Midwest Center for Structural Genomics deposits 500th
structure into Protein Data Bank
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ARGONNE, Ill. (Jan. 5, 2007) — Researchers from the Midwest
Center for Structural Genomics, located at the U.S. Department of Energy's
Argonne National Laboratory, have deposited their 500th structure to the Protein
Data Bank – identifying
the structure of an enzyme in the key bacterium for modifying and improving
crop production.
The Protein Data Bank is the single worldwide depository of information about
the three-dimensional structures of large biological molecules, found in all
organisms, including bacteria, yeast, plants, flies and mice, as well as humans.
Understanding the shape of a molecule helps scientists understand how it works.
The Protein Data Bank is a portal for information about these molecules, and
as such enables research and education about the molecular basis of life.
The 500th structure deposited in the data bank by MCSG researchers is a phosphofructokinase
from the bacteria Agrobacterium
tumefaciens, a plant pathogen. This
phosphofructokinase belongs to a ribokinase family of enzymes important in
regulating the process of fermentation, by which one molecule of the simple
sugar glucose is broken down to two molecules of pyruvic acid.
A. tumefaciens is harmful to plants and useful to scientists for the same
reason: It transfers DNA into plant genomes. Found in soil worldwide, A.
tumefaciens causes disease in plants by transferring its own DNA into plant cells. But
in the laboratory, the ability to move all sorts of genes into plants has made
the microbe the standard tool for investigating plant genetics and modifying
crops.
The Midwest Center for Structural Genomics is one of four large-scale research
centers of the Protein Structure Initiative, funded by the National
Institutes of Health (NIH). The MCSG, a consortium made up of scientists from Argonne
National Laboratory, European
Bioinformatics Institute, Northwestern
University,
University of Toronto, Washington
University, University
College London, University
of Virginia and the University
of Texas, has as its goal the discovery of three-dimensional
structures of proteins obtainable from knowledge of their corresponding DNA
sequences.
In the last 40 years, structural biology has been successful at addressing
fundamental mechanical and functional questions in biology. The complete understanding
of biological systems requires detailed knowledge of protein functions and
their interactions with other proteins and cellular components. Because protein
function is associated with 3-D protein structures, knowledge of the protein
structure is essential.
An important turning point for North American efforts in structural genomics
was Argonne's 1998 Structural Genomics meeting co-organized by MCSG Director
Andrzej Joachimiak. This meeting brought together researchers and members of
funding agencies who recognized that improvements in technology coupled with
the successes of genome sequencing projects had paved the way for a large-scale
structure determination project.
"X-ray crystallography of macromolecules, in particular, has seen remarkable
progress in recent years," said Joachimiak, who is also director of Argonne's Structural
Biology Center (SBC), a national user facility for macromolecular
crystallography. "These advances were made possible by the public investment
in the development of third-generation synchrotron sources."
The second, production phase of the NIH's Protein Structure Initiative, which
is currently underway, has a primary goal of large-scale structure determination
to maximize the coverage of protein sequence space by structural information.
A majority of the 500 structures solved by the MCSG have been derived from
human pathogens and have unique sequences. Among the characterized proteins
is the structure of Hcp1 protein from Pseudomonas
aeruginosa – an important
component of a new secretion apparatus. Determining these structures helps
scientists better understand function and biology of these organisms and in
some cases helps create uniquely designed, targeted drugs and vaccines.
New technology developed for structural genomics has greatly increased the
efficiency of protein structure determination. These advances have contributed
to the creation of one of the most efficient "high-throughput" pipelines, which
the MCSG applies to many novel protein families with no structural representative
and to biomedically important protein targets. The Argonne staff at the MCSG
is continuously improving and modernizing its capabilities to improve efficiency
and to determine structures of the most challenging protein targets.
"Forty years ago it took researchers worldwide 16 years to deposit the first
25 structures into the PDB," said Joachimiak. "By November 2003,
the MCSG had deposited its first 100 structures, and in the past three years
we have deposited an additional 400 structures. We have put together an outstanding
team and technology that contribute in many different ways to this project.
All structures are determined using the SBC beamlines that provide outstanding
facilities for data collection at the Advanced
Photon Source." — Andrea Cipriani
For more information, please
contact Steve McGregor (630/252-5580 or media@anl.gov)
at Argonne.
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