of the denatured state of staphylococcal nuclease, has been extended by obtaining long-range distance restraints between chain segments by paramagnetic relaxation enhancement. Fourteen unique PROXYL spin labels were introduced at sites that are solvent-exposed in ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Gillespie JR,Shortle D

    更新日期:1997-04-25 00:00:00

  • Native and non-native structure in a protein-folding intermediate: spectroscopic studies of partially reduced IGF-I and an engineered alanine model.

    abstract::The structure of a metastable folding intermediate of human insulin-like growth factor I (IGF-I) and an engineered model are investigated by circular dichroism and two-dimensional 1H NMR spectroscopy. The intermediate, which contains two of three native disulfide bonds, was trapped by acid quenching and isolated by re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Hua QX,Narhi L,Jia W,Arakawa T,Rosenfeld R,Hawkins N,Miller JA,Weiss MA

    更新日期:1996-06-07 00:00:00

  • Light-regulated catalysis by an RNA-cleaving deoxyribozyme.

    abstract::We describe light-induced switches for the catalytic activity of the small, RNA-cleaving 8-17 deoxyribozyme (DNAzyme), based on photochemically induced cis-trans isomerization of azobenzene (Az) moieties covalently tethered at various locations within the DNAzyme. Prior studies have shown that trans-azobenzene is able...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Liu Y,Sen D

    更新日期:2004-08-20 00:00:00

  • Morphology of sheet-like assemblies of pN-collagen, pC-collagen and procollagen studied by scanning transmission electron microscopy mass measurements.

    abstract::At high concentrations, type I pN-collagen, pC-collagen and procollagen (the first 2 generated from procollagen by enzymic cleavage of C-propeptides and N-propeptides, respectively) can all be made to assemble in vitro into thin D-periodic sheets or tapes. Scanning transmission electron microscopy mass measurements sh...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Holmes DF,Mould AP,Chapman JA

    更新日期:1991-07-05 00:00:00

  • Order-disorder phenomena in myelinated nerve sheaths: V. Effects of temperature on rat sciatic and optic nerves, and structural differences between the two types of nerve.

    abstract::We describe in this work X-ray scattering and electron microscope studies of rat sciatic and optic nerves as a function of temperature. The scattering experiments were analyzed as described in the previous papers of this series: a variety of parameters were determined, some of which characterize the lattice disorder, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Mateu L,Luzzati V,Vonasek E,Mateu E,Villegas GM,Vargas R

    更新日期:1995-01-13 00:00:00

  • The First Structure of an Active Mammalian dCTPase and its Complexes With Substrate Analogs and Products.

    abstract::Precise regulation of dNTPs within the cellular nucleotide pool is essential for high accuracy of DNA replication and is critical for retaining the genomic integrity. Recently, human dCTPase (deoxycytidine triphosphatase), also known as DCTPP1 (human all-alpha dCTP pyrophosphatase 1), has been revealed to be a key pla...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Scaletti E,Claesson M,Helleday T,Jemth AS,Stenmark P

    更新日期:2020-02-14 00:00:00

  • A pH-dependent dimer lock in spider silk protein.

    abstract::Spider dragline silk, one of the strongest polymers in nature, is composed of proteins termed major ampullate spidroin (MaSp) 1 and MaSp2. The N-terminal (NT) domain of MaSp1 produced by the nursery web spider Euprosthenops australis acts as a pH-sensitive relay, mediating spidroin assembly at around pH 6.3. Using ami...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Landreh M,Askarieh G,Nordling K,Hedhammar M,Rising A,Casals C,Astorga-Wells J,Alvelius G,Knight SD,Johansson J,Jörnvall H,Bergman T

    更新日期:2010-11-26 00:00:00

  • Contributions of residue pairing to beta-sheet formation: conservation and covariation of amino acid residue pairs on antiparallel beta-strands.

    abstract::In an effort to better understand beta-sheet assembly, we have investigated the evolutionary behavior of neighboring residues on adjacent antiparallel beta-strands. Residue pairs were classified according to solvent exposure as well as by whether their backbone NH and C==O groups are hydrogen bonded. The conservation ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Mandel-Gutfreund Y,Zaremba SM,Gregoret LM

    更新日期:2001-02-02 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


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

    更新日期:2003-11-28 00:00:00