Results tagged “highlight” from The SIBYLS Beamline

SAXS data collected at the SIBYLS beamline was used in conjunction with high resolution crystals structures to discern details of the unique interaction mode of of these key players in the autophagy pathway.


Atg7 is a noncanonical, homodimeric E1 enzyme that interacts with the noncanonical E2 enzyme, Atg3, to mediate conjugation of the ubiquitin-like protein (UBL) Atg8 during autophagy. Here we report that the unique N-terminal domain of Atg7 (Atg7NTD) recruits a unique “flexible region” from Atg3 (Atg3FR). The structure of an Atg7NTD-Atg3FR complex reveals hydrophobic residues from Atg3 engaging a conserved groove in Atg7, important for Atg8 conjugation. We also report the structure of the homodimeric Atg7 C-terminal domain, which is homologous to canonical E1s and bacterial antecedents. The structures, SAXS, and crosslinking data allow modeling of a full-length, dimeric (Atg7∼Atg8-Atg3)2 complex. The model and biochemical data provide a rationale for Atg7 dimerization: Atg8 is transferred in trans from the catalytic cysteine of one Atg7 protomer to Atg3 bound to the N-terminal domain of the opposite Atg7 protomer within the homodimer. The studies reveal a distinctive E1∼UBL-E2 architecture for enzymes mediating autophagy.

Taherbhoy AM, Tait SW, Kaiser SE, Williams AH, Deng A, Nourse A, Hammel M, Kurinov I, Rock CO, Green DR, Schulman BA. “Atg8 transfer from atg7 to atg3: a distinctive e1-e2 architecture and mechanism in the autophagy pathway.” Mol Cell 2011 Nov.;44(3):451-461.
The structure of XPD was solved using data collected at the SIBYLS beamline and published in Cell this past summer. Recently this outstanding work was featured in the ALS Science Highlights.

"XPD helicase is an enzyme that unwinds the DNA double helix; it is one component of an essential repair mechanism that maintains the integrity of DNA. XPD is unique, however, in that pinpoint mutations of this single protein are responsible for three different human diseases: in xeroderma pigmentosum (XP), extreme sensitivity to sunlight promotes cancer; Cockayne syndrome (CS) involves stunted growth and premature aging; trichothiodystrophy (TTD), characterized by brittle hair and scaly skin, is another form of greatly accelerated aging. At the ALS, researchers from Berkeley Lab and The Scripps Research Institute recently solved the structure of XPD. The structure gives novel insight into the processes of aging and cancer by revealing how discrete flaws--as seemingly insignificant as a change in either of two adjacent amino acid residues--can lead to diseases with completely different physical manifestations."

Li Fan, Jill O Fuss, Quen J Cheng, Andrew S Arvai, Michal Hammel, Victoria A Roberts, Priscilla K Cooper, John A Tainer. "XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations." Cell (2008) vol. 133 (5) pp. 789-800
In a recent article in the Journal of Molecular Biology a paper has been published exploring the ability of prokaryotic thermophiles to supply stable human protein homologs for structural biology. The authors have made use of an unusual deep-sea hydrothermal-vent worm called Alvinella pompejana. This worm has been found in temperatures averaging as high as 68 degrees C. The paper explores the structure, stability, and mechanism of Cu,Zn superoxide dismutase (SOD), an enzyme whose mutation is implicated in causing the neurodegenerative disease familial amyotrophic lateral sclerosis or Lou Gehrig's disease. The SAXS endstation of the SIBYLS beamline played a key role in providing confirmation of the dimeric state of the Alvinella pompejana SOD and its structural similarity to the Human SOD.


The structure of Sulfolobus acidocaldarius XPD has recently been solved and the biochemical activites of various disease causing mutations measured. Results are reported in the May 30th issue of Cell. LBNL has also done a nice write up.

As recently reported in the ALSNews:

“The veil has finally been lifted on an enzyme that is critical to the process of DNA transcription and replication and is a prime target of antibacterial and anticancer drugs. Researchers at Berkeley Lab and the University of California, Berkeley, have produced the first three-dimensional structural images of a DNA-bound type II topoisomerase (topo II) that is responsible for untangling coiled strands of the chromosome during cell division. Preventing topo II from disentangling a cell’s DNA is fatal to the cell, which is why drugs that target topo II serve as agents against bacterial infections and some forms of cancer. This first ever structural image of topo II should help in the development of future antibacterial and anticancer drugs that are even more effective and carry fewer potential side effects.”

The original publication in Nature can be found here: K.C. Dong and J.M. Berger, “Structural basis for Gate-DNA recognition and bending by type IIA topoisomerases,” Nature 250, 1201 (2007).

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