Structural bases for sulfide recognition in Lucina pectinata hemoglobin I.


:The X-ray crystal structure of the sulfide derivative of ferric Lucina pectinata hemoglobin component I (HbI) has been determined at 1.9 A resolution (R-factor 0.186). The heme pocket structural organization of HbI is in keeping with its ligand binding properties. The fast sulfide association rate constant can be related to the presence of Gln(64)E7, as the heme distal residue, together with the protein structural properties in the CD-E distal region. Moreover, the very high sulfide affinity for HbI is reflected by the exceptionally slow ligand dissociation rate. The stabilization of the heme-bound sulfide molecule is achieved through hydrogen bonding to Gln(64)E7, as well as by finely tuned aromatic-electrostatic interactions with the clustered residues Phe(29)B10, Phe(43)CD1 and Phe(68)E11. Such a peculiar arrangement of phenylalanyl residues at the distal ligand binding site has not been observed before in the globin family, and is unique to HbI, a protein functionally devoted to sulfide transport.


J Mol Biol


Rizzi M,Wittenberg JB,Coda A,Ascenzi P,Bolognesi M




Has Abstract


1996-04-26 00:00:00














  • Induced transcription of the mouse beta-globin transcription unit in erythroleukemia cells. Time-course of induction and of changes in chromatin structure.

    abstract::The transcription of the beta-globin genes in mouse erythroleukemia cells has been examined by hybridizing labeled RNA obtained from isolated nuclei after chain elongation in the presence of [alpha-32P]UTP. There is induction of at least 30-fold of beta maj globin transcription after cells are treated with either dime...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Salditt-Georgieff M,Sheffery M,Krauter K,Darnell JE Jr,Rifkind R,Marks PA

    更新日期:1984-02-05 00:00:00

  • Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9: similarities and differences in the folding of homologous proteins.

    abstract::The bacterial immunity proteins Im7 and Im9 fold with mechanisms of different kinetic complexity. Whilst Im9 folds in a two-state transition at pH 7.0 and 10 degrees C, Im7 populates an on-pathway intermediate under these conditions. In order to assess the role of sequence versus topology in the folding of these prote...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Friel CT,Capaldi AP,Radford SE

    更新日期:2003-02-07 00:00:00

  • Stability of a structural scaffold upon activity transfer: X-ray structure of a three fingers chimeric protein.

    abstract::Fasciculin 2 and toxin alpha proteins belong to the same structural family of three-fingered snake toxins. They act on different targets, but in each case the binding region involves residues from loops I and II. The superimposition of the two structures suggests that these functional regions correspond to structurall...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Le Du MH,Ricciardi A,Khayati M,Ménez R,Boulain JC,Ménez A,Ducancel F

    更新日期:2000-03-03 00:00:00

  • Energetics of MazG unfolding in correlation with its structural features.

    abstract::MazG is a homodimeric alpha-helical protein that belongs to the superfamily of all-alpha NTP pyrophosphatases. Its function has been connected to the regulation of the toxin-antitoxin module mazEF, implicated in programmed growth arrest/cell death of Escherichia coli cells under conditions of amino acid starvation. Th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Drobnak I,Korencic A,Loris R,Marianovsky I,Glaser G,Jamnik A,Vesnaver G,Lah J

    更新日期:2009-09-11 00:00:00

  • Expression-system-dependent modulation of HIV-1 envelope glycoprotein antigenicity and immunogenicity.

    abstract::Recombinant expression systems differ in the type of glycosylation they impart on expressed antigens such as the human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins, potentially affecting their biological properties. We performed head-to-head antigenic, immunogenic and molecular profiling of two distant...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kong L,Sheppard NC,Stewart-Jones GBE,Robson CL,Chen H,Xu X,Krashias G,Bonomelli C,Scanlan CN,Kwong PD,Jeffs SA,Jones IM,Sattentau QJ

    更新日期:2010-10-15 00:00:00

  • Role of beta-turn residues in beta-hairpin formation and stability in designed peptides.

    abstract::The sequence RGITVNGKTYGR has been reported as part of a de novo design peptide system. This peptide folds as a beta-hairpin structure with three residues per strand and two residue turns. Asn6 side-chain, the residue in position L1 of the beta-turn, appeared to be solvent exposed, interacting only within the turn but...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ramírez-Alvarado M,Blanco FJ,Niemann H,Serrano L

    更新日期:1997-11-07 00:00:00

  • UTP-bound and Apo structures of a minimal RNA uridylyltransferase.

    abstract::3'-Uridylylation of RNA is emerging as a phylogenetically widespread phenomenon involved in processing events as diverse as uridine insertion/deletion RNA editing in mitochondria of trypanosomes and small nuclear RNA (snRNA) maturation in humans. This reaction is catalyzed by terminal uridylyltransferases (TUTases), w...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Stagno J,Aphasizheva I,Rosengarth A,Luecke H,Aphasizhev R

    更新日期:2007-02-23 00:00:00

  • Close packing of an oligomeric eye lens beta-crystallin induces loss of symmetry and ordering of sequence extensions.

    abstract::beta-Crystallins are oligomeric eye lens proteins that are related to monomeric gamma-crystallins. The main sequence difference between the two families is the presence of sequence extensions in the beta-crystallins. A major question concerns the role that these extensions play in mediating interactions at the high pr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Nalini V,Bax B,Driessen H,Moss DS,Lindley PF,Slingsby C

    更新日期:1994-03-04 00:00:00

  • Non-receptor tyrosine kinases c-Abl and Arg regulate the activity of C/EBPbeta.

    abstract::The CCAAT/enhancer-binding protein beta (C/EBPbeta) is a critical transcription factor that regulates gene expression during numerous biological processes, including differentiation, metabolism, homeostasis, proliferation, tumorigenesis, inflammation, and apoptosis. In this study, interactions between C/EBPbeta and ei...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Li X,Liu X,Wang G,Zhu X,Qu X,Li X,Yang Y,Peng L,Li C,Li P,Huang W,Ma Q,Cao C

    更新日期:2009-08-28 00:00:00

  • Organization of the R family and other interspersed repetitive DNA sequences in the mouse genome.

    abstract::Six R sequences have been described as members of a new family of dispersed repetitive DNA in the mouse genome (Gebhard et al., 1982). Several sequenced regions were extended in the 5' direction (R1, R2 and R6) and two new sequences were determined (R7 and R8). On the basis of our sequence and blot hybridization data ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Gebhard W,Zachau HG

    更新日期:1983-10-25 00:00:00

  • Structural and functional analysis of the C-terminal domain of Nup358/RanBP2.

    abstract::The nuclear pore complex is the sole mediator of bidirectional transport between the nucleus and cytoplasm. Nup358 is a metazoan-specific nucleoporin that localizes to the cytoplasmic filaments and provides several binding sites for the mobile nucleocytoplasmic transport machinery. Here we present the crystal structur...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lin DH,Zimmermann S,Stuwe T,Stuwe E,Hoelz A

    更新日期:2013-04-26 00:00:00

  • Complete assignment of the 1H nuclear magnetic resonance spectrum of French bean plastocyanin. Sequential resonance assignments, secondary structure and global fold.

    abstract::Sequence-specific proton nuclear magnetic resonance (n.m.r.) assignments for all 99 amino acid residues of French bean Cu(I) plastocyanin are described. The assignments were made using standard sequential assignment procedures and were greatly facilitated by the availability of complete spin system assignments. The ch...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Chazin WJ,Wright PE

    更新日期:1988-08-05 00:00:00

  • Both N-Terminal and C-Terminal Histidine Residues of the Prion Protein Are Essential for Copper Coordination and Neuroprotective Self-Regulation.

    abstract::The cellular prion protein (PrPC) comprises two domains: a globular C-terminal domain and an unstructured N-terminal domain. Recently, copper has been observed to drive tertiary contact in PrPC, inducing a neuroprotective cis interaction that structurally links the protein's two domains. The location of this interacti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Schilling KM,Tao L,Wu B,Kiblen JTM,Ubilla-Rodriguez NC,Pushie MJ,Britt RD,Roseman GP,Harris DA,Millhauser GL

    更新日期:2020-07-24 00:00:00

  • Structure determination of the glutamate dehydrogenase from the hyperthermophile Thermococcus litoralis and its comparison with that from Pyrococcus furiosus.

    abstract::Glutamate dehydrogenase catalyses the oxidative deamination of glutamate to 2-oxoglutarate with concomitant reduction of NAD(P)(+), and has been shown to be widely distributed in nature across species ranging from psychrophiles to hyperthermophiles. Extensive characterisation of this enzyme isolated from hyperthermoph...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Britton KL,Yip KS,Sedelnikova SE,Stillman TJ,Adams MW,Ma K,Maeder DL,Robb FT,Tolliday N,Vetriani C,Rice DW,Baker PJ

    更新日期:1999-11-12 00:00:00

  • Accomodation of S-cis-tamoxifen-N(2)-guanine adduct within a bent and widened DNA minor groove.

    abstract::The non-steroidal anti-estrogen tamoxifen [TAM] has been in clinical use over the last two decades as a potent adjunct chemotherapeutic agent for treatment of breast cancer. It has also been given prophylactically to women with a strong family history of breast cancer. However, tamoxifen treatment has also been associ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Shimotakahara S,Gorin A,Kolbanovskiy A,Kettani A,Hingerty BE,Amin S,Broyde S,Geacintov N,Patel DJ

    更新日期:2000-09-15 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


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

    更新日期:1999-12-17 00:00:00

  • Nuclear magnetic resonance solution structure of dendrotoxin K from the venom of Dendroaspis polylepis polylepis.

    abstract::The solution structure of dendrotoxin K (Toxin K), a protein consisting of one polypeptide chain with 57 residues purified from the venom of the black mamba, Dendroaspis polylepis polylepis, was determined by nuclear magnetic resonance (NMR) spectroscopy. On the basis of virtually complete sequence-specific 1H NMR ass...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Berndt KD,Güntert P,Wüthrich K

    更新日期:1993-12-05 00:00:00

  • Features of the plasmid pMV158-encoded MobM, a protein involved in its mobilization.

    abstract::The streptococcal promiscuous plasmid pMV158 can be mobilized between a number of bacterial species by means of three elements: (i) the plasmid-encoded nicking-closing protein MobM, involved in the initiation and termination of the conjugative transfer; (ii) the DNA sequence where the MobM-mediated nick takes place (t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: de Antonio C,Farías ME,de Lacoba MG,Espinosa M

    更新日期:2004-01-16 00:00:00

  • (GT)n repetitive tracts affect several stages of RecA-promoted recombination.

    abstract::The effect of GT/CA dinucleotide repeat tracts on RecA-dependent homologous recombination was examined in vitro. By measuring the binding of RecA protein to oligonucleotides containing GT or CA repeats using the surface plasmon resonance (BIAcore), we show that the efficiency of RecA protein binding is sequence depend...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Dutreix M

    更新日期:1997-10-17 00:00:00

  • Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions.

    abstract::Contradictory reports in the literature have emphasised either the sequence of small interfering RNAs (siRNA) or the structure of their target molecules to be the major determinant of the efficiency of RNA interference (RNAi) approaches. In the present study, we analyse systematically the contributions of these parame...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Schubert S,Grünweller A,Erdmann VA,Kurreck J

    更新日期:2005-05-13 00:00:00

  • DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site.

    abstract::Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleot...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kearney BM,Johnson CW,Roberts DM,Swartz P,Mattos C

    更新日期:2014-02-06 00:00:00

  • Self-assembly of brome mosaic virus protein into capsids. Initial and final states of aggregation.

    abstract::The pH and ionic strength dependence of the states of aggregation of brome mosaic virus protein has been investigated by small angle neutron scattering, quasielastic light-scattering, analytical centrifugation and electron microscopy. At pH above neutrality, protein oligomers are found in dynamical equilibrium, compri...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Cuillel M,Zulauf M,Jacrot B

    更新日期:1983-03-15 00:00:00

  • A mechanistic insight into SMAC peptide interference with XIAP-Bir2 inhibition of executioner caspases.

    abstract::X-linked inhibitor of apoptosis protein (XIAP) inhibits apoptosis mainly through inhibition of caspase-9 and executioner caspases of -3 and -7. The inhibition of the former protease is implemented through the bacculoviral inhibitory repeat-3 (Bir3) domain, while the inhibition of the latter is accomplished by the inte...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Abhari BA,Davoodi J

    更新日期:2008-09-05 00:00:00

  • Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs.

    abstract::X-ray, phylogenetic and quantum chemical analysis of molecular interactions and conservation patterns of cis Watson-Crick (W.C.) A/G base-pairs in 16S rRNA, 23S rRNA and other molecules was carried out. In these base-pairs, the A and G nucleotides interact with their W.C. edges with glycosidic bonds oriented cis relat...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Sponer J,Mokdad A,Sponer JE,Spacková N,Leszczynski J,Leontis NB

    更新日期:2003-07-25 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

  • Electrostatic interactions in the denatured state and in the transition state for protein folding: effects of denatured state interactions on the analysis of transition state structure.

    abstract::The development of electrostatic interactions during the folding of the N-terminal domain of the ribosomal protein L9 (NTL9) is investigated by pH-dependent rate equilibrium free energy relationships. We show that Asp8, among six acidic residues, is involved in non-native, electrostatic interactions with K12 in the tr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Cho JH,Raleigh DP

    更新日期:2006-06-23 00:00:00

  • A novel photoactive GAF domain of cyanobacteriochrome AnPixJ that shows reversible green/red photoconversion.

    abstract::We report the discovery of a novel cyanobacteriochrome, the green/red photoreceptor AnPixJ (All1069), isolated from the heterocyst-forming cyanobacterium Anabaena (Nostoc) sp. PCC 7120. Cyanobacteriochromes are a recently emerging tetrapyrrole-based photoreceptor superfamily that are distantly related to the conventio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Narikawa R,Fukushima Y,Ishizuka T,Itoh S,Ikeuchi M

    更新日期:2008-07-25 00:00:00

  • Reversible peptide folding in solution by molecular dynamics simulation.

    abstract::Long-standing questions on how peptides fold are addressed by the simulation at different temperatures of the reversible folding of a peptide in solution in atomic detail. Molecular dynamics simulations correctly predict the structure that is thermodynamically stable at 298 K, irrespective of the initial peptide confo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Daura X,Jaun B,Seebach D,van Gunsteren WF,Mark AE

    更新日期:1998-07-31 00:00:00

  • HDEA, a periplasmic protein that supports acid resistance in pathogenic enteric bacteria.

    abstract::The X-ray crystal structure of the Escherichia coli stress response protein HDEA has been determined at 2.0 A resolution. The single domain alpha-helical protein is found in the periplasmic space, where it supports an acid resistance phenotype essential for infectivity of enteric bacterial pathogens, such as Shigella ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Gajiwala KS,Burley SK

    更新日期:2000-01-21 00:00:00

  • A structural perspective of the sequence variability within botulinum neurotoxin subtypes A1-A4.

    abstract::Botulinum neurotoxin (BoNT) is a category A toxin that has been classified within seven serotypes, designated A-G. Recently, it has been discovered that sequence variability occurs in BoNTs produced by serotype A (BoNT/A) variant strains, designated as subtypes A1 and A2, which have significantly different antibody-bi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Arndt JW,Jacobson MJ,Abola EE,Forsyth CM,Tepp WH,Marks JD,Johnson EA,Stevens RC

    更新日期:2006-09-29 00:00:00