Enzymes articles within Nature

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  • Letter |

    Two complexes of RNA-binding proteins, Sm and Lsm2–8, act sequentially on telomerase RNA during its biogenesis: the Sm ring promotes 3′-cleavage and facilitates hypermethylation of the 5′-cap, whereas the Lsm2–8 complex aids binding of the telomerase catalytic subunit and prevents degradation of the RNA.

    • Wen Tang
    • , Ram Kannan
    •  & Peter Baumann

  • Letter |

    The epoxidase PaaABCE, which converts phenylacetyl-CoA into its ring-1,2-epoxide, is shown to be also able to mediate the NADPH-dependent removal of that epoxide, ensuring that the intracellular concentrations of the toxic epoxide does not exceed a certain ‘acceptable’ concentration.

    • Robin Teufel
    • , Thorsten Friedrich
    •  & Georg Fuchs

  • News & Views |

    The orchestration of cell division requires a programme of events choreographed by protein modification. A study shows that the relative activity of a phosphatase enzyme towards its substrates imposes order during the final act of division.

    • Curt Wittenberg

  • Brief Communications Arising |

    • Christopher J. Phiel
    • , Christina A. Wilson
    •  & Peter S. Klein

  • News & Views |

    Caspase-1 is one of the main culprits behind sepsis, a form of systemic inflammation. The related enzyme caspase-11 is also involved, but the relative roles of the two proteins have been confusing, until now. See Letter p.117

    • Douglas R. Green

  • Letter |

    Eukaryotic cells have several DNA ligases. DNA ligase III (Lig3) forms a complex with Xrcc1 that can function in nuclear repair. But, Lig3 null animals cannot be made; is this nuclear role in base excision repair its critical function? This is one of two papers showing that the role of Lig3 in the nucleus is non-essential. Rather, the catalytic activity of Lig3, but not Xrcc1, is essential for the maintenance of mitochondria.

    • Deniz Simsek
    • , Amy Furda
    •  & Maria Jasin

  • News & Views |

    The protein Sae2 mediates the repair of double-strand breaks in DNA. It emerges that Sae2 activity is controlled by both its modification with acetyl groups and its degradation by the process of autophagy. See Article p.74

    • Catherine J. Potenski
    •  & Hannah L. Klein

  • Letter |

    Haematopoietic stem cells (HSCs) are very sensitive to energetic and oxidative stress, and modulation of the balance between their quiescence and proliferation is needed to respond to metabolic stress while preserving HSCs' long-term regenerative capacity. Here, and in two accompanying studies, it is shown that the tumour suppressor Lkb1 has a crucial role in maintaining energy homeostasis in haematopoietic cells.

    • Boyi Gan
    • , Jian Hu
    •  & Ronald A. DePinho

  • Article |

    tRNAs are synthesized in a premature form that requires trimming of the 5′ and 3′ ends and modification of specific nucleotides. RNase P, a complex containing a long catalytic RNA and a protein cofactor, catalyses the cleavage that generates the mature 5′ end. Here, the structure of RNase P bound to mature tRNAPhe is solved. Recognition of the leader sequence and its mechanism of cleavage is determined by soaking an oligonucleotide corresponding to the premature 5′ end into the crystal.

    • Nicholas J. Reiter
    • , Amy Osterman
    •  & Alfonso Mondragón

  • Letter |

    Mononuclear iron-containing oxygenases have many important roles in the cell, including the demethylation of DNA and histones. These authors crystallized the AlkB oxygenase in complex with various modified DNAs. By growing the crystals under anaerobic conditions and then exposing them to dioxygen to initiate oxidation, two different intermediates were trapped. A third type of intermediate was determined using additional computational analysis. These structures provide insight into how these enzymes perform oxidative demethylation.

    • Chengqi Yi
    • , Guifang Jia
    •  & Chuan He

  • Letter |

    These authors identify the human enzyme responsible for menaquinone-4 biosynthesis, a naturally occurring form of vitamin K. They find that UbiA prenyltransferase containing 1, a human homologue of a prenyltransferase gene from Escherichia coli, encodes an enzyme that can convert vitamin K derivatives into menaquinone-4.

    • Kimie Nakagawa
    • , Yoshihisa Hirota
    •  & Toshio Okano

  • Letter |

    The ends of chromosomes, known as telomeres, look like ends generated by double-strand breaks, but if treated as such the DNA damage repair system would initiate a checkpoint response and cause telomere–telomere fusions. These authors show that telomeres lack two types of histone modification that are required for recruitment of Crb2b53BP1, without which the checkpoint cannot be activated even if other DNA damage response proteins are recruited to a Taz1-deficient telomere.

    • Tiago Carneiro
    • , Lyne Khair
    •  & Miguel Godinho Ferreira

  • Letter |

    Propionyl-coenzyme A carboxylase (PCC) is a biotin-dependent enzyme that is essential for the catabolism of several amino acids, cholesterol and some fatty acids. Here, the crystal structure of a bacterial PCC is presented, along with a cryo-electron microscopy reconstruction showing a similar structure for human PCC. The structural information establishes a molecular basis for understanding the known disease-causing mutations in PCC, and is relevant to the holoenzymes of other biotin-dependent carboxylases.

    • Christine S. Huang
    • , Kianoush Sadre-Bazzaz
    •  & Liang Tong

  • News & Views |

    The protein OTUB1 inhibits DNA repair without using its enzymatic activity. Instead, it sequesters a protein that is required for the assembly of certain forms of ubiquitin chain, which function as key signals during repair.

    • April Rose
    •  & Christian Schlieker

  • Letter |

    The repair enzyme (6–4) photolyase uses light energy to cleave the ultraviolet-induced bond between pyrimidine dimers. These authors use ultrafast spectroscopy to examine the detailed electron and proton movements during the catalytic photocycle. Histidine 364 is identified as the crucial residue involved in the rate-limiting step.

    • Jiang Li
    • , Zheyun Liu
    •  & Dongping Zhong

  • Article |

    Ultraviolet radiation causes damage to DNA in skin cells, blocking DNA replication and causing mutations that can lead to cancer. One way in which the cell deals with such damage involves specialized DNA polymerases, such as Polη, that can bypass lesions. Here the crystal structure of Polη is presented at four consecutive steps during DNA synthesis through thymine dimers. Polη acts like a 'molecular splint' to stabilize damaged DNA, and accommodates the thymine dimer in an atypically large active site.

    • Christian Biertümpfel
    • , Ye Zhao
    •  & Wei Yang

  • News & Views |

    Ultraviolet radiation can cause cancer through DNA damage — specifically, by linking adjacent thymine bases. Crystal structures show how the enzyme DNA polymerase η accurately bypasses such lesions, offering protection.

    • Suse Broyde
    •  & Dinshaw J. Patel

  • News & Views |

    The enzyme co-substrate S-adenosylmethionine is a potential source of two different free radicals, yet only one seemed to occur in nature. The discovery of an unusual enzyme reveals that both radicals can be formed.

    • Joan B. Broderick

  • Letter |

    It is shown here that the methylation of histone proteins regulates lifespan in Caenorhabditis elegans. Deficiencies in members of the ASH-2 complex, which trimethylates histone H3 at lysine 4 (H3K4), extend worm lifespan. Meanwhile, the H3K4 demethylase RBR-2 is required for normal lifespan. These findings are consistent with the idea that an excess of H3K4 trimethylation reduces longevity. The extension of lifespan caused by ASH-2 deficiency requires an intact adult germline and the continuous production of mature eggs.

    • Eric L. Greer
    • , Travis J. Maures
    •  & Anne Brunet

  • Letter |

    Topoisomerases are enzymes that transiently make breaks in DNA, to prevent the build-up of topological stress and tangles as the genome is transcribed, replicated or repaired. Type II topoisomerases have been postulated to use a two-metal mechanism to break duplex DNA. Now, the structure of the DNA-binding and cleavage core of a yeast type II topoisomerase has been solved, showing that the enzyme uses a variation of the classical mechanism, and can also carry out the type of cleavage performed by type IA topoisomerases.

    • Bryan H. Schmidt
    • , Alex B. Burgin
    •  & James M. Berger

  • Article |

    Complex I is an enzyme of the respiratory chain, and is crucial to cellular energy production: it couples electron transfer between NADH and quinine to proton translocation. Here, structures are presented of the membrane domain of complex I from Escherichia coli, and of the entire complex I from Thermus thermophilus. It is proposed that conformational changes at the interface of the two main domains drive a particular 110-Å-long a-helix in a piston-like motion, tilting nearby transmembrane helices and causing proton translocation.

    • Rouslan G. Efremov
    • , Rozbeh Baradaran
    •  & Leonid A. Sazanov

  • News & Views |

    The membrane-spanning enzyme known as complex I couples the movement of electrons to that of protons as a way of converting energy. Crystal structures suggest how electron transfer drives proton pumping from afar.

    • Tomoko Ohnishi

  • Letter |

    Toxoplasma gondii is an opportunistic human pathogen that secretes organelles called micronemes during infection. This is important for parasite motility, host-cell invasion and egress. It is now shown that the secretion of micronemes is dependent on the T. gondii calcium-dependent protein kinase 1. This kinase is not found in the parasite's mammalian hosts, and might represent a valid drug target.

    • Sebastian Lourido
    • , Joel Shuman
    •  & L. David Sibley

  • Letter |

    The enzyme inositol polyphosphate phosphatase 4A (INPP4A) removes phosphate groups from phosphatidylinositol-3,4-bisphosphate, a key cellular lipid. Here, a crucial role for INPP4A in maintaining the integrity of the brain is described. Mice that lack this enzyme suffer from neurodegeneration in the striatum of the brain, as well as severe involuntary movements. When present, INPP4A protects neurons from a particular type of cell death.

    • Junko Sasaki
    • , Satoshi Kofuji
    •  & Takehiko Sasaki

  • Letter |

    The ability of plants to 'green' in the dark is attributed to the activity of the dark-operative protochlorophyllide oxidoreductase (DPOR). This enzyme catalyses the stereospecific reduction of the C17≡C18 double bond of protochlorophyllide to form chlorophyllide a, the direct precursor of chlorophyll a. The X-ray crystal structure of the catalytic component of DPOR has now been solved. A chemical mechanism is proposed by which the reduction of the double bond may occur.

    • Norifumi Muraki
    • , Jiro Nomata
    •  & Yuichi Fujita

  • Letter |

    Polycomb group (PcG) proteins are transcriptional repressors that modify chromatin and regulate important developmental genes. One PcG-associated, chromatin-modifying activity is an enzyme that ubiquitinates histone H2A of chromatin. Here, a fruitfly PcG complex that is associated with H2A deubiquitination, and thereby with gene repression, is identified. PcG-mediated gene silencing might thus involve a dynamic balance between ubiquitination and deubiquitination of H2A.

    • Johanna C. Scheuermann
    • , Andrés Gaytán de Ayala Alonso
    •  & Jürg Müller

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