All publications
2025
Activity and structure of human (d)CTP deaminase CDADC1.
Slyvka A, Rathore I, Yang R, Gewartowska O, Kanai T, Lountos GT, Skowronek K, Czarnocki-Cieciura M, Wlodawer A, Bochtler M.
Proc Natl Acad Sci U S A. 2025
How the technologies behind self-driving cars, social networks, ChatGPT, and DALL-E2 are changing structural biology.
Bochtler M.
Bioessays. 2025
2024
Structural analysis of the BisI family of modification dependent restriction endonucleases.
Szafran K, Rafalski D, Skowronek K, Wojciechowski M, Kazrani AA, Gilski M, Xu SY, Bochtler M.
Nucleic Acids Res. 2024
Cytosine analogues as DNA methyltransferase substrates.
Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D, Bochtler M.
Nucleic Acids Res. 2024
Characterization of winged helix domain fusion endonucleases as N6-methyladenine-dependent type IV restriction systems.
Helbrecht I, Heiter D, Yang W, Vincze T, Hanneman A, Lutz T, Ettwiller L, Bochtler M, Xu SY.
Front Microbiol. 2024
RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short-chain L-asparaginases.
Di Zhang D, Czapinska H, Bochtler M, Wlodawer A, Lubkowski J.
Protein Sci. 2024
2023
Modification of DNA by a viral enzyme and charged tRNA.
Silva RMB, Slyvka A, Lee Y-J, Guan C, Lund SR, Raleigh EA, Skowronek K, Bochtler M, Weigele PR.
bioRxiv. 2023
The Bacteroidetes Q-rule and glutaminyl cyclase activity increase the stability of extracytoplasmic proteins.
Szczęśniak K, Veillard F, Scavenius C, Chudzik K, Ferenc K, Bochtler M, Potempa J, Mizgalska D.
mBio.. 2023
Bicarbonate Activation of the Monomeric Photosystem II-PsbS/Psb27 Complex.
Fantuzzi A, Haniewicz P, Farci D, Loi MC, Park K, Büchel C, Bochtler M, Rutherford AW, Piano D.
Plant Physiol.. 2023
Clustered PHD domains in KMT2/MLL proteins are attracted by H3K4me3 and H3 acetylation-rich active promoters and enhancers.
Stroynowska-Czerwinska AM, Klimczak M, Pastor M, Kazrani AA, Misztal K, Bochtler M.
Cell Mol Life Sci. 2023
2022
Competition between electrostatic interactions and halogen bonding in the protein–ligand system: structural and thermodynamic studies of 5,6-dibromobenzotriazole-hCK2α complexes.
Winiewska‑Szajewska M, Czapinska H, Kaus‑Drobek M, Fricke A, Mieczkowska K, Dadlez M, Bochtler M, Poznański J.
Sci Rep. 2022
Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function.
Ravichandran M, Rafalski D, Davies CI, Ortega-Recalde O, Nan X, Glanfield CR, Kotter A, Misztal K, Wang AH, Wojciechowski M, Rażew M, Mayyas IM, Kardailsky O, Schwartz U, Zembrzycki K, Morison IM, Helm M, Weichenhan D, Jurkowska RZ, Krueger F, Plass C, Zacharias M, Bochtler M, Hore TA, Jurkowski TP.
Sci Adv. 2022
Adar-mediated A-to-I editing is required for embryonic patterning and innate immune response regulation in zebrafish.
Niescierowicz K#, Pryszcz L#, Navarrete C#, Tralle E#, Sulej A#, Abu Nahia K, Kasprzyk ME, Misztal K, Pateria A, Pakuła A, Bochtler M, Winata C.
# Contributed equally
Nat Commun. 2022
The Nε-rule for serine, but not cysteine catalytic triads.
Czapińska H, Bochtler M.
Angew Chem Int Ed Engl. 2022
2021
Distinction between self and non-self in restriction modification: The mysterious case of type IIL enzymes.
Bochtler M.
Structure. 2021
Halogen Atoms in the Protein-Ligand System. Structural and Thermodynamic Studies of the Binding of Bromobenzotriazoles by the Catalytic Subunit of Human Protein Kinase CK2.
Czapinska H, Winiewska-Szajewska M, Szymaniec-Rutkowska A, Piasecka A, Bochtler M, Poznański J.
J Phys Chem B.. 2021
Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA.
Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz T, Xu S, Bochtler M.
Nucleic Acids Res.. 2021
DNA adenine methylation in eukaryotes: Enzymatic mark or a form of DNA damage?
Bochtler M, Fernandes H.
BioEssays. 2021
2020
Targeted RNA Knockdown by a Type III CRISPR-Cas Complex in Zebrafish.
Fricke T, Smalakyte D, Lapinski M, Pateria A, Weige C, Pastor M, Kolano A, Winata C, Siksnys V, Tamulaitis G, Bochtler M.
CRISPR J.. 2020
Protein Domain Guided Screen for Sequence Specific and Phosphorothioate-Dependent Restriction Endonucleases.
Lutz T, Czapinska H, Fomenkov A, Potapov V, Heiter DF, Cao B, Dedon P, Bochtler M, Xu S.
Front. Microbiol.. 2020
Restriction endonucleases that cleave RNA/DNAheteroduplexes bind dsDNA in A-like conformation.
Kisiala M, Kowalska M, Pastor M, Korza HJ, Czapinska H, Bochtler M.
Nucleic Acids Res.. 2020
In Vitro Directed Evolution of a Restriction Endonuclease With More Stringent Specificity.
Skowronek KJ, Bochtler M.
J Vis Exp . 2020
2019
Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping.
Slyvka A, Zagorskaitė E, Czapinska H, Sasnauskas G, Bochtler M.
Nucleic Acids Res.. 2019
A protein architecture guided screen for modification dependent restriction endonucleases.
Lutz T, Flodman K, Copelas A, Czapinska H, Mabuchi M, Fomenkov A, He X, Bochtler M, Xu S.
Nucleic Acids Res.. 2019
Crystal Structure and Directed Evolution of Specificity of NlaIV Restriction Endonuclease.
Czapinska H, Siwek W, Szczepanowski RH, Bujnicki JM, Bochtler M, Skowronek KJ.
J Mol Biol.. 2019
Structural bases of peptidoglycan recognition by lysostaphin SH3b domain.
Mitkowski P, Jagielska E, Nowak E, Bujnicki JM, Stefaniak F, Niedziałek D, Bochtler M, Sabała I.
Sci Rep.. 2019
2018
Shifting meiotic to mitotic spindle assembly in oocytes disrupts chromosome alignment.
Bennabi I, Quéguiner I, Kolano A, Boudier T, Mailly P, Verlhac MH, Terret ME.
EMBO Rep.. 2018
The Bacteroidetes Q-Rule: Pyroglutamate in Signal Peptidase I Substrates.
Bochtler M, Mizgalska D, Veillard F, Nowak ML, Houston J, Veith P, Reynolds EC, Potempa J.
Front Microbiol.. 2018
Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family.
Tamulaitiene G, Manakova E, Jovaisaite V, Tamulaitis G, Grazulis S, Bochtler M, Siksnys V.
Nucleic Acids Res.. 2018
Specificity of MLL1 and TET3 CXXC domains towards naturally occurring cytosine modifications.
Stroynowska-Czerwinska A, Piasecka A, Bochtler M.
Biochim Biophys Acta Gene Regul Mech.. 2018
Crystal structure of human Acinus RNA recognition motif domain.
Fernandes H, Czapinska H, Grudziaz K, Bujnicki JM, Nowacka M.
PeerJ.. 2018
Crystal structure of the modification-dependent SRA-HNH endonuclease TagI
Kisiala M, Copelas A, Czapinska H, Xu S, Bochtler M.
Nucleic Acids Res.. 2018
Activity and structure of EcoKMcrA.
Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M.
Nucleic Acids Res.. 2018
The Y. bercovieri Anbu crystal structure sheds light on the evolution of highly (pseudo)symmetric multimers.
Piasecka A, Czapinska H, Vielberg MT, Szczepanowski RH, Kiefersauer R, Reed S, Groll M, Bochtler M.
J Mol Biol.. 2018
2017
Nei-like 1 (NEIL1) excises 5-carboxylcytosine directly and stimulates TDG-mediated 5-formyl and 5-carboxylcytosine excision.
Slyvka A, Mierzejewska K, Bochtler M.
Sci Rep.. 2017
A TALE-inspired computational screen for proteins that contain approximate tandem repeats.
Perycz M, Krwawicz J, Bochtler M.
PLoS One. 2017
2016
DNA demethylation pathways: Additional players and regulators
Bochtler M, Kolano A, Xu G-L
Bioessays. 2016
Type III CRISPR complexes from Thermus thermophilus
Szychowska M, Siwek W, Pawolski D, Kazrani AA, Pyrc K, Bochtler M
Acta Biochim Pol. 2016
Haloferax volcanii UbaA, catalytic engine for sampylation and sulfur transfer
Bochtler M., Piasecka A
FEBS J. 2016
On the role of steric clashes in methylation control of restriction endonuclease activity
Mierzejewska K, Bochtler M, Czapinska H
Nucleic Acids Res. 2016
Isolation of Plant Photosystem II Complexes by Fractional Solubilization
Haniewicz P, Floris D, Farci D, Kirkpatrick J, Loi MC, Büchel C, Bochtler M, Piano D
Front Plant Sci. 2016
2015
High resolution structure of an M23 peptidase with a substrate analogue
Grabowska M, Jagielska E, Czapinska H, Bochtler M, Sabala I
Sci Rep. 2015
Functional Analysis of Porphyromonas gingivalis W83 CRISPR-Cas Systems
Burmistrz M, Dudek B, Staniec D, Rodriguez Martinez JI, Bochtler M, Potempa J, Pyrc K
J Bacteriol. 2015
2014
Carboxy terminus of GATA4 transcription factor is required for its cardiogenic activity and interaction with CDK4
Gallagher JM, Yamak A, Kirilenko P, Black S, Bochtler M, Lefebvre C, Nemer M, Latinkić BV
Mech Dev. 2014
Crystal structure of the antimicrobial peptidase lysostaphin from Staphylococcus simulans
Sabala I, Jagielska E, Bardelang PT, Czapinska H, Dahms SO, Sharpe JA, James R, Than ME, Thomas NR, Bochtler M
FEBS J. 2014
Structural basis of the methylation specificity of R.DpnI
Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M
Nucleic Acids Res.. 2014
Insights into DNA hydroxymethylation in the honeybee from in-depth analyses of TET dioxygenase
Wojciechowski M, Rafalski D, Kucharski R, Misztal K, Maleszka J, Bochtler M, Maleszka R
Open Biol. 2014
Crystal structure of the 5hmC specific endonuclease PvuRts1I
Kazrani AA, Kowalska M, Czapinska H, Bochtler M
Nucleic Acids Res.. 2014
NMR structural studies of the first catalytic half-domain of ubiquitin activating enzyme
Jaremko M, Jaremko L, Nowakowski M, Wojciechowski M, Szczepanowski RH, Panecka R, Zhukov I, Bochtler M, Ejchart A
J Struct Biol. 2014
2013
Isolation of monomeric photosystem II that retains the subunit PsbS
Haniewicz P, De Sanctis D, Büchel C, Schröder WP, Loi MC, Kieselbach T, Bochtler M, Piano D
Photosynth Res. 2013
CpG Underrepresentation and the Bacterial CpG Specific DNA Methyltransferase M.MpeI
Wojciechowski M, Czapinska H, Bochtler M
Proc Natl Acad Sci U S A.. 2013
2012
Anti-staphylococcal activities of lysostaphin and LytM catalytic domain
Sabala I, Jonsson IM, Tarkowski A, Bochtler M
BMC Microbiol. 2012
Crystal structure and mechanism of action of the N6-methyladenine dependent type IIM restriction endonuclease
Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek K
Nucleic Acids Res. 2012
RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes
Chojnowski G, Bujnicki JM, Bochtler M
Bioinformatics. 2012
2011
Importance of single molecular determinants in the fidelity of expanded genetic codes
Antonczak AK, Simova Z, Yonemoto IT, Bochtler M, Piasecka A, Czapinska H, Brancale A, Tippmann EM
Proc Natl Acad Sci U S A.. 2011
Amyloid-associated nucleic acid hybridisation
Braun S, Humphreys C, Fraser E, Brancale A, Bochtler M, Dale TC
PLoS One. 2011
DNA intercalation without flipping in the specific ThaI-DNA complex
Firczuk M, Wojciechowski M, Czapinska H, Bochtler M
Nucleic Acids Res. 2011
Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis
Sokolowska M, Czapinska H, Bochtler M
Nucleic Acids Res. 2011
2010
Alu-repeat-induced deletions within the NCF2 gene causing p67-phox-deficient chronic granulomatous disease (CGD)
Gentsch M, Kaczmarczyk A, van Leeuwen K, de Boer M, Kaus-Drobek M, Dagher MC, Kaiser P, Arkwright PD, Gahr M, Rösen-Wolff A, Bochtler M, Secord E, Britto-Williams P, Saifi GM, Maddalena A, Dbaibo G, Bustamante J, Casanova JL, Roos D, Roesler J
Hum Mutat. 2010
1.45 A resolution crystal structure of recombinant PNP in complex with a pM multisubstrate analogue inhibitor bearing one feature of the postulated transition state
Chojnowski G, Breer K, Narczyk M, Wielgus-Kutrowska B, Czapinska H, Hashimoto M, Hikishima S, Yokomatsu T, Bochtler M, Girstun A, Staroń K, Bzowska A
Biochem Biophys Res Commun. 2010
Crystallization of the Photosystem II core complex and its chlorophyll binding subunit CP43 from transplastomic plants of Nicotiana tabacum
Piano D, El Alaoui S, Korza HJ, Filipek R, Sabala I, Haniewicz P, Buechel C, De Sanctis D, Bochtler M
Photosynth Res. 2010
2009
Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA
Sokolowska M, Czapinska H, Bochtler M
Nucleic Acids Res. 2009
2008
Central base pair flipping and discrimination by PspGI
Szczepanowski RH, Carpenter MA, Czapinska H, Zaremba M, Tamulaitis G, Siksnys V, Bhagwat AS, Bochtler M
Nucleic Acids Res. 2008
How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets
Tamulaitis G, Zaremba M, Szczepanowski RH, Bochtler M, Siksnys V
Nucleic Acids Res. 2008
Thermodynamic studies of interactions of calf spleen PNP with acyclic phosphonate inhibitors
Breer K, Wielgus-Kutrowska B, Hashimoto M, Hikishima S, Yokomatsu T, Szczepanowski RH, Bochtler M, Girstun A, Starón K, Bzowska A
Nucleic Acids Symp Ser (Oxf). 2008
The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution
Sukackaite R, Grazulis S, Bochtler M, Siksnys V.
J Mol Biol. 2008
Crystal structure and mechanism of the Staphylococcus cohnii virginiamycin B lyase (Vgb)
Lipka M, Filipek R, Bochtler M
Biochemistry. 2008
2007
The highest reflection intensity in a resolution shell
Bochtler M, Chojnowski G
Acta Crystallogr A. 2007
Mutational analysis of peptidoglycan amidase MepA
Firczuk M, Bochtler M.
Biochemistry. 2007
Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically
Kaus-Drobek M, Czapinska H, Sokołowska M, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M
Nucleic Acids Res. 2007
Restriction endonucleases that resemble a component of the bacterial DNA repair machinery
Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Siksnys V, Bochtler M
Cell Mol Life Sci. 2007
Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA.
Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M
J Mol Biol. 2007
Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence
Tamulaitis G, Zaremba M, Szczepanowski RH, Bochtler M, Siksnys V
Nucleic Acids Res. 2007
2006
Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease
Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis S, Czapinska H, Manakova E, Siksnys V
EMBO J. 2006
2005
Characterization of the HslU chaperone affinity for HslV protease
Azim MK, Goehring W, Song HK, Ramachandran R, Bochtler M, Goettig P
Protein Sci. 2005
Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene
Dandanell G,Szczepanowski RH, Kierdaszuk B, Shugar D, Bochtler M
J Mol Biol. 2005
A comparison of staphostatin B with standard mechanism serine protease inhibitors
Filipek R, Potempa J, Bochtler M
J Biol Chem. 2005
Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease.
Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V
Proc Natl Acad Sci U S A. 2005
Molecular machines for protein degradation.
Groll M, Bochtler M, Brandstetter H, Clausen T, Huber R
Chembiochem. 2005
Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow.
Korza HJ, Bochtler M
J Biol Chem. 2005
Staphylococcus aureus aminopeptidase S is a founding member of a new peptidase clan
Odintsov SG, Sabała I, Bourenkov G, Rybin V, Bochtler M
J Biol Chem. 2005
Substrate access to the active sites in aminopeptidase T, a representative of a new metallopeptidase clan.
Odintsov SG, Sabała I, Bourenkov G, Rybin V, Bochtler M
J Mol Biol. 2005
Crystal structure of a fragment of mouse ubiquitin-activating enzyme.
Szczepanowski RH, Filipek R, Bochtler M
J Biol Chem. 2005
Fighting an enemy within: cytoplasmic inhibitors of bacterial cysteine proteases
Potempa J, Golonka E, Filipek R, Shaw LN
Mol Microbiol. 2005
Peptydoglycan amidase MepA is a LAS metallopeptidase
Marcyjaniak M, Odintsov SG, Sabala I, Bochtler M
J Biol Chem. 2005
2004
Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidases.
Bochtler M, Odintsov SG, Marcyjaniak M, Sabala I
Protein Sci. 2004
Prostaphopain B structure: a comparison of proregion-mediated and staphostatin-mediated protease inhibition
Filipek R, Szczepanowski R, Sabat A, Potempa J, Bochtler M
Biochemistry. 2004
Peptidoglycan amidase MepA is a LAS metallopeptidase
Marcyjaniak M, Odintsov SG, Sabala I, Bochtler M.
J Biol Chem. 2004
Genetic characterization of staphopain genes in Staphylococcus aureus
Golonka E, Filipek R, Sabat A, Sinczak A, Potempa J
Biol Chem. 2004
2003
A novel class of cysteine protease inhibitors: solution structure of staphostatin A from Staphylococcus aureus.
Dubin G, Krajewski M, Popowicz G, Stec-Niemczyk J, Bochtler M, Potempa J, Dubin A, Holak TA
Biochemistry. 2003
The Staphostatin-staphopain complex: a forward binding inhibitor in complex with its target cysteine protease.
Filipek R, Rzychon M, Oleksy A, Gruca M, Dubin A, Potempa J, Bochtler M
J Biol Chem. 2003
Staphostatins resemble lipocalins, not cystatins in fold
Rzychon M, Filipek R, Sabat A, Kosowska K, Dubin A, Potempa J, Bochtler M
Protein Sci. 2003
2002
Functional interactions of HslV (ClpQ) with the ATPase HslU (ClpY)
Ramachandran R, Hartmann C, Song HK, Huber R, Bochtler M
Proc Natl Acad Sci U S A. 2002
2001