I don't find section about polymerases
where is it ?
http://www.eurekalert.org/pub_releases/2008-07/dnl-nd071508.php
Public release date: 15-Jul-2008
Contact: Steve McGregor
smcgregor@anl.gov
630-252-5580
DOE/Argonne National Laboratory
Newly described 'dragon' protein could be key to bird flu cure
ARGONNE, Ill. (July 15, 2008) -- Scientists and researchers have taken a big step closer to a cure for the most common strain of avian influenza, or "bird flu," the potential pandemic that has claimed more than 200 lives and infected nearly 400 people in 14 countries since it was identified in 2003.
Researchers at the U.S. Department of Energy's (DOE) Argonne National Laboratory, in conjunction with scientists from China and Singapore, have crystallized and characterized the structure of one of the most important protein complexes of the H5N1 virus, the most common strain of bird flu.
All viruses, including H5N1, contain only a small number of proteins that govern all of the viruses' functions. In H5N1, perhaps the most important of these proteins is RNA polymerase, which contains the instructions that allows the virus to copy itself along with all of its genetic material. The Argonne study focused on H5N1's RNA polymerase protein, which contains three subunits: PA, PB1 and PB2.
After performing X-ray crystallography on the protein crystals at Argonne's Structural Biology Center 19ID beamline at the Advanced Photon Source, the researchers saw a surprising resemblance in the protein structure's image. "When we mapped out the PA subunit, it looked very much like the head of a dragon," said Argonne biophysicist Andrzej Joachimiak. "One domain looked like the dragon's brains, and the other looked like its mouth."
During RNA replication – the phase during which the virus "reproduces" – all three of the subunits of the protein assemble themselves in a particular configuration. In order for this congregation to take place, the researchers determined the end of the PB1 subunit has to insert itself and bind to the "dragon's mouth" part of the PA subunit.
This unexpected relationship between the two subunits could inspire a number of different therapies or vaccines for H5N1 that rely on muzzling the "dragon's" jaws with another molecule or chemical compound that would block the PB1 subunit's access to the PA site, according to Joachimiak. "If we can put a bit in the dragon's mouth, we can slow or even potentially someday stop the spread of avian flu," he said. "Since we are talking about a relatively small protein surface area, finding a way to inhibit RNA replication in H5N1 seems very feasible."
Joachimiak hopes to more precisely identify the types of compounds that could inhibit RNA replication in H5N1 by looking at the atomic-level grooves and pockets within the PA "mouth" region. According to Joachimiak, scientists must gain a more thorough understanding of the geometry of that small region in order to effectively synthesize drugs that could prevent the further spread of bird flu.
The results of the study will be reported in an upcoming issue of Nature and can be found online at http://dx.doi.org/10.1038/nature07120. The work was funded by the National Natural Science Foundation of China as well as the Chinese Ministry of Science and Technology and the U.S. Department of Energy's Office of Biological and Environmental Research.
About Argonne
The U.S. Department of Energy's Argonne National Laboratory brings the world's brightest scientists and engineers together to find exciting and creative new solutions to pressing national problems in science and technology. The nation's first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America's scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy's Office of Science.
http://www.nature.com/nature/journa...l;jsessionid=46598356F0F97E619B442762F0473F50
Letter
Nature advance online publication 9 July 2008 | <abbr title="Digital Object Identifier">doi</abbr>:10.1038/nature07120; Received 25 March 2008; Accepted 23 May 2008; Published online 9 July 2008
Crystal structure of the polymerase PA<sub>C</sub>–PB1<sub>N</sub> complex from an avian influenza H5N1 virus
Xiaojing He<sup>1</sup>, Jie Zhou<sup>1</sup>, Mark Bartlam<sup>2</sup>, Rongguang Zhang<sup>3</sup>, Jianyuan Ma<sup>1</sup>, Zhiyong Lou<sup>4</sup>, Xuemei Li<sup>1,</sup><sup>4</sup>, Jingjing Li<sup>1</sup>, Andrzej Joachimiak<sup>3</sup>, Zonghao Zeng<sup>1</sup>, Ruowen Ge<sup>5</sup>, Zihe Rao<sup>1,</sup><sup>2,</sup><sup>4</sup> & Yingfang Liu<sup>1</sup>
Top of pageThe recent emergence of highly pathogenic avian influenza A virus strains with subtype H5N1 pose a global threat to human health<sup>1</sup>. Elucidation of the underlying mechanisms of viral replication is critical for development of anti-influenza virus drugs<sup>2</sup>. The influenza RNA-dependent RNA polymerase (RdRp) heterotrimer has crucial roles in viral RNA replication and transcription. It contains three proteins: PA, PB1 and PB2. PB1 harbours polymerase and endonuclease activities and PB2 is responsible for cap binding<sup>3, </sup><sup>4</sup>; PA is implicated in RNA replication<sup>5, </sup><sup>6, </sup><sup>7, </sup><sup>8, </sup><sup>9, </sup><sup>10</sup> and proteolytic activity<sup>11, </sup><sup>12, </sup><sup>13, </sup><sup>14</sup>, although its function is less clearly defined. Here we report the 2.9 ångström structure of avian H5N1 influenza A virus PA (PA<sub>C</sub>, residues 257–716) in complex with the PA-binding region of PB1 (PB1<sub>N</sub>, residues 1–25). PA<sub>C</sub> has a fold resembling a dragon's head with PB1<sub>N</sub> clamped into its open 'jaws'. PB1<sub>N</sub> is a known inhibitor that blocks assembly of the polymerase heterotrimer and abolishes viral replication. Our structure provides details for the binding of PB1<sub>N</sub> to PA<sub>C</sub> at the atomic level, demonstrating a potential target for novel anti-influenza therapeutics. We also discuss a potential nucleotide binding site and the roles of some known residues involved in polymerase activity. Furthermore, to explore the role of PA in viral replication and transcription, we propose a model for the influenza RdRp heterotrimer by comparing PA<sub>C</sub> with the
3 reovirus polymerase structure, and docking the PA<sub>C</sub> structure into an available low resolution electron microscopy map.
where is it ?
http://www.eurekalert.org/pub_releases/2008-07/dnl-nd071508.php
Public release date: 15-Jul-2008
Contact: Steve McGregor
smcgregor@anl.gov
630-252-5580
DOE/Argonne National Laboratory
Newly described 'dragon' protein could be key to bird flu cure
ARGONNE, Ill. (July 15, 2008) -- Scientists and researchers have taken a big step closer to a cure for the most common strain of avian influenza, or "bird flu," the potential pandemic that has claimed more than 200 lives and infected nearly 400 people in 14 countries since it was identified in 2003.
Researchers at the U.S. Department of Energy's (DOE) Argonne National Laboratory, in conjunction with scientists from China and Singapore, have crystallized and characterized the structure of one of the most important protein complexes of the H5N1 virus, the most common strain of bird flu.
All viruses, including H5N1, contain only a small number of proteins that govern all of the viruses' functions. In H5N1, perhaps the most important of these proteins is RNA polymerase, which contains the instructions that allows the virus to copy itself along with all of its genetic material. The Argonne study focused on H5N1's RNA polymerase protein, which contains three subunits: PA, PB1 and PB2.
After performing X-ray crystallography on the protein crystals at Argonne's Structural Biology Center 19ID beamline at the Advanced Photon Source, the researchers saw a surprising resemblance in the protein structure's image. "When we mapped out the PA subunit, it looked very much like the head of a dragon," said Argonne biophysicist Andrzej Joachimiak. "One domain looked like the dragon's brains, and the other looked like its mouth."
During RNA replication – the phase during which the virus "reproduces" – all three of the subunits of the protein assemble themselves in a particular configuration. In order for this congregation to take place, the researchers determined the end of the PB1 subunit has to insert itself and bind to the "dragon's mouth" part of the PA subunit.
This unexpected relationship between the two subunits could inspire a number of different therapies or vaccines for H5N1 that rely on muzzling the "dragon's" jaws with another molecule or chemical compound that would block the PB1 subunit's access to the PA site, according to Joachimiak. "If we can put a bit in the dragon's mouth, we can slow or even potentially someday stop the spread of avian flu," he said. "Since we are talking about a relatively small protein surface area, finding a way to inhibit RNA replication in H5N1 seems very feasible."
Joachimiak hopes to more precisely identify the types of compounds that could inhibit RNA replication in H5N1 by looking at the atomic-level grooves and pockets within the PA "mouth" region. According to Joachimiak, scientists must gain a more thorough understanding of the geometry of that small region in order to effectively synthesize drugs that could prevent the further spread of bird flu.
###
Argonne researchers Joachimiak and Rongguang Zhang collaborated with Zihe Rao and Yingfang Liu, both members of the Institute of Biophysics of Chinese Academy of Sciences. Rao is one of the most influential Chinese crystallographers and biophysicists, Joachimiak said. The protein samples were manufactured in China and crystals were shipped to Argonne for data collection and structural analysis.The results of the study will be reported in an upcoming issue of Nature and can be found online at http://dx.doi.org/10.1038/nature07120. The work was funded by the National Natural Science Foundation of China as well as the Chinese Ministry of Science and Technology and the U.S. Department of Energy's Office of Biological and Environmental Research.
About Argonne
The U.S. Department of Energy's Argonne National Laboratory brings the world's brightest scientists and engineers together to find exciting and creative new solutions to pressing national problems in science and technology. The nation's first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America's scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy's Office of Science.
http://www.nature.com/nature/journa...l;jsessionid=46598356F0F97E619B442762F0473F50
Letter
Nature advance online publication 9 July 2008 | <abbr title="Digital Object Identifier">doi</abbr>:10.1038/nature07120; Received 25 March 2008; Accepted 23 May 2008; Published online 9 July 2008
Crystal structure of the polymerase PA<sub>C</sub>–PB1<sub>N</sub> complex from an avian influenza H5N1 virus
Xiaojing He<sup>1</sup>, Jie Zhou<sup>1</sup>, Mark Bartlam<sup>2</sup>, Rongguang Zhang<sup>3</sup>, Jianyuan Ma<sup>1</sup>, Zhiyong Lou<sup>4</sup>, Xuemei Li<sup>1,</sup><sup>4</sup>, Jingjing Li<sup>1</sup>, Andrzej Joachimiak<sup>3</sup>, Zonghao Zeng<sup>1</sup>, Ruowen Ge<sup>5</sup>, Zihe Rao<sup>1,</sup><sup>2,</sup><sup>4</sup> & Yingfang Liu<sup>1</sup>
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences and Tianjin State Laboratory of Protein Sciences, Nankai University, Tianjin 300071, China
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
Top of pageThe recent emergence of highly pathogenic avian influenza A virus strains with subtype H5N1 pose a global threat to human health<sup>1</sup>. Elucidation of the underlying mechanisms of viral replication is critical for development of anti-influenza virus drugs<sup>2</sup>. The influenza RNA-dependent RNA polymerase (RdRp) heterotrimer has crucial roles in viral RNA replication and transcription. It contains three proteins: PA, PB1 and PB2. PB1 harbours polymerase and endonuclease activities and PB2 is responsible for cap binding<sup>3, </sup><sup>4</sup>; PA is implicated in RNA replication<sup>5, </sup><sup>6, </sup><sup>7, </sup><sup>8, </sup><sup>9, </sup><sup>10</sup> and proteolytic activity<sup>11, </sup><sup>12, </sup><sup>13, </sup><sup>14</sup>, although its function is less clearly defined. Here we report the 2.9 ångström structure of avian H5N1 influenza A virus PA (PA<sub>C</sub>, residues 257–716) in complex with the PA-binding region of PB1 (PB1<sub>N</sub>, residues 1–25). PA<sub>C</sub> has a fold resembling a dragon's head with PB1<sub>N</sub> clamped into its open 'jaws'. PB1<sub>N</sub> is a known inhibitor that blocks assembly of the polymerase heterotrimer and abolishes viral replication. Our structure provides details for the binding of PB1<sub>N</sub> to PA<sub>C</sub> at the atomic level, demonstrating a potential target for novel anti-influenza therapeutics. We also discuss a potential nucleotide binding site and the roles of some known residues involved in polymerase activity. Furthermore, to explore the role of PA in viral replication and transcription, we propose a model for the influenza RdRp heterotrimer by comparing PA<sub>C</sub> with the
