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  • Fragel, S. M., Montada, A., Heermann, R., Baumann, U., Schacherl, M., and Schnetz, K. (2019) Characterization of the pleiotropic LysR-type transcription regulator LeuO of Escherichia coli. Nucleic Acids Res. 10.1093/nar/gkz506

  • Pichlo, C., Juetten, L., Wojtalla, F., Schacherl, M., Diaz, D., and Baumann, U. (2019) Molecular determinants of the mechanism and substrate specificity of Clostridium difficile proline-proline endopeptidase-1. J. Biol. Chem. 10.1074/jbc.RA119.009029

  • Teuscher, A. C., Jongsma, E., Davis, M. N., Statzer, C., Gebauer, J. M., Naba, A., and Ewald, C. Y. (2019) The in-silico characterization of the Caenorhabditis elegans matrisome and proposal of a novel collagen classification. Matrix Biology Plus. 10.1016/j.mbplus.2018.11.001
  • Schehr, M., Ianes, C., Weisner, J., Heintze, L., Müller, M. P., Pichlo, C., Charl, J., Brunstein, E., Ewert, J., Lehr, M., Baumann, U., Rauh, D., Knippschild, U., Peifer, C., and Herges, R. (2019) 2-Azo-, 2-diazocine-thiazols and 2-azo-imidazoles as photoswitchable kinase inhibitors: limitations and pitfalls of the photoswitchable inhibitor approach. Photochem. Photobiol. Sci. 10.1039/c9pp00010k


  • Gebauer, J. M., Köhler, A., Dietmar, H., Gompert, M., Neundorf, I., Zaucke, F., Koch, M., and Baumann, U. (2018) COMP and TSP-4 interact specifically with the novel GXKGHR motif only found in fibrillar collagens. Sci Rep. 8, 17187

  • Lange, J., Demir, F., Huesgen, P. F., Baumann, U., von Elert, E., and Pichlo, C. (2018) Heterologous expression and characterization of a novel serine protease from Daphnia magna: A possible role in susceptibility to toxic cyanobacteria. Aquat. Toxicol. 205, 140–147

  • Hermanns, T., Pichlo, C., Woiwode, I., Klopffleisch, K., Witting, K. F., Ovaa, H., Baumann, U., and Hofmann, K. (2018) A family of unconventional deubiquitinases with modular chain specificity determinants. Nature Communications. 9, 799
  • García-Reyes, B., Witt, L., Jansen, B., Karasu, E., Gehring, T., Leban, J., Henne-Bruns, D., Pichlo, C., Brunstein, E., Baumann, U., Wesseler, F., Rathmer, B., Schade, D., Peifer, C., and Knippschild, U. (2018) Discovery of Inhibitor of Wnt Production 2 (IWP-2) and related compounds as selective ATP-competitive inhibitors of Casein Kinase 1 (CK1) δ/εJ. Med. Chem (2018) in press
  • Pichlo, C., Toelzer, C., Chojnacki, K., Öcal, S., Uthoff, M., Ruegenberg, S., Hermanns, T., Schacherl, M., Denzel, M. S., Hofmann, K., Niefind, K., and Baumann, U. (2018) Improved protein-crystal identification by using 2,2,2-trichloroethanol as a fluorescence enhancer. Acta Cryst F (2018)  F74, 307-314
  • Arefyeva, N., Sandleben, A., Krest, A., Baumann, U., Schäfer, M., Kempf, M., and Klein, A. (2018) [2 × 2] Molecular Grids of Ni(II) and Zn(II) with Redox-Active 1,4-Pyrazine-Bis(thiosemicarbazone) Ligands. Inorganics. 6, 51
  • Uthoff, M., and Baumann, U. (2018) Conformational flexibility of pore loop-1 gives insights into substrate translocation by the AAA+ protease FtsH. Journal of Structural Biology. 10.1016/j.jsb.2018.08.009



  • Dolde, C., Bischof, J., Grüter, S., Montada, A., Halekotte, J., Peifer, C., Kalbacher, H., Baumann, U., Knippschild, U., and Suter, B. (2017) A CK1 FRET biosensor reveals that DDX3X is an essential activator of CK1ϵ. J. Cell. Sci. 10.1242/jcs.207316
  • Halekotte, J., Witt, L., Ianes, C., Krüger, M., Bührmann, M., Rauh, D., Pichlo, C., Brunstein, E., Luxenburger, A., Baumann, U., Knippschild, U., Bischof, J., and Peifer, C. (2017) Optimized 4,5-Diarylimidazoles as Potent/Selective Inhibitors of Protein Kinase CK1δ and Their Structural Relation to p38α MAPK. Molecules. 10.3390/molecules22040522
  • Cauble M, Yang P, Baumann U, Gebauer JM, Orr BG, Duong LT, Banaszak Holl MM (2017) Microstructure Dependent Binding of Pigment Epithelium Derived Factor (PEDF) to Type I Collagen Fibrils. J Struct Biol S1047-8477(17)30095-3
  • Schacherl M, Gompert M, Pardon E, Lamkemeyer T, Steyaert J, Baumann U (2017) Crystallographic and biochemical characterization of the dimeric architecture of site-2 protease Biochim Biophys Acta. 2017 May 11. pii: S0005-2736(17)30159-1 


  • Pichlo C, Montada AA, Schacherl M, Baumann U (2016) Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD J Vis Exp. 2016 Dec 30;(118)
  • Schacherl, M., and Baumann, U. (2016) Feeding Anthrax: The Crystal Structure of Bacillus anthracis InhA Protease. Structure. 24, 1–2
  • Oecal, S., Socher E., Uthoff M., Ernst C., Zaucke F., Sticht H., Bauman, U., and Gebauer, J.M.. (2016). “The pH-Dependent Client Release from the Collagen-Specific Chaperone HSP47 Is Triggered by a Tandem Histidine Pair.” Journal of Biological Chemistry 291 (24): 12612–26


  • Schacherl, M., Pichlo, C., Neundorf, I., and Baumann, U. (2015) Structural Basis of Proline-Proline Peptide Bond Specificity of the Metalloprotease Zmp1 Implicated in Motility of Clostridium difficile. Structure. 23, 1632–1642
  • Vostrukhina, M., Popov, A., Brunstein, E., Lanz, M. A., Baumgartner, R., Bieniossek, C., Schacherl, M., and Baumann, U. (2015) The structure of Aquifex aeolicus FtsH in the ADP-bound state reveals a C2-symmetric hexamer. Acta Crystallogr. D Biol. Crystallogr. 71, 1307–1318
  • Bräutigam, M., Teusch, N., Schenk, T., Sheikh, M., Aricioglu, R. Z., Borowski, S. H., Neudörfl, J.-M., Baumann, U., Griesbeck, A. G., and Pietsch, M. (2015) Selective Inhibitors of Glutathione Transferase P1 with Trioxane Structure as Anticancer Agents. ChemMedChem. 10.1002/cmdc.201402553
  • Kuhlmann, N., Wroblowski, S., Knyphausen, P., de Boor, S., Brenig, J., Zienert, A. Y., Meyer-Teschendorf, K., Praefcke, G. J. K., Nolte, H., Krüger, M., Schacherl, M., Baumann, U., James, L. C., Chin, J. W., and Lammers, M. (2015) Structural and mechanistic insights into the regulation of the fundamental Rho-regulator RhoGDIα by lysine acetylation. J. Biol. Chem. 10.1074/jbc.M115.707091
  • Schacherl, M., Montada, A. A. M., Brunstein, E., and Baumann, U. (2015) The first crystal structure of the peptidase domain of the U32 peptidase family. Acta Crystallographica Section D Biological Crystallography. 71, 2505–2512



  • Stubbs MT, Baumann U (2012). No End in Sight. Biol Chem 393, 1025-26.
  • Graef, C., Schacherl, M., Waltersperger, S., and Baumann, U. (2012) Crystal Structures of Archaemetzincin Reveal a Moldable Substrate-Binding Site. PLoS ONE 7, e43863 
  • Widmer, C., Gebauer, J. M., Brunstein, E., Rosenbaum, S., Zaucke, F., Drögemüller, C., Leeb, T., and Baumann, U. (2012) Molecular basis for the action of the collagen-specific chaperone Hsp47/SERPINH1 and its structure-specific client recognition. Proc. Natl. Acad. Sci. U.S.A. 109, 13243-13247
  • Trachsel, C., Widmer, C., Kämpfer, U., Bühr, C., Baumann, T., Kuhn-Nentwig, L., Schürch, S., Schaller, J., and Baumann, U. (2012) Structural and biochemical characterization of native and recombinant single insulin-like growth factor-binding domain protein (SIBD-1) from the Central American Hunting Spider Cupiennius salei (Ctenidae). Proteins: Structure, Function, and Bioinformatics 80, 2323-2329
  • Langklotz, S., Baumann, U., and Narberhaus, F. (2012) Structure and function of the bacterial AAA protease FtsH. Biochim. Biophys. Acta 1823, 40–48


  • Navdaeva, V., Zurbriggen, A., Waltersperger, S., Schneider, P., Oberholzer, A. E., Bähler, P., Bächler, C., Grieder, A., Baumann, U., and Erni, B. (2011) Phosphoenolpyruvate: sugar phosphotransferase system from the hyperthermophilic Thermoanaerobacter tengcongensis. Biochemistry 50, 1184–1193


  • Tallant C, García-Castellanos R, Baumann U, Gomis-Rüth FX (2010). On the relevance of the Met-turn methionine in metzincins. J Biol Chem 285, 13951 -7.
  • Zurbriggen A, Schneider P, Bähler P, Erni B, Baumann U (2010). Expression, purification, crystallization and preliminary X-ray analysis of the EIICGlc domain of the Escherichia coli glucose transporter. Acta Crystallogr Section F 66, 664-8.
  • Mermod M, Mourlane F, Walstersperger S, Oberholzer AE, Baumann U, Solioz M (2010). Structure and Function of CinD (YtjD) of Lactococcus lactis, a Copper-Induced Nitroreductase Involved in Defense Against Oxidative Stress. J Bacteriol  192, 4172-80.
  • Waltersperger S, Widmer C, Wang M, Baumann U (2010). Crystal structure of archaemetzincin amza from Methanopyrus kandleri at 1.5 Å resolution. Proteins 78, 2720-3.



  • Oberholzer AE, Bumann M, Hege T, Russo S, Baumann U  (2009). Metzincin's canonical methionine is responsible for the structural integrity of the zinc-binding site. Biol Chem 390, 875-81.
  • Drögemüller C, Becker D, Brunner A, Haase B, Kircher P, Seeliger F, Fehr M, Baumann U, Lindblad-Toh K, Leeb T (2009). A missense mutation in the SERPINH1 gene in Dachshunds with osteogenesis imperfecta. PLoS Genet. 2009 Jul;5(7):e1000579. Epub 2009 Jul 24.
  • Oberholzer AE, Schneider P, Siebold C, Baumann U, Erni B (2009). Crystal structure of enzyme I of the phosphoenolpyruvate:Sugar phosphotransferase system in the dephosphorylated state. J Biol Chem 284, 33169 - 76.
  • Tan K, Borovilos M, Zhou M, Horer S, Clancy S, Moy S, Volkart LL, Sassoon J, Baumann U, Joachimiak A (2009). The Mannitol Operon Repressor MtlR Belongs to a New Class of Transcription Regulators in Bacteria. J Biol Chem 284, 36670-79.
  • Bieniossek C, Niederhauser B, Baumann UM (2009). The Crystal Structure of apo-FtsH Reveals Domain Movements Necessary for Substrate Unfolding and Translocation. Proc Natl Acad Sci USA 106, 21579-84.


  • Schutz P, Bumann M, Oberholzer A, Bieniossek C, Trachsel H, Altmann M, Baumann U (2008). Crystal structure of the yeast eIF4A-eIF4G complex: An RNA helicase controlled by protein-protein interactions. Proc Natl Acad Sci USA 105, 9564-69.
  •  Zurbriggen A, Jeckelmann JM, Christen S, Bieniossek C, Baumann U, Erni B (2008). X-ray structures of the three l. lactis dihydroxyacetone kinase subunits and of a transient inter subunit complex. J Biol Chem 283, 35789-96.



  • Garcia-Castellanos R, Cynthiatallant, Marrero A, Sola M, Baumann U, Gomis-Ruth FX (2007). Substrate specificity of a metalloprotease of the pappalysin family revealed by an inhibitor and a product complex. Arch Biochem Biophys. 457, 57-72.
  • Meier R, Drepper T, Swensson V, Jaeger KE* Baumann U (2007). A calcium-gated lid and a large beta -roll sandwich are revealed by the crystal structure of extracellular lipase from Serratia marcescens. J Biol Chem 282, 31477-83.
  • Tallant C, García-Castellanos R, Marrero A, Canals F, Yang Y, Reymond JL, Solà M, Baumann U, Gomis-Rüth FX (2007). Activity of ulilysin, an archaeal PAPP-A-related gelatinase and IGFBP protease. Biol Chem. 388, 1243-53.




  • Bieniossek C, Schalch T, Bumann M, Meister M, Meier R, Baumann U (2006). The molecular architecture of the metalloprotease FtsH. Proc Natl Acad Sci USA 103, 3066-71.
  • Erni B, Siebold C, Christen S, Srinivas A, Oberholzer A, Baumann U (2006). Small substrate, big surprise: fold, function and phylogeny of dihydroxyacetone kinases. Cell Mol Life Sci 63, 890-900
  • Tallant C, Garcia-Castellanos R, Seco J, Baumann U, Gomis-Ruth FX (2006). Molecular analysis of ulilysin, the structural prototype of a new family of metzincin metalloproteases. J Biol Chem 28, 17920-28
  • Oberholzer AE, Schneider P, Baumann U, Erni B (2006).Crystal Structure of the Nucleotide-binding Subunit DhaL of the Escherichia coli Dihydroxyacetone Kinase. J Mol Biol 359, 539-45
  • Christen S, Srinivas A, Bahler P, Zeller A, Pridmore D, Bieniossek C, Baumann U, Erni B. (2006). Regulation of the DHA operon of lactococcus lactis: A deviation from the rule followed by the tetr family of transcription regulators. J Biol Chem 281, 23129-37
  • Bieniossek C, Schutz P, Bumann M, Limacher A, Uson I, Baumann U  (2006). The crystal structure of the carboxy-terminal domain of human translation initiation factor eIF5. J Mol Biol 360, 457-65. 




  • Oberholzer AE, Bumann M, Schneider P, Bachler C, Siebold C, Baumann U, Erni B (2005). Crystal Structure of the Phosphoenolpyruvate-binding Enzyme I-Domain from the Thermoanaerobacter tengcongensis PEP: Sugar Phosphotransferase System (PTS).  J Mol Biol. 346, 521-32.
  • Zheng L, Manetsch R, Woggon WD, Baumann U, Reymond JL (2005). Mechanistic study of proton transfer and hysteresis in catalytic antibody 16E7 by site-directed mutagenesis and homology modeling. Bioorg Med Chem. 13, 1021-29.



  • Zheng L, Baumann U, Reymond JL (2004). Molecular mechanism of enantioselective proton transfer to carbon in catalytic antibody 14D9. Proc Natl Acad Sci U S A. 101, 3387-92.
  • Bumann M, Djafarzadeh S, Oberholzer AE, Bigler P, Altmann M, Trachsel H, Baumann U (2004). Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits.  J Biol Chem. 279, 37087-94.
  • Zheng L, Goddard JP, Baumann U, Reymond JL (2004). Expression Improvement and Mechanistic Study of the Retro-Diels-Alderase Catalytic Antibody 10F11 by Site-directed Mutagenesis. J Mol Biol  341, 807-14.
  • Zheng L, Baumann U, Reymond JL (2004). An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res 32, E115.
  • Russo S, Baumann U (2004). Crystal structure of a tetrahedral shaped dodecameric aminopeptidase. J Biol Chem 279, 51275-81.
  • Garcia-Alles LF, Siebold C, Nyffeler TL, Flukiger-Bruhwiler K, Schneider P, Burgi HB, Baumann U, Erni B (2004). Phosphoenolpyruvate- and ATP-dependent dihydroxyacetone kinases: covalent substrate-binding and kinetic mechanism. Biochemistry 43, 13037-45. 


  • Meier R, Tomizaki T, Schulze-Briese C, Baumann U, Stocker A (2003). The molecular basis of vitamin E retention: structure of human alpha-tocopherol transfer protein.  J Mol Biol 331,725-34. 
  • Siebold C, García-Alles LF, Erni B & Baumann U (2003). A mechanism of covalent substrate binding in the x-ray structure of subunit K of the Escherichia coli dihydroxyacetone kinase. Proc Natl Acad Sci U S A. 100, 8188 -92.
  • Zheng L, Baumann U, Reymond JL (2003). Production of a Functional Catalytic Antibody ScFv-NusA Fusion Protein in Bacterial Cytoplasm. J Biochem .133, 577-81.
  • Stocker A, Baumann U (2003). Supernatant Protein Factor in Complex with RRR-alpha-Tocopherylquinone: A Link Between Oxidized Vitamin E and Cholesterol Biosynthesis.  J Mol Biol 332, 759-65
  • Siebold C, Arnold I, Garcia-Alles LF, Baumann U, Erni B (2003). Crystal structure of the Citrobacter freundii dihydroxyacetone kinase reveals an eight-stranded alpha -helical barrel ATP-binding domain. J Biol Chem. 278, 48236-44.



  • Hugot M, Bensel N, Reymond M, Reymond JL, Baumann, U (2002). The crystal structure of a retro-Diels-Alder catalytic antibody: evidence for a catalytic aromatic residue. Proc Natl Acad Sci USA. 99, 9674-78 
  • Stocker A., Tomazaki T., Briese-Schulze C,  Baumann U (2002). The crystal structure of human supernatant protein factor. Structure 10, 1533 -40.



  • Sasson J*, Hörer S, Mooibroek H, Stoop J & Baumann U (2001). Crystallization and preliminary crystallographic analysis of mannitol dehydrogenase from the common mushroom Agaricus bisporus. Acta Cryst D 57, 711- 13.
  • Hörer S, Mooibroek H, Stoop J, Baumann U,  Sassoon J(2001). The crystallographic structure of the mannitol dehydrogenase NADP+ binary complex from Agaricus bisporus.  J Biol Chem 276, 27555 –61.
  • Gutknecht R, Beutler R, Garcia-Alles LF, Baumann U, Erni B* (2001). The dihydroxyacetone kinase of Escherichia coli utilizes a phosphoprotein instead of ATP as phosphoryl donor. EMBO J 20, 2480-86
  • Sassoon J*, Baumann U, Kohli J (2001). Biochemical characterization of the structure specific DNA binding protein Cmb1 from Schizosaccharomyces pombe. J Mol Biol 309, 1101-15.
  • Hege T, Feltzer RE, Gray RD & Baumann U* (2001). Crystal structure of a complex between Pseudomonas aeruginosa alkaline protease and its cognate inhibitor: inhibition by a zinc-NH2 coordinative bond. J Biol Chem 276, 35087 –92.
  • Hege T, Baumann U  (2001). Protease C of Erwinia chrysanthemi: The crystal structure and role of amino acids Y228 and E189. J Mol Biol 314, 187 –93.
  • Hege T, Baumann U (2001). The conserved methionine of the metzincins – a site-directed mutagenesis study. J Mol Biol 314, 181 -86.


  • Lilie H, Haehnel W, Rudolph R, Baumann U (2000). Folding of a synthetic parallel ß-roll protein. FEBS Lett 470, 173 –77.
  • Snell K, Baumann U, Byrne PC, Chave KJ, Renwick SB, Sanders PG, Whitehouse SK (2000). The genetic organization and protein crystallographic structure of human serine hydroxymethyl-transferase.  Adv Enzyme Regul 40, 353-403. 

earlier than 2000


  • Bode W, Mayr I, Baumann U, Huber R, Hofsteenge S (1988). The refined 1.92 Å Structure of human thrombin. EMBO J  8, 3467 - 75.
  • Schmittel M,  Baumann U (1990). Stability and cyclization of enol radical cations. Angew. Chemie Int. Edit. 29, 541 - 43
  • Schulze A, Baumann U, Knof S, Jäger E, Huber R, Laurell CB (1990). Structural transition of alpha1-antitrypsin by a peptide sequentially similar to beta-strand s4A. Europ J Biochem 194, 51 - 56.
  • Baumann U, Huber R, Bode W, Grosse D, Lesjak M, Laurell CB (1991). Crystal structure of active site cleaved human alpha1-antichymotrypsin at 2.7 Å resolution.  J Mol Biol 218, 595-606.
  • Baumann U, Potempa J,Bode W, Huber R, Travis J (1992). Three-dimensional structure of the intracellular Serpin leucocyte elastase inhibitor from horse. J Mol Biol  226, 1207 -18.
  • Faber JP, Poller W,  Olek K, Baumann U, Carlson J, Lindmark B, Eriksson S (1993). The molecular basis of alpha1-antichymotrypsin deficiency in a heterozygote with liver and lung disease.  J Hepatology 18, 313-21.
  • Baumann U, Wu S, Flaherty KM, McKay DB (1993). Three-dimensional structure of the alkaline protease of Ps. aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif.  EMBO J  12, 3357 -64.
  • Baumann U (1994). Crystal structure of the 50 kDa metallo protease from Serratia marcescens.  J Mol Biol  242, 244 - 51
  • Baumann U, Bauer M, Letoffe S, Delepelaire P, Wandersman C (1995). Crystal structure of a complex between Serratia protease and an inhibitor from Erwinia chrysanthemi. J Mol Biol 248, 653 -61.
  • Stoecker W, Grams F,Baumann U, Reinemer P, Gomis-Ruth FX, McKay DB & Bode W (1995). The metzincins - topological and sequential relations between the astacins,  adamalysins, serralysins and matrixins (collagenases) define a superfamily of zinc-peptidases. Prot Science 4, 823 - 40.
  • Bode W, Grams F, Reinemer P, Gomis-Rüth FX, Baumann U, McKay DB, Stöcker W (1996). The metzincin-superfamily of zinc-peptidases. Adv Exp Med Biol  389, 1-11
  • Engh R, Brandstetter H, Sucher G, Eichinger A, Baumann U, Bode W, Huber R, Poll T, Rudolph R, Vondersaal W (1996). Enzyme flexibility, solvent and weak interactions characterize thrombin-ligand interactions - implications for drug design. Structure 4, 1353 - 62.
  • Renwick SB, Skelly JV, Chave KJ, Sanders PG, Snell K, Baumann U (1998). Purification, crystallization and preliminary X-ray analysis of human recombinant cytosolic serine hydroxymethyltransferase. Acta Cryst D 54, 1030.
  • Renwick SB, Snell K ,  Baumann, U (1998). The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy. Structure 6, 1105-116.
  • Benz J, Trachsel H,  Baumann U (1999). Crystal structure of the ATPase domain of translation initiation factor 4A from Saccharomyces cerevisiae - the prototype of a DEAD box protein family. Structure Fold. Des. 7, 671 -79.
  • Dominguez D, Altmann M, Benz J, Baumann, U & Trachsel, H (1999). Interaction of Translation Initiation Factor eIF4G with eIF4A in the Yeast Saccharomyces cerevisiae J Biol Chem 274, 26720-26.
  • Skelly JV, Sanderson MR, Suter DA, Baumann U, Read MA, Gregory DSJ, Bennett M, Hobbs SM & Neidle S. (1999). Crystal structure of human DT-Diaphorase: A model for interaction with the cytotxic prodrug 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB1954). J Med Chem 42, 4325 –30.