Protein structures solved by Dohnalek's laboratory

PDB: 8Q3I, 8QN8, 8QU6, 8R3M, 8R2M, 8R6P, 8R6R, 8QTI

Mycobacterial HelD 

Kovaľ, T., Borah, N., Sudzinová, P. et al. 

Mycobacterial HelD connects RNA polymerase recycling with transcription initiation. 

DOI: https://doi.org/10.1038/s41467-024-52891-5

Nat Commun 15, 8740 (2024)

PDB: 8QJL, 8QJM, 8QJN, 8QJO, 8QJP, 8QJQ, 9EMG

Stenotrophomonas maltophilia nuclease SmNuc1 with ligands

Kristýna Adámková; Mária Trundová; Tomáš Kovaľ; Blanka Husťáková; Petr Kolenko; Jarmila Dušková; Tereza Skálová; Jan Dohnalek

Substrate preference, RNA binding and active site versatility of Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study

FEBS Journal 292 (2025), 129-152 , https://doi.org/10.1111/febs.17265

PDB: 8AQ8 

FAD-dependent monooxygenase from Stenotrophomonas maltophilia

Malý, Martin; Kolenko, Petr; Stránský, Jan; Švecová, Leona; Dušková, Jarmila; Koval', Tomáš; Skálová, Tereza; Trundová, Mária; Adámková, Kristýna; Černý, Jiří; Božíková, Paulína; Dohnálek, Jan

Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia

DOI: https://doi.org/10.1107/S2053230X23005381

PDB: 7QTA 

S1 nuclease from Aspergillus oryzae in complex with uridine

Adámková, Kristýna - Koval, Tomáš - Ostergaard, L. H. - Dušková, Jarmila - Malý, Martin - Švecová, Leona - Skálová, Tereza - Kolenko, Petr - Dohnálek, Jan

Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects.

DOI: 10.1107/s2059798322008397

PDB: 7QTB 

S1 nuclease from Aspergillus oryzae in complex with cytidine-5'-monophosphate

Adámková, Kristýna - Koval, Tomáš - Ostergaard, L. H. - Dušková, Jarmila - Malý, Martin - Švecová, Leona - Skálová, Tereza - Kolenko, Petr - Dohnálek, Jan

Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects.

DOI: 10.1107/s2059798322008397

PDB: 6TVK 

Alpha-L-fucosidase isoenzyme 2 from Paenibacillus thiaminolyticus

Kovaľová, T., Kovaľ, T., Stránský, J., Kolenko, P., Dušková, J., Švecová, L., Vodičková, P., Spiwok, V., Benešová, E., Lipovová, P., Dohnálek, J.

The first structure–function study of GH151 α-l-fucosidase uncovers new oligomerization pattern, active site complementation, and selective substrate specificity

https://doi.org/10.1111/febs.16387 

PDB: 5MGR 

Human receptor NKR-P1 in glycosylated form

Blaha, J. - Skálová, Tereza - Kalousková, B. - Skořepa, O. - Cmunt, D. - Grobárová, V. - Pažický, S. - Polachova, E. - Abreu, C. -

Stránský, Jan - Koval, Tomáš - Dušková, Jarmila - Zhao, Y. - Harlos, K. - Hašek, Jindřich - Dohnálek, Jan - Vaněk, O.

Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse.

https://doi.org/10.1038/S41467-022-32577-6

PDB: 5MGS 

Human receptor NKR-P1 in deglycosylated form

Blaha, J. - Skálová, Tereza - Kalousková, B. - Skořepa, O. - Cmunt, D. - Grobárová, V. - Pažický, S. - Polachova, E. - Abreu, C. -

Stránský, Jan - Koval, Tomáš - Dušková, Jarmila - Zhao, Y. - Harlos, K. - Hašek, Jindřich - Dohnálek, Jan - Vaněk, O.

Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse.

https://doi.org/10.1038/S41467-022-32577-6

PDB: 5MGT 

Complex of human NKR-P1 and LLT1 in deglycosylated forms

Blaha, J. - Skálová, Tereza - Kalousková, B. - Skořepa, O. - Cmunt, D. - Grobárová, V. - Pažický, S. - Polachova, E. - Abreu, C. -

Stránský, Jan - Koval, Tomáš - Dušková, Jarmila - Zhao, Y. - Harlos, K. - Hašek, Jindřich - Dohnálek, Jan - Vaněk, O.

Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse.

https://doi.org/10.1038/S41467-022-32577-6

PDB: 6T3O

Crystal structure of the human myomesin domain 10

Kuchar, M., Kosztyu, P., Daniel Liskova, V., Cerny, J., Petrokova, H., Vroblova, E., Maly, M., Vankova, L., Krupka, M., Raskova Kafkova, L., Turanek Knotigova, P., Duskova, J., Dohnalek, J., Masek, J., Turanek, J., Raska, M., Maly, P.

Myomedin scaffold variants targeted to 10E8 HIV-1 broadly neutralizing antibody mimic gp41 epitope and elicit HIV-1 virus-neutralizing sera in mice.

Virulence (2021), 12, 1271-1287

DOI: 10.1080/21505594.2021.1920251

PDB: 6OTD

Globin sensor domain of AfGcHK in monomeric form, with imidazole

Skalova, T., Lengalova, A., Dohnalek, J., Harlos, K., Mihalcin, P., Kolenko, P., Stranava, M., Blaha, J., Shimizu, T. and Martínková, M.

Disruption of the dimerization interface of the sensing domain in the dimeric heme-based oxygen sensor AfGcHK abolishes bacterial signal transduction

J. Biol. Chem.(2020) 295(6) 1587–1597

http://www.jbc.org/cgi/doi/10.1074/jbc.RA119.01157

PDB: 6YXU (electron microscopy)

Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State I, primary channel engaged

Kouba, T., Kovaľ, T., Sudzinodá, P., Pospíšil, J., Brezovská, B., Hnilicová, J., Šanderová, H., Janoušková, M., Šiková, M., Halada, P., Sýkora, M., Barvík, I., Nováček, J., Trundová, M., Dušková, J., Skálová, T., Chon, U., Murakami, K. S., Dohnálek, J., Krásný, L.

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase
Nature communications (2020) 11:6419
https://doi.org/10.1038/s41467-020-20158-4

PDB: 6YYS (electron microscopy)

Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State II, primary channel engaged and active site interfering

Kouba, T., Kovaľ, T., Sudzinodá, P., Pospíšil, J., Brezovská, B., Hnilicová, J., Šanderová, H., Janoušková, M., Šiková, M., Halada, P., Sýkora, M., Barvík, I., Nováček, J., Trundová, M., Dušková, J., Skálová, T., Chon, U., Murakami, K. S., Dohnálek, J., Krásný, L.

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase
Nature communications (2020) 11:6419
https://doi.org/10.1038/s41467-020-20158-4

PDB: 6VSX 

X-ray crystal structure of the C-terminal domain of Bacillus subtilis RNA polymerase binding helicase HelD

Kouba, T., Kovaľ, T., Sudzinodá, P., Pospíšil, J., Brezovská, B., Hnilicová, J., Šanderová, H., Janoušková, M., Šiková, M., Halada, P., Sýkora, M., Barvík, I., Nováček, J., Trundová, M., Dušková, J., Skálová, T., Chon, U., Murakami, K. S., Dohnálek, J., Krásný, L.

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase
Nature communications (2020) 11:6419
https://doi.org/10.1038/s41467-020-20158-4

PDB: 6I3L

Bilirubin oxidase from Myrothecium verrucaria, mutant W396F

Koval, T.,Svecova, L.,Ostergaard, L.H.,Skalova, T.,Duskova, J.,Hasek, J.,Kolenko, P.,Fejfarova, K.,Stransky, J.,Trundova, M.,Dohnalek, J.

Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer

Journal: Sci Rep.

DOI: 10.1038/s41598-019-50105-3

PDB: 6I3K

Bilirubin oxidase from Myrothecium verrucaria, mutant W396A in complex with ferricyanide

Koval, T.,Svecova, L.,Ostergaard, L.H.,Skalova, T.,Duskova, J.,Hasek, J.,Kolenko, P.,Fejfarova, K.,Stransky, J.,Trundova, M.,Dohnalek, J.

Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer

Journal: Sci Rep.

DOI: 10.1038/s41598-019-50105-3

PDB: 6GN6

α-l-fucosidase (isoenzyme 1) from Paenibacillus thiaminolyticus

Kovaľová, T.,  Kovaľ, T.,  Benešová, E., Vodičková, P.,  Spiwok, V., Lipovová, P., Dohnálek, J.

Active site complementation and hexameric arrangement in the GH family 29; a structure–function study of α-l-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus

Glycobiology (2019), 29 (1), 59–73

https://doi.org/10.1093/glycob/cwy078

PDB: 5OHE

Globin sensor domain of AfGcHK (FeIII form) in complex with cyanide

Stranava, M., Man, P., Skalova, T., Kolenko, P., Blaha, J. ,Fojtikova, V. ,Martinek, V. ,Dohnalek, J. ,Lengalova, A. ,Rosulek, M. ,Shimizu, T. ,Martinkova, M. 

Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intrapr otein signal transduction.

J. Biol. Chem. (2017), 292(51), 20921–20935.

SBGrid Data Bank: 776

PDB: 5FB9

S1 nuclease from Aspergillus oryzae with unoccupied active site

Kovaľ T, Østergaard LH, Lehmbeck J, Nørgaard A, Lipovová P, Dušková J, Skálová T, Trundová M, Kolenko P, Fejfarová K, Stránský J, Švecová L, Hašek J, Dohnálek J. Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. PLoS ONE 11 e0168832 (2016)

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168832

PDB: 5FBA

S1 nuclease from Aspergillus oryzae in complex with phosphate

Kovaľ T, Østergaard LH, Lehmbeck J, Nørgaard A, Lipovová P, Dušková J, Skálová T, Trundová M, Kolenko P, Fejfarová K, Stránský J, Švecová L, Hašek J, Dohnálek J. 

Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. 

PLoS ONE 11 e0168832 (2016)

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168832

PDB: 5FBB

S1 nuclease from Aspergillus oryzae in complex with phosphate and adenosine 5'-monophosphate

Kovaľ T, Østergaard LH, Lehmbeck J, Nørgaard A, Lipovová P, Dušková J, Skálová T, Trundová M, Kolenko P, Fejfarová K, Stránský J, Švecová L, Hašek J, Dohnálek J. 

Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. PLoS ONE 11 e0168832 (2016)

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168832

PDB: 5FBC

S1 nuclease from Aspergillus oryzae in complex with 2'-deoxyadenosine-5'-thio-monophosphate (5'dAMP(S))

Kovaľ T, Østergaard LH, Lehmbeck J, Nørgaard A, Lipovová P, Dušková J, Skálová T, Trundová M, Kolenko P, Fejfarová K, Stránský J, Švecová L, Hašek J, Dohnálek J. 

Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. 

PLoS ONE 11 e0168832 (2016)

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168832

PDB: 5FBD

S1 nuclease from Aspergillus oryzae in complex with phosphate and 2'-deoxycytidine

Kovaľ T, Østergaard LH, Lehmbeck J, Nørgaard A, Lipovová P, Dušková J, Skálová T, Trundová M, Kolenko P, Fejfarová K, Stránský J, Švecová L, Hašek J, Dohnálek J. 

Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. 

PLoS ONE 11 e0168832 (2016)

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168832

PDB: 5FBF

S1 nuclease from Aspergillus oryzae in complex with two molecules of 2'-deoxycytidine-5'-monophosphate

Kovaľ T, Østergaard LH, Lehmbeck J, Nørgaard A, Lipovová P, Dušková J, Skálová T, Trundová M, Kolenko P, Fejfarová K, Stránský J, Švecová L, Hašek J, Dohnálek J. 

Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. 

PLoS ONE 11 e0168832 (2016)

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168832

PDB: 5FBG

S1 nuclease from Aspergillus oryzae mutant D65N, in complex with phosphate, 2'-deoxycytidine and 2'-deoxyguanosine

Kovaľ T, Østergaard LH, Lehmbeck J, Nørgaard A, Lipovová P, Dušková J, Skálová T, Trundová M, Kolenko P, Fejfarová K, Stránský J, Švecová L, Hašek J, Dohnálek J. 

Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. 

PLoS ONE 11 e0168832 (2016)

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168832

PDB: 4JDG

Tomato multifunctional nuclease TBN1

J. Stransky, T. Koval', T. Podzimek, A. Tycova, P. Lipovova, J. Matousek, P. Kolenko, K. Fejfarova, J. Duskova, T. Skalova, J. Hasek and J. Dohnalek 

The structure of a mutant of tomato multifunctional nuclease TBN1 with phosphate ion bound in the active centre explains the stabilization of the conserved crystal-packing motif of molecular superhelices.

Acta Cryst. (2015). F71, 1408-1415 [http://dx.doi.org/10.1107/S2053230X15018324]

Acta Crystallographica Section F: Structural Biology Communications, 2015, Volume F71, pages 1408-1415

PDB: 4QKH 

Deglycosylated human LLT1, a ligand of human NKR-P1, in dimeric form

T. Skálová, J. Bláha, K. Harlos, J. Dušková, T. Koval', J. Stránský, J. Hašek, O. Vaněk and J. Dohnálek

Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states

Acta Cryst. (2015). D71, 578-591 [ doi:10.1107/S1399004714027928 ]

SBGrid Data Bank: 723

PDB: 4QKI 

Deglycosylated human LLT1, a ligand of human NKR-P1, in dimeric form 

T. Skálová, J. Bláha, K. Harlos, J. Dušková, T. Koval', J. Stránský, J. Hašek, O. Vaněk and J. Dohnálek

Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states 

Acta Cryst. (2015). D71, 578-591 [ doi:10.1107/S1399004714027928 ] 

SBGrid Data Bank: 724

PDB: 4QKJ

Glycosylated human LLT1, a ligand of human NKR-P1, in hexameric form - compact packing of three dimers 

T. Skálová, J. Bláha, K. Harlos, J. Dušková, T. Koval', J. Stránský, J. Hašek, O. Vaněk and J. Dohnálek

Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states

 Acta Cryst. (2015). D71, 578-591 [ doi:10.1107/S1399004714027928 ] 

SBGrid Data Bank: 726

PDB: 3RVA

Organophosphorous acid anhydrolase from Alteromonas macleodii

Andrea Štěpánková, Jarmila Dušková,   Tereza Skálová,   Jindřich Hašek, Tomáš Koval', Lars Henrik Ostergaard and Jan Dohnálek

Organophosphorous acid anhydrolase from Alteromonas macleodii - a structural study and functional relationship to prolidases

Acta Cryst. (2013) F69, 346-354.

PDB: 3SNG

Plant multifunctional nuclease TBN1

Tomáš Koval’, Petra Lipovová, Tomáš Podzimek, Jaroslav Matoušek, Jarmila Dušková, Tereza Skálová, Andrea Štěpánková, Jindřich Hašek and Jan Dohnálek

Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis

Acta Cryst. (2013). D69, 213–226

PDB: 4DJ4

Plant multifunctional nuclease TBN1 with mutation N211D

Tomáš Koval’, Petra Lipovová, Tomáš Podzimek, Jaroslav Matoušek, Jarmila Dušková, Tereza Skálová, Andrea Štěpánková, Jindřich Hašek and Jan Dohnálek 

Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis

 Acta Cryst. (2013). D69, 213–2262012

PDB: 3RS1

Data DOI: 10.15785/SBGRID/713

Mouse Clr-g, a ligand for NK Cell activation receptor NKR-P1F

Tereza Skalova, Kristyna Kotynkova, Jarmila Duskova, Jindrich Hasek, Tomas Koval, Petr Kolenko, Petr Novak, Petr Man, Pavel Hanc, Ondrej Vanek, Karel Bezouska, and Jan Dohnalek

Mouse Clr-g, a Ligand for NK Cell Activation Receptor NKR-P1F: Crystal Structure and Biophysical Properties

J. of Immunology, 2012, 189 (10), 4881-4889, [DOI: 10.4049/jimmunol.1200880 ]

SBGrid Data Bank: 713

PDB: 3T3A

Mouse receptor NKR-P1A - mutant H107R

P. Kolenko, D. Rozbeský, O. Vanek, K. Bezouska, J. Hasek and J. Dohnálek

Structure of the H107R variant of the extracellular domain of mouse NKR-P1A at 2.3 Å resolution

Acta Cryst. (2011). F67, 1519-1523 [ doi:10.1107/S1744309111046203 ]

PDB: 3KW8

Data DOI: 10.15785/SBGRID/717

Small laccase from Streptomyces coelicolor with bound hexacyanoferrate

Skalova, T; Duskova, J; Hasek, J; Stepankova, A; Koval, T; Ostergaard L.H. and  Dohnalek, J.

Structure of laccase from Streptomyces coelicolor after soaking with potassium hexacyanoferrate and at an improved resolution of 2.3 A

Acta Cryst. (2011). F67, 27-32. http://dx.doi.org/10.1107/S1744309110046099

SBGrid Data Bank: 717

PDB: 3RJ8

Carbohydrate oxidase from Microdochium nivale

Duskova, J; Dohnalek, J; Skalova, T; Oestergaard, LH; Fuglsang, CC; Kolenko, P; Stepankova, A; Hasek, J

Crystallization of carbohydrate oxidase from Microdochium nivale

ACTA CRYSTALLOGRAPHICA, 2009, F65, 638-640.

SBGrid Data Bank: 796

PDB: 2RGS

Fc fragment of immunoglobulin at 2.1 A

Kolenko, P; Dohnalek, J; Duskova, J; Skalova, T; Collard, R; Hasek, J

New insights into intra- and intermolecular interactions of immunoglobulins; Crystal structure of mouse IgG2b-Fc at 2.1 Å resolution

IMMUNOLOGY, 2009, 126, 378-385.

PDB: 1ZJ7

Mutant of HIV-1 protease with bound inhibitor SE

Skalova, T; Dohnalek, J; Duskova, J; Petrokova, H; Hradilek, M; Soucek, M; Konvalinka, J; Hasek, J

HIV-1 protease mutations and inhibitor modifications monitored on a series of complexes. Structural basis for the effect of the A71V mutation on the active site

JOURNAL OF MEDICINAL CHEMISTRY, 2006, 49(19), 5777-5784

SBGrid Data Bank: 725

PDB: 1ZLF

Mutant of HIV-1 protease with bound inhibitor SQ

Skalova, T; Dohnalek, J; Duskova, J; Petrokova, H; Hradilek, M; Soucek, M; Konvalinka, J; Hasek, J

HIV-1 protease mutations and inhibitor modifications monitored on a series of complexes. Structural basis for the effect of the A71V mutation on the active site

JOURNAL OF MEDICINAL CHEMISTRY, 2006, 49(19), 5777-5784

SBGrid Data Bank: 721

PDB: 1YQ2

Cold-active beta-galactosidase from Arthrobacter sp C2-2

Skalova, T; Dohnalek, J; Spiwok, V; Lipovova, P; Vondrackova, E; Petrokova, H; Duskova, J; Strnad, H; Kralova, B; Hasek, J 

Cold-active beta-galactosidase from Arthrobacter sp C2-2 forms compact 660 kDa hexamers: Crystal structure at 1.9 angstrom resolution JOURNAL OF MOLECULAR BIOLOGY, 2005, 353(2), 282-294

SBGrid Data Bank: 855