当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Flexibility and variability of TIMP binding: X-ray structure of the complex between collagenase-3/MMP-13 and TIMP-2.

Flexibility and variability of TIMP binding: X-ray structure of the complex between collagenase-3/MMP-13 and TIMP-2.

Abstract：

:The excessive activity of matrix metalloproteinases (MMPs) contributes to pathological processes such as arthritis, tumor growth and metastasis if not balanced by the tissue inhibitors of metalloproteinases (TIMPs). In arthritis, the destruction of fibrillar (type II) collagen is one of the hallmarks, with MMP-1 (collagenase-1) and MMP-13 (collagenase-3) being identified as key players in arthritic cartilage. MMP-13, furthermore, has been found in highly metastatic tumors. We have solved the 2.0 A crystal structure of the complex between the catalytic domain of human MMP-13 (cdMMP-13) and bovine TIMP-2. The overall structure resembles our previously determined MT1-MMP/TIMP-2 complex, in that the wedge-shaped TIMP-2 inserts with its edge into the entire MMP-13 active site cleft. However, the inhibitor is, according to a relative rotation of approximately 20 degrees, oriented differently relative to the proteinase. Upon TIMP binding, the catalytic zinc, the zinc-ligating side chains, the enclosing MMP loop and the S1' wall-forming segment move significantly and in concert relative to the rest of the cognate MMP, and the active site cleft constricts slightly, probably allowing a more favourable interaction between the Cys1(TIMP) alpha-amino group of the inhibitor and the catalytic zinc ion of the enzyme. Thus, this structure supports the view that the central N-terminal TIMP segment essentially defines the relative positioning of the TIMP, while the flanking edge loops determine the relative orientation, depending on the individual target MMP.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Maskos K,Lang R,Tschesche H,Bode W

doi

10.1016/j.jmb.2006.11.072

subject

Has Abstract

pub_date

2007-03-02 00:00:00

pages

1222-31

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(06)01631-7

journal_volume

366

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Structural and biophysical characterization of the Syk activation switch.

    abstract：:Syk is an essential non-receptor tyrosine kinase in intracellular immunological signaling, and the control of Syk kinase function is considered as a valuable target for pharmacological intervention in autoimmune or inflammation diseases. Upon immune receptor stimulation, the kinase activity of Syk is regulated by bind...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.11.007

    authors： Grädler U,Schwarz D,Dresing V,Musil D,Bomke J,Frech M,Greiner H,Jäkel S,Rysiok T,Müller-Pompalla D,Wegener A

    更新日期：2013-01-23 00:00:00

  • Kinetic isotope effects reveal the presence of significant secondary structure in the transition state for the folding of the N-terminal domain of L9.

    abstract：:Our present understanding of the nature of the transition state for protein folding depends predominantly on studies where individual side-chain contributions are mapped out by mutational analysis (phi value analysis). This approach, although extremely powerful, does not in general provide direct information about the...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.02.084

    authors： Sato S,Raleigh DP

    更新日期：2007-07-06 00:00:00

  • Structural studies of the final enzyme in the alpha-aminoadipate pathway-saccharopine dehydrogenase from Saccharomyces cerevisiae.

    abstract：:The 1.64 A structure of the apoenzyme form of saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae shows the enzyme to be composed of two domains with similar dinucleotide binding folds with a deep cleft at the interface. The structure reveals homology to alanine dehydrogenase, despite low primary sequence s...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.08.044

    authors： Burk DL,Hwang J,Kwok E,Marrone L,Goodfellow V,Dmitrienko GI,Berghuis AM

    更新日期：2007-10-26 00:00:00

  • Dramatic stabilization of an SH3 domain by a single substitution: roles of the folded and unfolded states.

    abstract：:The N-terminal SH3 domain of the Drosophila drk protein (drkN SH3) exists in equilibrium between folded and unfolded states under non-denaturing buffer conditions. In order to examine the origins of this instability, we have made mutations in the domain and characterized the thermodynamics and kinetics of folding. Res...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4521

    authors： Mok YK,Elisseeva EL,Davidson AR,Forman-Kay JD

    更新日期：2001-03-30 00:00:00

  • Purification and secondary structure determination of simian immunodeficiency virus p27.

    abstract：:We have developed a novel method for the expression and purification of p27, the major core protein of simian immunodeficiency virus. Circular dichroism measurements of purified p27 were used to determine the relative amounts of alpha-helix, beta-sheet and unordered secondary structural elements. These empirically det...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(05)80308-0

    authors： Burns NR,Craig S,Lee SR,Richardsons MH,Stenner N,Adams SE,Kingsman SM,Kingsman AJ

    更新日期：1990-11-20 00:00:00

  • Correlation between calculated local stability and hydrogen exchange rates in proteins.

    abstract：:The attempt is made to find new correlations between local structural characteristics of proteins and the hydrogen exchange rates of their individual main-chain amides, and to relate such correlations to possible mechanisms of hydrogen exchange. It is found that in bovine pancreatic trypsin inhibitor (BPTI) the surfac...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90317-2

    authors： Rashin AA

    更新日期：1987-11-20 00:00:00

  • Observing membrane protein diffusion at subnanometer resolution.

    abstract：:Single sodium-driven rotors from a bacterial ATP synthase were embedded into a lipid membrane and observed in buffer solution at subnanometer resolution using atomic force microscopy (AFM). Time-lapse AFM topographs show the movement of single proteins within the membrane. Subsequent analysis of their individual traje...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00206-7

    authors： Müller DJ,Engel A,Matthey U,Meier T,Dimroth P,Suda K

    更新日期：2003-04-11 00:00:00

  • A highly conserved lysine residue in phi29 DNA polymerase is important for correct binding of the templating nucleotide during initiation of phi29 DNA replication.

    abstract：:DNA polymerases that initiate replication by protein-priming are able to catalyze terminal protein (TP)-primed initiation, the following transition steps and finally DNA-primed elongation. Therefore, their structures must be able to position sequentially both primers, TP and DNA, at a common binding site. For DNA-temp...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/S0022-2836(02)00022-0

    authors： Truniger V,Lázaro JM,Blanco L,Salas M

    更新日期：2002-04-19 00:00:00

  • Structural studies of MFE-1: the 1.9 A crystal structure of the dehydrogenase part of rat peroxisomal MFE-1.

    abstract：:The 1.9 A structure of the C-terminal dehydrogenase part of the rat peroxisomal monomeric multifunctional enzyme type 1 (MFE-1) has been determined. In this construct (residues 260-722 and referred to as MFE1-DH) the N-terminal hydratase part of MFE-1 has been deleted. The structure of MFE1-DH shows that it consists o...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.10.085

    authors： Taskinen JP,Kiema TR,Hiltunen JK,Wierenga RK

    更新日期：2006-01-27 00:00:00

  • Design and evolution of artificial M13 coat proteins.

    abstract：:Using simple design and selective pressure, we have evolved an artificial M13 bacteriophage coat protein. M13 coat proteins first reside in the bacterial inner membrane and subsequently surround the DNA core of the assembled virus. The artificial coat protein (ACP) was designed and evolved to mimic both functions of t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3845

    authors： Weiss GA,Sidhu SS

    更新日期：2000-06-30 00:00:00

  • Crystals of seryl-tRNA synthetase from Escherichia coli. Preliminary crystallographic data.

    abstract：:Crystals of seryl-tRNA synthetase from Escherichia coli can be grown from ammonium sulphate/octyl glucoside solutions in two days. The crystals appear to be very suitable for X-ray analysis, diffracting to at least 2.8 A resolution and being resistant to radiation damage. The crystals are monoclinic (space group C2) w...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90232-4

    authors： Leberman R,Berthet-Colominas C,Cusack S,Härtlein M

    更新日期：1987-01-20 00:00:00

  • AMP sensing by DEAD-box RNA helicases.

    abstract：:In eukaryotes, cellular levels of adenosine monophosphate (AMP) signal the metabolic state of the cell. AMP concentrations increase significantly upon metabolic stress, such as glucose deprivation in yeast. Here, we show that several DEAD-box RNA helicases are sensitive to AMP, which is not produced during ATP hydroly...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.05.006

    authors： Putnam AA,Jankowsky E

    更新日期：2013-10-23 00:00:00

  • The elastic I-band region of titin is assembled in a "modular" fashion by weakly interacting Ig-like domains.

    abstract：:The vertebrate striated muscle protein titin is thought to play a critical rôle in myofibril assembly and passive tension. The recently determined complete primary structure of titin revealed a modular architecture that opens the way to a structural characterisation and the understanding of essential properties of thi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0050

    authors： Politou AS,Gautel M,Improta S,Vangelista L,Pastore A

    更新日期：1996-02-02 00:00:00

  • Analysis of human Pex19p's domain structure by pentapeptide scanning mutagenesis.

    abstract：:Pex19p, a primarily cytosolic protein, is essential for the biogenesis of numerous peroxisomal membrane proteins (PMPs); however, its precise function is unclear. Pex19p might function as a PMP-specific chaperone, a cycling PMP-receptor protein, a PMP membrane insertion factor, or an association/dissociation factor of...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.01.013

    authors： Fransen M,Vastiau I,Brees C,Brys V,Mannaerts GP,Van Veldhoven PP

    更新日期：2005-03-11 00:00:00

  • In vivo characterization of mutants of the bacteriophage f1 gene V protein isolated by saturation mutagenesis.

    abstract：:The gene V protein of bacteriophage f1 binds to single-stranded nucleic acids and is essential for propagation of phage f1. We tested the function of gene V protein mutants with single amino acid substitutions in two ways: by the ability of the mutant proteins to support phage growth, and by the ability of the mutant ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1165

    authors： Terwilliger TC,Zabin HB,Horvath MP,Sandberg WS,Schlunk PM

    更新日期：1994-02-18 00:00:00

  • Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin gamma1 chain harboring the nidogen binding site.

    abstract：:The structure of three consecutive laminin-type EGF-like (LE) modules of mouse laminin gammma1 chain, gamma1III3-5 (positions 738 to 899), has been determined by multiple isomorphous replacement in a crystal of space group p6(4)22 (a=b=74.57 angstroms, c = 185.11 angstroms and gamma = 120 degrees). The crystal structu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0191

    authors： Stetefeld J,Mayer U,Timpl R,Huber R

    更新日期：1996-04-05 00:00:00

  • The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 A resolution.

    abstract：:The crystal structure of dihydrodipicolinate synthase from E. coli was determined by multiple isomorphous replacement methods. The structure was refined at a resolution of 2.5 A and the final R-factor is 19.6% for 32,190 reflections between 10.0 A and 2.5 A and F > 2 sigma (F). The crystallographic asymmetric unit con...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.0078

    authors： Mirwaldt C,Korndörfer I,Huber R

    更新日期：1995-02-10 00:00:00

  • Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction.

    abstract：:beta-Barrel membrane proteins are found in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Little is known about how residues in membrane beta-barrels interact preferentially with other residues on adjacent strands. We have developed probabilistic models to quantify propensities of residu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.09.094

    authors： Jackups R Jr,Liang J

    更新日期：2005-12-09 00:00:00

  • High-resolution three-dimensional structure of horse heart cytochrome c.

    abstract：:The 1.94 A resolution three-dimensional structure of oxidized horse heart cytochrome c has been elucidated and refined to a final R-factor of 0.17. This has allowed for a detailed assessment of the structural features of this protein, including the presence of secondary structure, hydrogen-bonding patterns and heme ge...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(90)90200-6

    authors： Bushnell GW,Louie GV,Brayer GD

    更新日期：1990-07-20 00:00:00

  • ABCF ATPases Involved in Protein Synthesis, Ribosome Assembly and Antibiotic Resistance: Structural and Functional Diversification across the Tree of Life.

    abstract：:Within the larger ABC superfamily of ATPases, ABCF family members eEF3 in Saccharomyces cerevisiae and EttA in Escherichia coli have been found to function as ribosomal translation factors. Several other ABCFs including biochemically characterized VgaA, LsaA and MsrE confer resistance to antibiotics that target the pe...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2018.12.013

    authors： Murina V,Kasari M,Takada H,Hinnu M,Saha CK,Grimshaw JW,Seki T,Reith M,Putrinš M,Tenson T,Strahl H,Hauryliuk V,Atkinson GC

    更新日期：2019-08-23 00:00:00

  • Stochastic switching in gene networks can occur by a single-molecule event or many molecular steps.

    abstract：:Due to regulatory feedback, biological networks can exist stably in multiple states, leading to heterogeneous phenotypes among genetically identical cells. Random fluctuations in protein numbers, tuned by specific molecular mechanisms, have been hypothesized to drive transitions between these different states. We deve...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.11.035

    authors： Choi PJ,Xie XS,Shakhnovich EI

    更新日期：2010-02-12 00:00:00

  • Functional characterization and modulation of the DNA cleavage efficiency of type III restriction endonuclease EcoP15I in its interaction with two sites in the DNA target.

    abstract：:EcoP15I is a Type III restriction endonuclease requiring the interaction with two inversely oriented 5'-CAGCAG recognition sites for efficient DNA cleavage. Diverse models have been developed to explain how enzyme complexes bound to both sites move toward each other, DNA translocation, DNA looping and simple diffusion...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.02.047

    authors： Möncke-Buchner E,Rothenberg M,Reich S,Wagenführ K,Matsumura H,Terauchi R,Krüger DH,Reuter M

    更新日期：2009-04-17 00:00:00

  • Direct visualisation of conformational changes in EF(0)F(1) by electron microscopy.

    abstract：:The isolated H(+)-ATPase from Escherichia coli (EF(0)F(1)) was investigated by electron microscopy of samples of negatively stained monodisperse molecules, followed by single-particle image processing. The resulting three-dimensional maps showed that the F(1)-part is connected by a prominent stalk to a more peripheral...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3435

    authors： Böttcher B,Bertsche I,Reuter R,Gräber P

    更新日期：2000-02-18 00:00:00

  • Domain Interactions Determine the Amyloidogenicity of Antibody Light Chain Mutants.

    abstract：:In antibody light chain amyloidosis (AL), mutant light chains (LCs) or their variable domains (VLs) form fibrils, which accumulate in organs and lead to their failure. The molecular mechanism of this disease is still poorly understood. One of the key open issues is whether the mutant VLs and LCs differ in fibril forma...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.10.005

    authors： Weber B,Hora M,Kazman P,Pradhan T,Rührnößl F,Reif B,Buchner J

    更新日期：2020-11-20 00:00:00

  • Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain.

    abstract：:Many essential biological processes are mediated by complex molecular machines comprising multiple subunits. Knowledge on the architecture of individual subunits and their positions within the overall multimeric complex is key to understanding the molecular mechanisms of macromolecular assemblies. The anaphase-promoti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2015.08.023

    authors： Cronin NB,Yang J,Zhang Z,Kulkarni K,Chang L,Yamano H,Barford D

    更新日期：2015-10-09 00:00:00

  • Properties of supercoiled DNA in gel electrophoresis. The V-like dependence of mobility on topological constraint. DNA-matrix interactions.

    abstract：:The dependence of the electrophoretic mobility of small DNA rings on topological constraint was investigated in acrylamide or agarose gels as a function of DNA size (from approximately 350 to 1400 base-pairs), gel concentration and nucleotide sequence. Under appropriate adjustment between the size of the DNA and the g...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90282-2

    authors： Zivanovic Y,Goulet I,Prunell A

    更新日期：1986-12-05 00:00:00

  • Cooperation of TOM and TIM23 complexes during translocation of proteins into mitochondria.

    abstract：:Translocation of the majority of mitochondrial proteins from the cytosol into mitochondria requires the cooperation of TOM and TIM23 complexes in the outer and inner mitochondrial membranes. The molecular mechanisms underlying this cooperation remain largely unknown. Here, we present biochemical and genetic evidence t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2014.07.015

    authors： Waegemann K,Popov-Čeleketić D,Neupert W,Azem A,Mokranjac D

    更新日期：2015-03-13 00:00:00

  • The human IgE-encoding transcriptome to assess antibody repertoires and repertoire evolution.

    abstract：:Upon encounter with antigen, the B lymphocyte population responds by producing a diverse set of antigen-specific antibodies of various isotypes. The vast size of the responding populations makes it very difficult to study clonal evolution and repertoire composition occurring during these processes in humans. Here, we ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.06.062

    authors： Andréasson U,Flicker S,Lindstedt M,Valenta R,Greiff L,Korsgren M,Borrebaeck CA,Ohlin M

    更新日期：2006-09-15 00:00:00

  • A study of electrophoretic mobility of DNA in agarose and polyacrylamide gels.

    abstract：:The aim of this paper is to clarify the mechanism of gel electrophoresis of DNA under constant-field conditions. We have conducted a large number of experiments on double-stranded DNA varying in length between approximately 10 and approximately 50,000 base-pairs, in both agarose and polyacrylamide gels ranging from 0....

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)80187-y

    authors： Calladine CR,Collis CM,Drew HR,Mott MR

    更新日期：1991-10-05 00:00:00

  • Mutation spectrum following transfection of ultraviolet-irradiated single-stranded or double-stranded shuttle vector DNA into monkey cells.

    abstract：:We designed a shuttle vector system that allowed a comparison of the mutation spectrum on the supF target gene after transfection of single-stranded or double-stranded DNA into monkey cells. Single-strand-derived plasmids exhibited a spontaneous mutation frequency tenfold higher than double-strand-derived ones. These ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90252-2

    authors： Madzak C,Sarasin A

    更新日期：1991-04-20 00:00:00