TY  - JOUR
A1  - Bangalore, Disha M.
A1  - Heil, Hannah S.
A1  - Mehringer, Christian F.
A1  - Hirsch, Lisa
A1  - Hemmen, Katharina
A1  - Heinze, Katrin G.
A1  - Tessmer, Ingrid
T1  - Automated AFM analysis of DNA bending reveals initial lesion sensing strategies of DNA glycosylases
JF  - Scientific Reports
N2  - Base excision repair is the dominant DNA repair pathway of chemical modifications such as deamination, oxidation, or alkylation of DNA bases, which endanger genome integrity due to their high mutagenic potential. Detection and excision of these base lesions is achieved by DNA glycosylases. To investigate the remarkably high efficiency in target site search and recognition by these enzymes, we applied single molecule atomic force microscopy (AFM) imaging to a range of glycosylases with structurally different target lesions. Using a novel, automated, unbiased, high-throughput analysis approach, we were able to resolve subtly different conformational states of these glycosylases during DNA lesion search. Our results lend support to a model of enhanced lesion search efficiency through initial lesion detection based on altered mechanical properties at lesions. Furthermore, its enhanced sensitivity and easy applicability also to other systems recommend our novel analysis tool for investigations of diverse, fundamental biological interactions.
KW  - atomic-force microscopy
KW  - base pairs
KW  - molecular structure
KW  - crystal structure
KW  - structural basis
KW  - repair
KW  - recognition
KW  - 8-oxoguanine
KW  - thymine
KW  - mismatches
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-231338
VL  - 10
ER  - 
TY  - JOUR
A1  - Metje-Sprink, Janina
A1  - Groffmann, Johannes
A1  - Neumann, Piotr
A1  - Barg-Kues, Brigitte
A1  - Ficner, Ralf
A1  - Kühnel, Karin
A1  - Schalk, Amanda M.
A1  - Binotti, Beyenech
T1  - Crystal structure of the Rab33B/Atg16L1 effector complex
JF  - Scientific Reports
N2  - The Atg12-Atg5/Atg16L1 complex is recruited by WIPI2b to the site of autophagosome formation. Atg16L1 is an effector of the Golgi resident GTPase Rab33B. Here we identified a minimal stable complex of murine Rab33B(30-202) Q92L and Atg16L1(153-210). Atg16L1(153-210) comprises the C-terminal part of the Atg16L1 coiled-coil domain. We have determined the crystal structure of the Rab33B Q92L/Atg16L1(153-210) effector complex at 3.47 angstrom resolution. This structure reveals that two Rab33B molecules bind to the diverging alpha -helices of the dimeric Atg16L1 coiled-coil domain. We mutated Atg16L1 and Rab33B interface residues and found that they disrupt complex formation in pull-down assays and cellular co-localization studies. The Rab33B binding site of Atg16L1 comprises 20 residues and immediately precedes the WIPI2b binding site. Rab33B mutations that abolish Atg16L binding also abrogate Rab33B association with the Golgi stacks. Atg16L1 mutants that are defective in Rab33B binding still co-localize with WIPI2b in vivo. The close proximity of the Rab33B and WIPI2b binding sites might facilitate the recruitment of Rab33B containing vesicles to provide a source of lipids during autophagosome biogenesis.
KW  - autophagosome formation
KW  - ATG12-ATG5 conjugate
KW  - LC3 lipidation
KW  - binding sites
KW  - ATG proteins
KW  - RAB GTPases
KW  - family
KW  - membrane
KW  - recognition
KW  - proppins
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-230396
VL  - 10
ER  - 
TY  - JOUR
A1  - Peissert, Stefan
A1  - Sauer, Florian
A1  - Grabarczyk, Daniel B.
A1  - Braun, Cathy
A1  - Sander, Gudrun
A1  - Poterszman, Arnaud
A1  - Egly, Jean-Marc
A1  - Kuper, Jochen
A1  - Kisker, Caroline
T1  - In TFIIH the Arch domain of XPD is mechanistically essential for transcription and DNA repair
JF  - Nature Communications
N2  - The XPD helicase is a central component of the general transcription factor TFIIH which plays major roles in transcription and nucleotide excision repair (NER). Here we present the high-resolution crystal structure of the Arch domain of XPD with its interaction partner MAT1, a central component of the CDK activating kinase complex. The analysis of the interface led to the identification of amino acid residues that are crucial for the MAT1-XPD interaction. More importantly, mutagenesis of the Arch domain revealed that these residues are essential for the regulation of (i) NER activity by either impairing XPD helicase activity or the interaction of XPD with XPG; (ii) the phosphorylation of the RNA polymerase II and RNA synthesis. Our results reveal how MAT1 shields these functionally important residues thereby providing insights into how XPD is regulated by MAT1 and defining the Arch domain as a major mechanistic player within the XPD scaffold.
KW  - nucleotide excision repair
KW  - nuclear receptors
KW  - helicase
KW  - transactivation
KW  - fluorescence
KW  - recognition
KW  - subunit
KW  - binding
KW  - sulfur
KW  - kinease
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-229857
VL  - 11
IS  - 1
ER  -