101
|
Hashimoto H. Structural and mutation studies of two DNA demethylation related glycosylases: MBD4 and TDG. Biophysics (Nagoya-shi) 2014; 10:63-8. [PMID: 27493500 PMCID: PMC4629659 DOI: 10.2142/biophysics.10.63] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/23/2014] [Indexed: 12/01/2022] Open
Abstract
Two mammalian DNA glycosylases, methyl-CpG binding domain protein 4 (MBD4) and thymine DNA glycosylase (TDG), are involved in active DNA demethylation via the base excision repair pathway. Both MBD4 and TDG excise the mismatch base from G:X, where X is uracil, thymine, and 5-hydroxymethyluracil (5hmU). In addition, TDG excises 5mC oxidized bases i.e. when X is 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) not 5-hydroxymethylcytosine (5hmC). A MBD4 inactive mutant and substrate crystal structure clearly explains how MBD4 glycosylase discriminates substrates: 5mC are not able to be directly excised, but a deamination process from 5mC to thymine is required. On the other hand, TDG is much more complicated; in this instance, crystal structures show that TDG recognizes G:X mismatch DNA containing DNA and G:5caC containing DNA from the minor groove of DNA, which suggested that TDG might recognize 5mC oxidized product 5caC like mismatch DNA. In mutation studies, a N157D mutation results in a more 5caC specific glycosylase, and a N191A mutation inhibits 5caC activity while that when X=5fC or T remains. Here I revisit the recent MBD4 glycos ylase domain co-crystal structures with DNA, as well as TDG glycosylase domain co-crystal structures with DNA in conjunction with its mutation studies.
Collapse
Affiliation(s)
- Hideharu Hashimoto
- Department of Biochemistry, Emory University, 1510 Clifton Road, Atlanta Georgia 30322, USA
| |
Collapse
|
102
|
Wang G, He Q, Feng C, Liu Y, Deng Z, Qi X, Wu W, Mei P, Chen Z. The atomic resolution structure of human AlkB homolog 7 (ALKBH7), a key protein for programmed necrosis and fat metabolism. J Biol Chem 2014; 289:27924-36. [PMID: 25122757 PMCID: PMC4183825 DOI: 10.1074/jbc.m114.590505] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 07/31/2014] [Indexed: 11/06/2022] Open
Abstract
ALKBH7 is the mitochondrial AlkB family member that is required for alkylation- and oxidation-induced programmed necrosis. In contrast to the protective role of other AlkB family members after suffering alkylation-induced DNA damage, ALKBH7 triggers the collapse of mitochondrial membrane potential and promotes cell death. Moreover, genetic ablation of mouse Alkbh7 dramatically increases body weight and fat mass. Here, we present crystal structures of human ALKBH7 in complex with Mn(II) and α-ketoglutarate at 1.35 Å or N-oxalylglycine at 2.0 Å resolution. ALKBH7 possesses the conserved double-stranded β-helix fold that coordinates a catalytically active iron by a conserved HX(D/E) … Xn … H motif. Self-hydroxylation of Leu-110 was observed, indicating that ALKBH7 has the potential to catalyze hydroxylation of its substrate. Unlike other AlkB family members whose substrates are DNA or RNA, ALKBH7 is devoid of the "nucleotide recognition lid" which is essential for binding nucleobases, and thus exhibits a solvent-exposed active site; two loops between β-strands β6 and β7 and between β9 and β10 create a special outer wall of the minor β-sheet of the double-stranded β-helix and form a negatively charged groove. These distinct features suggest that ALKBH7 may act on protein substrate rather than nucleic acids. Taken together, our findings provide a structural basis for understanding the distinct function of ALKBH7 in the AlkB family and offer a foundation for drug design in treating cell death-related diseases and metabolic diseases.
Collapse
Affiliation(s)
- Guoqiang Wang
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193 and
| | - Qingzhong He
- the Department of Biochemistry and Molecular Biology, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Chong Feng
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193 and
| | - Yang Liu
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193 and
| | - Zengqin Deng
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193 and
| | - Xiaoxuan Qi
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193 and
| | - Wei Wu
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193 and
| | - Pinchao Mei
- the Department of Biochemistry and Molecular Biology, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Zhongzhou Chen
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193 and
| |
Collapse
|
103
|
Lu L, Zhu C, Xia B, Yi C. Oxidative Demethylation of DNA and RNA Mediated by Non-Heme Iron-Dependent Dioxygenases. Chem Asian J 2014; 9:2018-29. [DOI: 10.1002/asia.201402148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 11/10/2022]
|
104
|
Mielecki D, Grzesiuk E. Ada response - a strategy for repair of alkylated DNA in bacteria. FEMS Microbiol Lett 2014; 355:1-11. [PMID: 24810496 PMCID: PMC4437013 DOI: 10.1111/1574-6968.12462] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/04/2014] [Accepted: 05/05/2014] [Indexed: 11/29/2022] Open
Abstract
Alkylating agents are widespread in the environment and also occur endogenously. They can be cytotoxic or mutagenic to the cells introducing alkylated bases to DNA or RNA. All organisms have evolved multiple DNA repair mechanisms to counteract the effects of DNA alkylation: the most cytotoxic lesion, N3-methyladenine (3meA), is excised by AlkA glycosylase initiating base excision repair (BER); toxic N1-methyladenine (1meA) and N3-methylcytosine (3meC), induced in DNA and RNA, are removed by AlkB dioxygenase; and mutagenic and cytotoxic O6-methylguanine (O6meG) is repaired by Ada methyltransferase. In Escherichia coli, Ada response involves the expression of four genes, ada, alkA, alkB, and aidB, encoding respective proteins Ada, AlkA, AlkB, and AidB. The Ada response is conserved among many bacterial species; however, it can be organized differently, with diverse substrate specificity of the particular proteins. Here, an overview of the organization of the Ada regulon and function of individual proteins is presented. We put special effort into the characterization of AlkB dioxygenases, their substrate specificity, and function in the repair of alkylation lesions in DNA/RNA.
Collapse
Affiliation(s)
- Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | | |
Collapse
|
105
|
Abstract
DNA base flipping is a fundamental theme in DNA biophysics. The dynamics for a B-DNA base to spontaneously flip out of the double helix has significant implications in various DNA-protein interactions but are still poorly understood. The spontaneous base-flipping rate obtained previously via the imino proton exchange assay is most likely the rate of base wobbling instead of flipping. Using the diffusion-decelerated fluorescence correlation spectroscopy together with molecular dynamics simulations, we show that a base of a single mismatched base pair (T-G, T-T, or T-C) in a double-stranded DNA can spontaneously flip out of the DNA duplex. The extrahelical lifetimes are on the order of 10 ms, whereas the intrahelical lifetimes range from 0.3 to 20 s depending on the stability of the base pairs. These findings provide detailed understanding on the dynamics of DNA base flipping and lay down foundation to fully understand how exactly the repair proteins search and locate the target mismatched base among a vast excess of matched DNA bases.
Collapse
|
106
|
Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Nature 2014; 510:422-426. [PMID: 24814345 PMCID: PMC4066111 DOI: 10.1038/nature13263] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 03/14/2014] [Indexed: 12/24/2022]
Abstract
2-Oxoglutarate (2OG)-dependent oxygenases play important roles in the regulation of gene expression via demethylation of N-methylated chromatin components1,2, hydroxylation of transcription factors3, and of splicing factor proteins4. Recently, 2OG-oxygenases that catalyze hydroxylation of tRNA5-7 and ribosomal proteins8, have been shown to play roles in translation relating to cellular growth, TH17-cell differentiation and translational accuracy9-12. The finding that the ribosomal oxygenases (ROX) occur in organisms ranging from prokaryotes to humans8 raises questions as to their structural and evolutionary relationships. In Escherichia coli, ycfD catalyzes arginine-hydroxylation in the ribosomal protein L16; in humans, Mina53 (MYC-induced nuclear antigen) and NO66 (Nucleolar protein 66) catalyze histidine-hydroxylation in ribosomal proteins rpL27a and rpL8, respectively. The functional assignments of the ROX open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in residue- and protein-selectivities of prokaryotic and eukaryotic ROX, crystal structures of ycfD and ycfDRM from E. coli and Rhodothermus marinus with those of human Mina53 and NO66 (hROX) reveal highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-oxygenases. ROX structures in complex with/without their substrates, support their functional assignments as hydroxylases, but not demethylases and reveal how the subfamily has evolved to catalyze the hydroxylation of different residue sidechains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-hydroxylases including the hypoxia-inducible factor asparaginyl-hydroxylase (FIH) and histone Nε-methyl lysine demethylases (KDMs) identifies branchpoints in 2OG-oxygenase evolution and distinguishes between JmjC-hydroxylases and -demethylases catalyzing modifications of translational and transcriptional machinery. The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate oxidizing species reacts. This coordination flexibility has likely contributed to the evolution of the wide range of reactions catalyzed by iron-oxygenases.
Collapse
|
107
|
Xu C, Liu K, Tempel W, Demetriades M, Aik W, Schofield CJ, Min J. Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation. J Biol Chem 2014; 289:17299-311. [PMID: 24778178 DOI: 10.1074/jbc.m114.550350] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N(6)-Methyladenosine (m(6)A) is the most prevalent internal RNA modification in eukaryotes. ALKBH5 belongs to the AlkB family of dioxygenases and has been shown to specifically demethylate m(6)A in single-stranded RNA. Here we report crystal structures of ALKBH5 in the presence of either its cofactors or the ALKBH5 inhibitor citrate. Catalytic assays demonstrate that the ALKBH5 catalytic domain can demethylate both single-stranded RNA and single-stranded DNA. We identify the TCA cycle intermediate citrate as a modest inhibitor of ALKHB5 (IC50, ∼488 μm). The structural analysis reveals that a loop region of ALKBH5 is immobilized by a disulfide bond that apparently excludes the binding of dsDNA to ALKBH5. We identify the m(6)A binding pocket of ALKBH5 and the key residues involved in m(6)A recognition using mutagenesis and ITC binding experiments.
Collapse
Affiliation(s)
- Chao Xu
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ke Liu
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, From the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China
| | - Wolfram Tempel
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Marina Demetriades
- the Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom, and
| | - WeiShen Aik
- the Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom, and
| | - Christopher J Schofield
- the Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom, and
| | - Jinrong Min
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, From the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China, the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
108
|
Feng C, Liu Y, Wang G, Deng Z, Zhang Q, Wu W, Tong Y, Cheng C, Chen Z. Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition. J Biol Chem 2014; 289:11571-11583. [PMID: 24616105 PMCID: PMC4002068 DOI: 10.1074/jbc.m113.546168] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
N(6)-Methylation of adenosine is the most ubiquitous and abundant modification of nucleoside in eukaryotic mRNA and long non-coding RNA. This modification plays an essential role in the regulation of mRNA translation and RNA metabolism. Recently, human AlkB homolog 5 (Alkbh5) and fat mass- and obesity-associated protein (FTO) were shown to erase this methyl modification on mRNA. Here, we report five high resolution crystal structures of the catalytic core of Alkbh5 in complex with different ligands. Compared with other AlkB proteins, Alkbh5 displays several unique structural features on top of the conserved double-stranded β-helix fold typical of this protein family. Among the unique features, a distinct "lid" region of Alkbh5 plays a vital role in substrate recognition and catalysis. An unexpected disulfide bond between Cys-230 and Cys-267 is crucial for the selective binding of Alkbh5 to single-stranded RNA/DNA by bringing a "flipping" motif toward the central β-helix fold. We generated a substrate binding model of Alkbh5 based on a demethylation activity assay of several structure-guided site-directed mutants. Crystallographic and biochemical studies using various analogs of α-ketoglutarate revealed that the active site cavity of Alkbh5 is much smaller than that of FTO and preferentially binds small molecule inhibitors. Taken together, our findings provide a structural basis for understanding the substrate recognition specificity of Alkbh5 and offer a foundation for selective drug design against AlkB members.
Collapse
Affiliation(s)
- Chong Feng
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yang Liu
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Guoqiang Wang
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Zengqin Deng
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Qi Zhang
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Wei Wu
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yufeng Tong
- the Structural Genomics Consortium and ,the Department of Pharmacology and Toxicology, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Changmei Cheng
- the Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China, , To whom correspondence may be addressed. Tel.: 86-10-62784642; Fax: 86-10-62784642; E-mail:
| | - Zhongzhou Chen
- From the State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China, , To whom correspondence may be addressed. Tel.: 86-10-6273-4078; Fax: 86-10-6273-4078; E-mail:
| |
Collapse
|
109
|
Affiliation(s)
- Guanqun Zheng
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| | - Ye Fu
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| | - Chuan He
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| |
Collapse
|
110
|
Shrivastav N, Fedeles BI, Li D, Delaney JC, Frick LE, Foti JJ, Walker GC, Essigmann JM. A chemical genetics analysis of the roles of bypass polymerase DinB and DNA repair protein AlkB in processing N2-alkylguanine lesions in vivo. PLoS One 2014; 9:e94716. [PMID: 24733044 PMCID: PMC3986394 DOI: 10.1371/journal.pone.0094716] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 03/18/2014] [Indexed: 01/06/2023] Open
Abstract
DinB, the E. coli translesion synthesis polymerase, has been shown to bypass several N2-alkylguanine adducts in vitro, including N2-furfurylguanine, the structural analog of the DNA adduct formed by the antibacterial agent nitrofurazone. Recently, it was demonstrated that the Fe(II)- and α-ketoglutarate-dependent dioxygenase AlkB, a DNA repair enzyme, can dealkylate in vitro a series of N2-alkyguanines, including N2-furfurylguanine. The present study explored, head to head, the in vivo relative contributions of these two DNA maintenance pathways (replicative bypass vs. repair) as they processed a series of structurally varied, biologically relevant N2-alkylguanine lesions: N2-furfurylguanine (FF), 2-tetrahydrofuran-2-yl-methylguanine (HF), 2-methylguanine, and 2-ethylguanine. Each lesion was chemically synthesized and incorporated site-specifically into an M13 bacteriophage genome, which was then replicated in E. coli cells deficient or proficient for DinB and AlkB (4 strains in total). Biochemical tools were employed to analyze the relative replication efficiencies of the phage (a measure of the bypass efficiency of each lesion) and the base composition at the lesion site after replication (a measure of the mutagenesis profile of each lesion). The main findings were: 1) Among the lesions studied, the bulky FF and HF lesions proved to be strong replication blocks when introduced site-specifically on a single-stranded vector in DinB deficient cells. This toxic effect disappeared in the strains expressing physiological levels of DinB. 2) AlkB is known to repair N2-alkylguanine lesions in vitro; however, the presence of AlkB showed no relief from the replication blocks induced by FF and HF in vivo. 3) The mutagenic properties of the entire series of N2-alkyguanines adducts were investigated in vivo for the first time. None of the adducts were mutagenic under the conditions evaluated, regardless of the DinB or AlkB cellular status. Taken together, the data indicated that the cellular pathway to combat bulky N2-alkylguanine DNA adducts was DinB-dependent lesion bypass.
Collapse
Affiliation(s)
- Nidhi Shrivastav
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bogdan I. Fedeles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Deyu Li
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - James C. Delaney
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Lauren E. Frick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - James J. Foti
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - John M. Essigmann
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
111
|
Zhu C, Yi C. Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
112
|
Zhu C, Yi C. Switching demethylation activities between AlkB family RNA/DNA demethylases through exchange of active-site residues. Angew Chem Int Ed Engl 2014; 53:3659-62. [PMID: 24596302 DOI: 10.1002/anie.201310050] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/04/2014] [Indexed: 01/14/2023]
Abstract
The AlkB family demethylases AlkB, FTO, and ALKBH5 recognize differentially methylated RNA/DNA substrates, which results in their distinct biological roles. Here we identify key active-site residues that contribute to their substrate specificity. Swapping such active-site residues between the demethylases leads to partially switched demethylation activities. Combined evidence from X-ray structures and enzyme kinetics suggests a role of the active-site residues in substrate recognition. Such a divergent active-site sequence may aid the design of selective inhibitors that can discriminate these homologue RNA/DNA demethylases.
Collapse
Affiliation(s)
- Chenxu Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871 (China)
| | | |
Collapse
|
113
|
Affiliation(s)
- Guanqun Zheng
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| | | | | |
Collapse
|
114
|
Abstract
TET-mediated 5-methyl cytosine (5mC) oxidation acts in epigenetic regulation, stem cell development, and cancer. Hu et al. now determine the crystal structure of the TET2 catalytic domain bound to DNA, shedding light on 5mC-DNA substrate recognition and the catalytic mechanism of 5mC oxidation.
Collapse
Affiliation(s)
- Chi-Lin Tsai
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John A Tainer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
115
|
Chen W, Zhang L, Zheng G, Fu Y, Ji Q, Liu F, Chen H, He C. Crystal structure of the RNA demethylase ALKBH5 from zebrafish. FEBS Lett 2014; 588:892-8. [PMID: 24561204 DOI: 10.1016/j.febslet.2014.02.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/27/2014] [Accepted: 02/08/2014] [Indexed: 12/22/2022]
Abstract
ALKBH5, a member of AlkB family proteins, has been reported as a mammalian N(6)-methyladenosine (m(6)A) RNA demethylase. Here we report the crystal structure of zebrafish ALKBH5 (fALKBH5) with the resolution of 1.65Å. Structural superimposition shows that fALKBH5 is comprised of a conserved jelly-roll motif. However, it possesses a loop that interferes potential binding of a duplex nucleic acid substrate, suggesting an important role in substrate selection. In addition, several active site residues are different between the two known m(6)A RNA demethylases, ALKBH5 and FTO, which may result in their slightly different pathways of m(6)A demethylation.
Collapse
Affiliation(s)
- Weizhong Chen
- Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA; Coordination Chemistry Institute and the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Liang Zhang
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Guanqun Zheng
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Ye Fu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Quanjiang Ji
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Fange Liu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Hao Chen
- Coordination Chemistry Institute and the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA.
| |
Collapse
|
116
|
Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 2014; 343:1247997. [PMID: 24505130 PMCID: PMC4184034 DOI: 10.1126/science.1247997] [Citation(s) in RCA: 748] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all Cas9 family members. The architectures of Cas9 enzymes define nucleic acid binding clefts, and single-particle electron microscopy reconstructions show that the two structural lobes harboring these clefts undergo guide RNA-induced reorientation to form a central channel where DNA substrates are bound. The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation.
Collapse
Affiliation(s)
- Martin Jinek
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
117
|
Aik W, Scotti JS, Choi H, Gong L, Demetriades M, Schofield CJ, McDonough MA. Structure of human RNA N⁶-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation. Nucleic Acids Res 2014; 42:4741-54. [PMID: 24489119 PMCID: PMC3985658 DOI: 10.1093/nar/gku085] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
ALKBH5 is a 2-oxoglutarate (2OG) and ferrous iron-dependent nucleic acid oxygenase (NAOX) that catalyzes the demethylation of N6-methyladenine in RNA. ALKBH5 is upregulated under hypoxia and plays a role in spermatogenesis. We describe a crystal structure of human ALKBH5 (residues 66–292) to 2.0 Å resolution. ALKBH566–292 has a double-stranded β-helix core fold as observed in other 2OG and iron-dependent oxygenase family members. The active site metal is octahedrally coordinated by an HXD…H motif (comprising residues His204, Asp206 and His266) and three water molecules. ALKBH5 shares a nucleotide recognition lid and conserved active site residues with other NAOXs. A large loop (βIV–V) in ALKBH5 occupies a similar region as the L1 loop of the fat mass and obesity-associated protein that is proposed to confer single-stranded RNA selectivity. Unexpectedly, a small molecule inhibitor, IOX3, was observed covalently attached to the side chain of Cys200 located outside of the active site. Modelling substrate into the active site based on other NAOX–nucleic acid complexes reveals conserved residues important for recognition and demethylation mechanisms. The structural insights will aid in the development of inhibitors selective for NAOXs, for use as functional probes and for therapeutic benefit.
Collapse
Affiliation(s)
- WeiShen Aik
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | | | | | | | | | | | | |
Collapse
|
118
|
Hashimoto H, Pais JE, Zhang X, Saleh L, Fu ZQ, Dai N, Corrêa IR, Zheng Y, Cheng X. Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA. Nature 2013; 506:391-5. [PMID: 24390346 PMCID: PMC4364404 DOI: 10.1038/nature12905] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 11/19/2013] [Indexed: 12/15/2022]
Abstract
Cytosine residues in mammalian DNA occur in five forms, cytosine (C), 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). The ten-eleven translocation (Tet) dioxygenases convert 5mC to 5hmC, 5fC and 5caC in three consecutive, Fe(II)- and α-ketoglutarate-dependent oxidation reactions1–4. The Tet family of dioxygenases is widely distributed across the tree of life5, including the heterolobosean amoeboflagellate Naegleria gruberi. The genome of Naegleria6 encodes homologs of mammalian DNA methyltransferase and Tet proteins7. Here we study biochemically and structurally one of the Naegleria Tet-like proteins (NgTet1), which shares significant sequence conservation (approximately 14% identity or 39% similarity) with mammalian Tet1. Like mammalian Tet proteins, NgTet1 acts on 5mC and generates 5hmC, 5fC and 5caC. The crystal structure of NgTet1 complexed with DNA containing a 5mCpG site revealed that NgTet1 uses a base-flipping mechanism to access 5mC. The DNA is contacted from the minor groove and bent towards the major groove. The flipped 5mC is positioned in the active site pocket with planar stacking contacts, Watson–Crick polar hydrogen bonds and van der Waals interactions specific for 5mC. The sequence conservation between NgTet1 and mammalian Tet1, including residues involved in structural integrity and functional significance, suggests structural conservation across phyla.
Collapse
Affiliation(s)
- Hideharu Hashimoto
- Departments of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - June E Pais
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, USA
| | - Xing Zhang
- Departments of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Lana Saleh
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, USA
| | - Zheng-Qing Fu
- 1] Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, USA [2] Sector 22, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Nan Dai
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, USA
| | - Yu Zheng
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, USA
| | - Xiaodong Cheng
- Departments of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| |
Collapse
|
119
|
Chen B, Gan J, Yang C. The complex structures of ALKBH2 mutants cross-linked to dsDNA reveal the conformational swing of β-hairpin. Sci China Chem 2013. [DOI: 10.1007/s11426-013-5029-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
120
|
Hu L, Li Z, Cheng J, Rao Q, Gong W, Liu M, Shi YG, Zhu J, Wang P, Xu Y. Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation. Cell 2013; 155:1545-55. [PMID: 24315485 DOI: 10.1016/j.cell.2013.11.020] [Citation(s) in RCA: 297] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 12/27/2022]
Abstract
TET proteins oxidize 5-methylcytosine (5mC) on DNA and play important roles in various biological processes. Mutations of TET2 are frequently observed in myeloid malignance. Here, we present the crystal structure of human TET2 bound to methylated DNA at 2.02 Å resolution. The structure shows that two zinc fingers bring the Cys-rich and DSBH domains together to form a compact catalytic domain. The Cys-rich domain stabilizes the DNA above the DSBH core. TET2 specifically recognizes CpG dinucleotide and shows substrate preference for 5mC in a CpG context. 5mC is inserted into the catalytic cavity with the methyl group orientated to catalytic Fe(II) for reaction. The methyl group is not involved in TET2-DNA contacts so that the catalytic cavity allows TET2 to accommodate 5mC derivatives for further oxidation. Mutations of Fe(II)/NOG-chelating, DNA-interacting, and zinc-chelating residues are frequently observed in human cancers. Our studies provide a structural basis for understanding the mechanisms of TET-mediated 5mC oxidation.
Collapse
Affiliation(s)
- Lulu Hu
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ze Li
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jingdong Cheng
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qinhui Rao
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wei Gong
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Mengjie Liu
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yujiang Geno Shi
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China; Division of Endocrinology, Diabetes and Hypertension, Department of Medicine and Department of Biological Chemistry & Molecular Pharmacology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jiayu Zhu
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Ping Wang
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
| |
Collapse
|
121
|
Chuan He. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/anie.201303444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
122
|
Chuan He. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
123
|
Zhou B, Han Z. Crystallization and preliminary X-ray diffraction of the RNA demethylase ALKBH5. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1231-4. [PMID: 24192356 DOI: 10.1107/s1744309113024858] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/05/2013] [Indexed: 01/12/2023]
Abstract
N(6)-methyladenosine (m6A) is a ubiquitous modification found in mammalian mRNA and long noncoding RNA. ALKBH5 is a member of the iron(II)- and 2-oxoglutarate-dependent AlkB oxygenase family and has been shown to catalyze the oxidative demethylation of N(6)-methyladenosine in RNA. The ALKBH5 protein was purified and crystallized using the hanging-drop vapour-diffusion method. The crystals diffracted to 2.4 Å resolution using synchrotron radiation. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 57.456, b = 83.406, c = 92.909 Å, α = β = γ = 90.00° and one molecule in the asymmetric unit.
Collapse
Affiliation(s)
- Bin Zhou
- College of Biological Sciences, China Agricultural University, Haidian District, Beijing 100094, People's Republic of China
| | | |
Collapse
|
124
|
Wickramaratne S, Mukherjee S, Villalta PW, Schärer OD, Tretyakova NY. Synthesis of sequence-specific DNA-protein conjugates via a reductive amination strategy. Bioconjug Chem 2013; 24:1496-506. [PMID: 23885807 DOI: 10.1021/bc400018u] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
DNA-protein cross-links (DPCs) are ubiquitous, structurally diverse DNA lesions formed upon exposure to bis-electrophiles, transition metals, UV light, and reactive oxygen species. Because of their superbulky, helix distorting nature, DPCs interfere with DNA replication, transcription, and repair, potentially contributing to mutagenesis and carcinogenesis. However, the biological implications of DPC lesions have not been fully elucidated due to the difficulty in generating site-specific DNA substrates representative of DPC lesions formed in vivo. In the present study, a novel approach involving postsynthetic reductive amination has been developed to prepare a range of hydrolytically stable lesions structurally mimicking the DPCs produced between the N7 position of guanine in DNA and basic lysine or arginine side chains of proteins and peptides.
Collapse
Affiliation(s)
- Susith Wickramaratne
- Masonic Cancer Center and the Departments of Chemistry and †Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | | | | | | | | |
Collapse
|
125
|
Hopkinson RJ, Tumber A, Yapp C, Chowdhury R, Aik W, Che KH, Li XS, Kristensen JBL, King ONF, Chan MC, Yeoh KK, Choi H, Walport LJ, Thinnes CC, Bush JT, Lejeune C, Rydzik AM, Rose NR, Bagg EA, McDonough MA, Krojer T, Yue WW, Ng SS, Olsen L, Brennan PE, Oppermann U, Muller-Knapp S, Klose RJ, Ratcliffe PJ, Schofield CJ, Kawamura A. 5-Carboxy-8-hydroxyquinoline is a Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor which Causes Iron Translocation. Chem Sci 2013; 4:3110-3117. [PMID: 26682036 PMCID: PMC4678600 DOI: 10.1039/c3sc51122g] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
2-Oxoglutarate and iron dependent oxygenases are therapeutic targets for human diseases. Using a representative 2OG oxygenase panel, we compare the inhibitory activities of 5-carboxy-8-hydroxyquinoline (IOX1) and 4-carboxy-8-hydroxyquinoline (4C8HQ) with that of two other commonly used 2OG oxygenase inhibitors, N-oxalylglycine (NOG) and 2,4-pyridinedicarboxylic acid (2,4-PDCA). The results reveal that IOX1 has a broad spectrum of activity, as demonstrated by the inhibition of transcription factor hydroxylases, representatives of all 2OG dependent histone demethylase subfamilies, nucleic acid demethylases and γ-butyrobetaine hydroxylase. Cellular assays show that, unlike NOG and 2,4-PDCA, IOX1 is active against both cytosolic and nuclear 2OG oxygenases without ester derivatisation. Unexpectedly, crystallographic studies on these oxygenases demonstrate that IOX1, but not 4C8HQ, can cause translocation of the active site metal, revealing a rare example of protein ligand-induced metal movement.
Collapse
Affiliation(s)
- Richard J. Hopkinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, UK
| | - Clarence Yapp
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - WeiShen Aik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Ka Hing Che
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
- Botnar Research Centre, Oxford Biomedical Research Unit, Oxford OX3 7LD, U.K
| | - Xuan Shirley Li
- Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Jan B. L. Kristensen
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Oliver N. F. King
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Mun Chiang Chan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7LD, U.K
| | - Kar Kheng Yeoh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7LD, U.K
| | - Hwanho Choi
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Louise J. Walport
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Cyrille C. Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Jacob T. Bush
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Clarisse Lejeune
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Anna M. Rydzik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Nathan R. Rose
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Eleanor A. Bagg
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Michael A. McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
| | - Wyatt W. Yue
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
| | - Stanley S. Ng
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
| | - Lars Olsen
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Paul E. Brennan
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, UK
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
- Botnar Research Centre, Oxford Biomedical Research Unit, Oxford OX3 7LD, U.K
| | | | - Robert J. Klose
- Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Peter J. Ratcliffe
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7LD, U.K
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7LD, UK
| |
Collapse
|
126
|
Mullins EA, Rubinson EH, Pereira KN, Calcutt MW, Christov PP, Eichman BF. An HPLC-tandem mass spectrometry method for simultaneous detection of alkylated base excision repair products. Methods 2013; 64:59-66. [PMID: 23876937 DOI: 10.1016/j.ymeth.2013.07.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/08/2013] [Accepted: 07/11/2013] [Indexed: 11/25/2022] Open
Abstract
DNA glycosylases excise a broad spectrum of alkylated, oxidized, and deaminated nucleobases from DNA as the initial step in base excision repair. Substrate specificity and base excision activity are typically characterized by monitoring the release of modified nucleobases either from a genomic DNA substrate that has been treated with a modifying agent or from a synthetic oligonucleotide containing a defined lesion of interest. Detection of nucleobases from genomic DNA has traditionally involved HPLC separation and scintillation detection of radiolabeled nucleobases, which in the case of alkylation adducts can be laborious and costly. Here, we describe a mass spectrometry method to simultaneously detect and quantify multiple alkylpurine adducts released from genomic DNA that has been treated with N-methyl-N-nitrosourea (MNU). We illustrate the utility of this method by monitoring the excision of N3-methyladenine (3 mA) and N7-methylguanine (7 mG) by a panel of previously characterized prokaryotic and eukaryotic alkylpurine DNA glycosylases, enabling a comparison of substrate specificity and enzyme activity by various methods. Detailed protocols for these methods, along with preparation of genomic and oligonucleotide alkyl-DNA substrates, are also described.
Collapse
Affiliation(s)
- Elwood A Mullins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | | | | | | | | | | |
Collapse
|
127
|
Li D, Fedeles BI, Shrivastav N, Delaney JC, Yang X, Wong C, Drennan CL, Essigmann JM. Removal of N-alkyl modifications from N(2)-alkylguanine and N(4)-alkylcytosine in DNA by the adaptive response protein AlkB. Chem Res Toxicol 2013; 26:1182-7. [PMID: 23773213 PMCID: PMC3748507 DOI: 10.1021/tx400096m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
The
AlkB enzyme is an Fe(II)- and α-ketoglutarate-dependent
dioxygenase that repairs DNA alkyl lesions by a direct reversal of
damage mechanism as part of the adaptive response in E. coli. The reported substrate scope of AlkB includes simple DNA alkyl
adducts, such as 1-methyladenine, 3-methylcytosine, 3-ethylcytosine,
1-methylguanine, 3-methylthymine, and N6-methyladenine, as well as more complex DNA adducts, such as 1,N6-ethenoadenine, 3,N4-ethenocytosine, and 1,N6-ethanoadenine.
Previous studies have revealed, in a piecemeal way, that AlkB has
an impressive repertoire of substrates. The present study makes two
additions to this list, showing that alkyl adducts on the N2 position of guanine and N4 position of cytosine are also substrates for AlkB. Using
high resolution ESI-TOF mass spectrometry, we show that AlkB has the
biochemical capability to repair in vitroN2-methylguanine, N2-ethylguanine, N2-furan-2-yl-methylguanine, N2-tetrahydrofuran-2-yl-methylguanine, and N4-methylcytosine in ssDNA but not in dsDNA.
When viewed together with previous work, the experimental data herein
demonstrate that AlkB is able to repair all simple N-alkyl adducts occurring at the Watson–Crick base
pairing interface of the four DNA bases, confirming AlkB as a versatile
gatekeeper of genomic integrity under alkylation stress.
Collapse
Affiliation(s)
- Deyu Li
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | | | | | | | | | |
Collapse
|
128
|
Giri NC, Passantino L, Sun H, Zoroddu MA, Costa M, Maroney MJ. Structural investigations of the nickel-induced inhibition of truncated constructs of the JMJD2 family of histone demethylases using X-ray absorption spectroscopy. Biochemistry 2013; 52:4168-83. [PMID: 23692052 PMCID: PMC3746964 DOI: 10.1021/bi400274v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Occupational and/or environmental exposure to nickel has been implicated in various types of cancer, and in vitro exposure to nickel compounds results in the accumulation of Ni(II) ions in cells. One group of major targets of Ni(II) ions inside the cell consists of Fe(II)- and αKG-dependent dioxygenases. Using JMJD2A and JMJD2C as examples, we show that the JMJD2 family of histone demethylases, which are products of putative oncogenes as well as Fe(II)- and αKG-dependent dioxygenases, are highly sensitive to inhibition by Ni(II) ions. In this work, X-ray absorption spectroscopy (XAS) has been used to investigate the Fe(II) active site of truncated JMJD2A and JMJD2C (1-350 amino acids) in the presence and absence of αKG and/or substrate to obtain mechanistic details of the early steps in catalysis that precede O2 binding in histone demethylation by the JMJD2 family of histone demethylases. Zinc K-edge XAS has been performed on the resting JMJD2A (with iron in the active site) to confirm the presence of the expected structural zinc site. XAS of the Ni(II)-substituted enzymes has also been performed to investigate the inhibition of these enzymes by Ni(II) ions. Our XAS results indicate that the five-coordinate Fe(II) center in the resting enzyme is retained in the binary and ternary complexes. In contrast, the Ni(II) center is six-coordinate in the resting enzyme and binary and ternary complexes. XAS results indicate that both Fe(II) and Ni(II) bind αKG in the binary and ternary complexes. The electron density buildup that is observed at the Fe(II) center in the presence of αKG and substrate is not observed at the Ni(II) center. Thus, both electronic and steric factors are responsible for Ni-induced inhibition of the JMJD2 family of histone demethylases. Ni-induced inhibition of these enzymes may explain the alteration of the epigenetic mechanism of gene expression that is responsible for Ni-induced carcinogenesis.
Collapse
Affiliation(s)
- Nitai Charan Giri
- Department of Chemistry University of Massachusetts, Amherst, Massachusetts 01003
| | - Lisa Passantino
- Department of Environmental Medicine, New York University School of Medicine, New York 10016
| | | | | | - Max Costa
- Department of Environmental Medicine, New York University School of Medicine, New York 10016
| | - Michael J. Maroney
- Department of Chemistry University of Massachusetts, Amherst, Massachusetts 01003
| |
Collapse
|
129
|
Pang X, Han K, Cui Q. A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: test of force field models and application to proteins in the AlkB family. J Comput Chem 2013; 34:1620-35. [PMID: 23666816 DOI: 10.1002/jcc.23305] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/09/2013] [Accepted: 04/03/2013] [Indexed: 12/25/2022]
Abstract
To facilitate computational study of proteins in the AlkB family and related α-ketoglutarate/Fe(II)-dependent dioxygenases, we have tested a simple modeling strategy for the non-heme Fe(II) site in which the iron is represented by a simple +2 point charge with Lennard-Jones parameters. Calculations for an AlkB active site model in the gas phase and ∼150 ns molecular dynamics (MD) simulations for two enzyme-dsDNA complexes (E. coli AlkB-dsDNA and ABH2-dsDNA) suggest that this simple modeling strategy provides a satisfactory description of structural properties of the Fe(II) site in AlkB enzymes, provided that care is exercised to control the binding mode of carboxylate (Asp) to the iron. MD simulations using the model for AlkB-dsDNA and ABH2-dsDNA systems find that although the structural features for the latter are overall in good agreement with the crystal structure, the dsDNA, and AlkB-dsDNA interface undergo substantial changes during the MD simulations from the crystal structure. Even for ABH2, new interactions form between a long loop region and dsDNA upon structural relaxation of the loop, supporting the role of this loop in DNA binding despite the lack of interactions between them in the crystal structure. Analysis of DNA backbone torsional distributions helps identify regions that adopt strained conformations. Collectively, the results highlight that crystal packing may have a significant impact on the structure of protein-DNA complexes; the simulations also provide additional insights regarding why AlkB and ABH2 prefer single-strand and double-strand DNA, respectively, as substrate.
Collapse
Affiliation(s)
- Xueqin Pang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, People's Republic of China
| | | | | |
Collapse
|
130
|
Hangasky JA, Taabazuing CY, Valliere MA, Knapp MJ. Imposing function down a (cupin)-barrel: secondary structure and metal stereochemistry in the αKG-dependent oxygenases. Metallomics 2013; 5:287-301. [PMID: 23446356 PMCID: PMC4109655 DOI: 10.1039/c3mt20153h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Fe(ii)/αketoglutarate (αKG) dependent oxygenases catalyze a diverse range of reactions significant in biological processes such as antibiotic biosynthesis, lipid metabolism, oxygen sensing, and DNA and RNA repair. Although functionally diverse, the eight-stranded β-barrel (cupin) and HX(D/E)XnH facial triad motifs are conserved in this super-family of enzymes. Crystal structure analysis of 25 αKG oxygenases reveals two stereoisomers of the Fe cofactor, Anti and Clock, which differ in the relative position of the exchangeable ligand position and the primary substrate. Herein, we discuss the relationship between the chemical mechanism and the secondary coordination sphere of the αKG oxygenases, within the constraints of the stereochemistry of the Fe cofactor. Sequence analysis of the cupin barrel indicates that a small subset of positions constitute the second coordination sphere, which has significant ramifications for the structure of the ferryl intermediate. The competence of both Anti and Clock stereoisomers of Fe points to a ferryl intermediate that is 5 coordinate. The small number of conserved close contacts within the active sites of αKG oxygenases can be extended to chemically related enzymes, such as the αKG-dependent halogenases SyrB2 and CytC3, and the non-αKG dependent dioxygenases isopenicillin N synthase (IPNS) and cysteine dioxygenase (CDO).
Collapse
Affiliation(s)
- John A. Hangasky
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Meaghan A. Valliere
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Michael J. Knapp
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| |
Collapse
|
131
|
Abstract
Base excision repair (BER) corrects DNA damage from oxidation, deamination and alkylation. Such base lesions cause little distortion to the DNA helix structure. BER is initiated by a DNA glycosylase that recognizes and removes the damaged base, leaving an abasic site that is further processed by short-patch repair or long-patch repair that largely uses different proteins to complete BER. At least 11 distinct mammalian DNA glycosylases are known, each recognizing a few related lesions, frequently with some overlap in specificities. Impressively, the damaged bases are rapidly identified in a vast excess of normal bases, without a supply of energy. BER protects against cancer, aging, and neurodegeneration and takes place both in nuclei and mitochondria. More recently, an important role of uracil-DNA glycosylase UNG2 in adaptive immunity was revealed. Furthermore, other DNA glycosylases may have important roles in epigenetics, thus expanding the repertoire of BER proteins.
Collapse
Affiliation(s)
- Hans E Krokan
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489 Trondheim, Norway.
| | | |
Collapse
|
132
|
Couvé S, Ishchenko AA, Fedorova OS, Ramanculov EM, Laval J, Saparbaev M. Direct DNA Lesion Reversal and Excision Repair in Escherichia coli. EcoSal Plus 2013; 5. [PMID: 26442931 DOI: 10.1128/ecosalplus.7.2.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Indexed: 06/05/2023]
Abstract
Cellular DNA is constantly challenged by various endogenous and exogenous genotoxic factors that inevitably lead to DNA damage: structural and chemical modifications of primary DNA sequence. These DNA lesions are either cytotoxic, because they block DNA replication and transcription, or mutagenic due to the miscoding nature of the DNA modifications, or both, and are believed to contribute to cell lethality and mutagenesis. Studies on DNA repair in Escherichia coli spearheaded formulation of principal strategies to counteract DNA damage and mutagenesis, such as: direct lesion reversal, DNA excision repair, mismatch and recombinational repair and genotoxic stress signalling pathways. These DNA repair pathways are universal among cellular organisms. Mechanistic principles used for each repair strategies are fundamentally different. Direct lesion reversal removes DNA damage without need for excision and de novo DNA synthesis, whereas DNA excision repair that includes pathways such as base excision, nucleotide excision, alternative excision and mismatch repair, proceeds through phosphodiester bond breakage, de novo DNA synthesis and ligation. Cell signalling systems, such as adaptive and oxidative stress responses, although not DNA repair pathways per se, are nevertheless essential to counteract DNA damage and mutagenesis. The present review focuses on the nature of DNA damage, direct lesion reversal, DNA excision repair pathways and adaptive and oxidative stress responses in E. coli.
Collapse
|
133
|
Abstract
Endogenous and exogenous factors constantly challenge cellular DNA, generating cytotoxic and/or mutagenic DNA adducts. As a result, organisms have evolved different mechanisms to defend against the deleterious effects of DNA damage. Among these diverse repair pathways, direct DNA-repair systems provide cells with simple yet efficient solutions to reverse covalent DNA adducts. In this review, we focus on recent advances in the field of direct DNA repair, namely, photolyase-, alkyltransferase-, and dioxygenase-mediated repair processes. We present specific examples to describe new findings of known enzymes and appealing discoveries of new proteins. At the end of this article, we also briefly discuss the influence of direct DNA repair on other fields of biology and its implication on the discovery of new biology.
Collapse
Affiliation(s)
- Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | | |
Collapse
|
134
|
Johannessen TCA, Prestegarden L, Grudic A, Hegi ME, Tysnes BB, Bjerkvig R. The DNA repair protein ALKBH2 mediates temozolomide resistance in human glioblastoma cells. Neuro Oncol 2012; 15:269-78. [PMID: 23258843 DOI: 10.1093/neuonc/nos301] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION Glioblastoma multiforme (GBM; World Health Organization astrocytoma grade IV) is the most frequent and most malignant primary brain tumor in adults. Despite multimodal therapy, all such tumors practically recur during the course of therapy, causing a median survival of only 14.6 months in patients with newly diagnosed GBM. The present study was aimed at examining the expression of the DNA repair protein AlkB homolog 2 (ALKBH2) in human GBM and determining whether it could promote resistance to temozolomide chemotherapy. METHODS ALKBH2 expression in GBM cell lines and in human GBM was determined by quantitative real-time PCR (qRT-PCR) and gene expression analysis, respectively. Drug sensitivity was assessed in GBM cells overexpressing ALKBH2 and in cells in which ALKBH2 expression was silenced by small-interfering (si)RNA. ALKBH2 expression following activation of the p53 pathway was examined by western blotting and qRT-PCR. RESULTS ALKBH2 was abundantly expressed in established GBM cell lines and human GBM, and temozolomide exposure increased cellular ALKBH2 expression levels. Overexpression of ALKBH2 in the U87 and U251 GBM cell lines enhanced resistance to the methylating agents temozolomide and methyl methanesulfonate but not to the nonmethylating agent doxorubicin. Conversely, siRNA-mediated knockdown of ALKBH2 increased sensitivity of GBM cells to temozolomide and methyl methanesulfonate but not to doxorubicin or cisplatin. Nongenotoxic activation of the p53 pathway by the selective murine double minute 2 antagonist nutlin-3 caused a significant decrease in cellular ALKBH2 transcription levels. CONCLUSION Our findings identify ALKBH2 as a novel mediator of temozolomide resistance in human GBM cells. Furthermore, we place ALKBH2 into a new cellular context by showing its regulation by the p53 pathway.
Collapse
|
135
|
Aik W, McDonough MA, Thalhammer A, Chowdhury R, Schofield CJ. Role of the jelly-roll fold in substrate binding by 2-oxoglutarate oxygenases. Curr Opin Struct Biol 2012; 22:691-700. [PMID: 23142576 DOI: 10.1016/j.sbi.2012.10.001] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 09/20/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
2-Oxoglutarate (2OG) and ferrous iron dependent oxygenases catalyze two-electron oxidations of a range of small and large molecule substrates, including proteins/peptides/amino acids, nucleic acids/bases, and lipids, as well as natural products including antibiotics and signaling molecules. 2OG oxygenases employ variations of a core double-stranded β-helix (DSBH; a.k.a. jelly-roll, cupin or jumonji C (JmjC)) fold to enable binding of Fe(II) and 2OG in a subfamily conserved manner. The topology of the DSBH limits regions directly involved in substrate binding: commonly the first, second and eighth strands, loops between the second/third and fourth/fifth DSBH strands, and the N-terminal and C-terminal regions are involved in primary substrate, co-substrate and cofactor binding. Insights into substrate recognition by 2OG oxygenases will help to enable selective inhibition and bioengineering studies.
Collapse
Affiliation(s)
- WeiShen Aik
- Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | | | | | | | | |
Collapse
|
136
|
Chen B, Ye F, Yu L, Jia G, Huang X, Zhang X, Peng S, Chen K, Wang M, Gong S, Zhang R, Yin J, Li H, Yang Y, Liu H, Zhang J, Zhang H, Zhang A, Jiang H, Luo C, Yang CG. Development of cell-active N6-methyladenosine RNA demethylase FTO inhibitor. J Am Chem Soc 2012; 134:17963-71. [PMID: 23045983 DOI: 10.1021/ja3064149] [Citation(s) in RCA: 295] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The direct nucleic acid repair dioxygenase FTO is an enzyme that demethylates N(6)-methyladenosine (m(6)A) residues in mRNA in vitro and inside cells. FTO is the first RNA demethylase discovered that also serves a major regulatory function in mammals. Together with structure-based virtual screening and biochemical analyses, we report the first identification of several small-molecule inhibitors of human FTO demethylase. The most potent compound, the natural product rhein, which is neither a structural mimic of 2-oxoglutarate nor a chelator of metal ion, competitively binds to the FTO active site in vitro. Rhein also exhibits good inhibitory activity on m(6)A demethylation inside cells. These studies shed light on the development of powerful probes and new therapies for use in RNA biology and drug discovery.
Collapse
Affiliation(s)
- Baoen Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
137
|
Mello LV, Rigden DJ. A new family of bacterial DNA repair proteins annotated by the integration of non-homology, distant homology and structural bioinformatic methods. FEBS Lett 2012; 586:3908-13. [DOI: 10.1016/j.febslet.2012.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/13/2012] [Accepted: 09/14/2012] [Indexed: 10/27/2022]
|
138
|
The potential of 2-oxoglutarate oxygenases acting on nucleic acids as therapeutic targets. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.ddstr.2012.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
139
|
Kundu S. Distribution and prediction of catalytic domains in 2-oxoglutarate dependent dioxygenases. BMC Res Notes 2012; 5:410. [PMID: 22862831 PMCID: PMC3475032 DOI: 10.1186/1756-0500-5-410] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/29/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The 2-oxoglutarate dependent superfamily is a diverse group of non-haem dioxygenases, and is present in prokaryotes, eukaryotes, and archaea. The enzymes differ in substrate preference and reaction chemistry, a factor that precludes their classification by homology studies and electronic annotation schemes alone. In this work, I propose and explore the rationale of using substrates to classify structurally similar alpha-ketoglutarate dependent enzymes. FINDINGS Differential catalysis in phylogenetic clades of 2-OG dependent enzymes, is determined by the interactions of a subset of active-site amino acids. Identifying these with existing computational methods is challenging and not feasible for all proteins. A clustering protocol based on validated mechanisms of catalysis of known molecules, in tandem with group specific hidden markov model profiles is able to differentiate and sequester these enzymes. Access to this repository is by a web server that compares user defined unknown sequences to these pre-defined profiles and outputs a list of predicted catalytic domains. The server is free and is accessible at the following URL (http://comp-biol.theacms.in/H2OGpred.html). CONCLUSIONS The proposed stratification is a novel attempt at classifying and predicting 2-oxoglutarate dependent function. In addition, the server will provide researchers with a tool to compare their data to a comprehensive list of HMM profiles of catalytic domains. This work, will aid efforts by investigators to screen and characterize putative 2-OG dependent sequences. The profile database will be updated at regular intervals.
Collapse
Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, Army College of Medical Sciences, Delhi Cantt., New Delhi 110010, India.
| |
Collapse
|
140
|
Crenshaw CM, Nam K, Oo K, Kutchukian PS, Bowman BR, Karplus M, Verdine GL. Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1. J Biol Chem 2012; 287:24916-28. [PMID: 22511791 PMCID: PMC3408145 DOI: 10.1074/jbc.m111.316497] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A poorly understood aspect of DNA repair proteins is their ability to identify exceedingly rare sites of damage embedded in a large excess of nearly identical undamaged DNA, while catalyzing repair only at the damaged sites. Progress toward understanding this problem has been made by comparing the structures and biochemical behavior of these enzymes when they are presented with either a target lesion or a corresponding undamaged nucleobase. Trapping and analyzing such DNA-protein complexes is particularly difficult in the case of base extrusion DNA repair proteins because of the complexity of the repair reaction, which involves extrusion of the target base from DNA followed by its insertion into the active site where glycosidic bond cleavage is catalyzed. Here we report the structure of a human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, in which a normal guanine from DNA has been forcibly inserted into the enzyme active site. Although the interactions of the nucleobase with the active site are only subtly different for G versus oxoG, hOGG1 fails to catalyze excision of the normal nucleobase. This study demonstrates that even if hOGG1 mistakenly inserts a normal base into its active site, the enzyme can still reject it on the basis of catalytic incompatibility.
Collapse
Affiliation(s)
- Charisse M. Crenshaw
- From the Departments of Molecular and Cellular Biology, ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Kwangho Nam
- Chemical and Chemical Biology, and ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138
| | | | - Peter S. Kutchukian
- Chemical and Chemical Biology, and ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Brian R. Bowman
- Chemical and Chemical Biology, and ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Martin Karplus
- Chemical and Chemical Biology, and ,the L'Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Gregory L. Verdine
- Chemical and Chemical Biology, and ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, ,the Program in Cancer Chemical Biology and Chemical Biology Initiative, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, and , To whom correspondence should be addressed. 12 Oxford St., Cambridge, MA 02138. Fax: 617-495-8755; E-mail:
| |
Collapse
|
141
|
Duplex interrogation by a direct DNA repair protein in search of base damage. Nat Struct Mol Biol 2012; 19:671-6. [PMID: 22659876 PMCID: PMC3392526 DOI: 10.1038/nsmb.2320] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 04/30/2012] [Indexed: 12/04/2022]
Abstract
ALKBH2 is a direct DNA repair dioxygenase guarding mammalian genome against N1-methyladenine, N3-methylcytosine, and 1,N6-ethenoadenine damage. A prerequisite for repair is to identify these lesions in the genome. Here we present crystal structures of ALKBH2 bound to different duplex DNAs. Together with computational and biochemical analyses, our results suggest that DNA interrogation by ALKBH2 displays two novel features: i) ALKBH2 probes base-pair stability and detects base pairs with reduced stability; ii) ALKBH2 does not have nor need a “damage-checking site”, which is critical for preventing spurious base-cleavage for several glycosylases. The demethylation mechanism of ALKBH2 insures that only cognate lesions are oxidized and reversed to normal bases, and that a flipped, non-substrate base remains intact in the active site. Overall, the combination of duplex interrogation and oxidation chemistry allows ALKBH2 to detect and process diverse lesions efficiently and correctly.
Collapse
|
142
|
Meza TJ, Moen MN, Vågbø CB, Krokan HE, Klungland A, Grini PE, Falnes PØ. The DNA dioxygenase ALKBH2 protects Arabidopsis thaliana against methylation damage. Nucleic Acids Res 2012; 40:6620-31. [PMID: 22532610 PMCID: PMC3413135 DOI: 10.1093/nar/gks327] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Escherichia coli AlkB protein (EcAlkB) is a DNA repair enzyme which reverses methylation damage such as 1-methyladenine (1-meA) and 3-methylcytosine (3-meC). The mammalian AlkB homologues ALKBH2 and ALKBH3 display EcAlkB-like repair activity in vitro, but their substrate specificities are different, and ALKBH2 is the main DNA repair enzyme for 1-meA in vivo. The genome of the model plant Arabidopsis thaliana encodes several AlkB homologues, including the yet uncharacterized protein AT2G22260, which displays sequence similarity to both ALKBH2 and ALKBH3. We have here characterized protein AT2G22260, by us denoted ALKBH2, as both our functional studies and bioinformatics analysis suggest it to be an orthologue of mammalian ALKBH2. The Arabidopsis ALKBH2 protein displayed in vitro repair activities towards methyl and etheno adducts in DNA, and was able to complement corresponding repair deficiencies of the E. coli alkB mutant. Interestingly, alkbh2 knock-out plants were sensitive to the methylating agent methylmethanesulphonate (MMS), and seedlings from these plants developed abnormally when grown in the presence of MMS. The present study establishes ALKBH2 as an important enzyme for protecting Arabidopsis against methylation damage in DNA, and suggests its homologues in other plants to have a similar function.
Collapse
Affiliation(s)
- Trine J Meza
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041 Blindern, N-0316 Oslo, Norway
| | | | | | | | | | | | | |
Collapse
|
143
|
Bleijlevens B, Shivarattan T, van den Boom KS, de Haan A, van der Zwan G, Simpson PJ, Matthews SJ. Changes in protein dynamics of the DNA repair dioxygenase AlkB upon binding of Fe(2+) and 2-oxoglutarate. Biochemistry 2012; 51:3334-41. [PMID: 22443471 DOI: 10.1021/bi201699e] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The Escherichia coli DNA repair enzyme AlkB is a 2-oxoglutarate (2OG)-dependent Fe(2+) binding dioxygenase that removes methyl lesions from DNA and RNA. To date, nine human AlkB homologues are known: ABH1 to ABH8 and the obesity-related FTO. Similar to AlkB, these homologues exert their activity on nucleic acids, although for some homologues the biological substrate remains to be identified. 2OG dioxygenases require binding of the cofactors Fe(2+) and 2OG in the active site to form a catalytically competent complex. We present a structural analysis of AlkB using NMR, fluorescence, and CD spectroscopy to show that AlkB is a dynamic protein exhibiting different folding states. In the absence of the cofactors Fe(2+) and 2OG, apoAlkB is a highly dynamic protein. Binding of either Fe(2+) or 2OG alone does not significantly affect the protein dynamics. Formation of a fully folded and catalytically competent holoAlkB complex only occurs when both 2OG and Fe(2+) are bound. These findings provide the first insights into protein folding of 2OG-dependent dioxygenases. A role for protein dynamics in the incorporation of the metal cofactor is discussed.
Collapse
Affiliation(s)
- Boris Bleijlevens
- Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| | | | | | | | | | | | | |
Collapse
|
144
|
Characterization of a Trypanosoma brucei Alkb homolog capable of repairing alkylated DNA. Exp Parasitol 2012; 131:92-100. [PMID: 22465611 DOI: 10.1016/j.exppara.2012.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 02/29/2012] [Accepted: 03/12/2012] [Indexed: 11/20/2022]
Abstract
Trypanosoma brucei encodes a protein (denoted TbABH) that is homologous to AlkB of Escherichia coli and AlkB homolog (ABH) proteins in other organisms, raising the possibility that trypanosomes catalyze oxidative repair of alkylation-damaged DNA. TbABH was cloned and expressed in E. coli, and the recombinant protein was purified and characterized. Incubation of anaerobic TbABH with Fe(II) and α-ketoglutarate (αKG) produces a characteristic metal-to-ligand charge-transfer chromophore, confirming its membership in the Fe(II)/αKG dioxygenase superfamily. The protein binds to DNA, with a clear preference for alkylated oligonucleotides according to results derived by electrophoretic mobility shift assays. Finally, the protozoan gene was shown to partially complement E. coli alkB cells when stressed with methylmethanesulfonate; thus confirming assignment of TbABH as a functional AlkB protein in T. brucei.
Collapse
|
145
|
Heinze RJ, Sekerina S, Winkler I, Biertümpfel C, Oretskaya TS, Kubareva E, Friedhoff P. Covalently trapping MutS on DNA to study DNA mismatch recognition and signaling. MOLECULAR BIOSYSTEMS 2012; 8:1861-4. [DOI: 10.1039/c2mb25086a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
146
|
Abstract
DNA hybridization, wherein strands of DNA form duplex or larger hybrids through noncovalent, sequence-specific interactions, is one of the most fundamental processes in biology. Developing a better understanding of the kinetic and dynamic properties of DNA hybridization will thus help in the elucidation of molecular mechanisms involved in numerous biochemical processes. Moreover, because DNA hybridization has been widely adapted in biotechnology, its study is invaluable to the development of a range of commercially important processes. In this Account, we examine recent studies of the kinetics and dynamics of DNA hybridization, including (i) intramolecular collision of random coil, single-stranded DNA (ssDNA), (ii) nucleic acid hairpin folding, and (iii) considerations of DNA hybridization from both a global view and a detailed base-by-base view. We also examine the spontaneous single-base-pair flipping in duplex DNA because of its importance to both DNA hybridization and repair. Intramolecular collision of random coil ssDNA, with chemical relaxation times ranging from hundreds of nanoseconds to a few microseconds, is investigated both theoretically and experimentally. The first passage time theory of Szabo, Schulten, and Schulten, which determines the average reaction time of the intrachain collision, was tested. Although it was found to provide an acceptable approximation, a more sophisticated theoretical treatment is desirable. Nucleic acid hairpin folding has been extensively investigated as an important model system of DNA hybridization. The relaxation time of hairpin folding and unfolding strongly depends on the stem length, and it may range from hundreds of microseconds to hundreds of milliseconds. The traditional two-state model has been revised to a multistate model as a result of new experimental observations and theoretical study, and partially folded intermediate states have been introduced to the folding energy landscape. On the other hand, new techniques are needed to provide more accurate and detailed information on the dynamics of DNA hairpin folding in the time domain of sub-milliseconds to tens of milliseconds. From a global view, the hybridization of unstructured ssDNA goes through an entropy-controlled nucleation step, whereas the hybridization of ssDNA with a hairpin structure must overcome an extra, enthalpy-controlled energy barrier to eliminate the hairpin. From a detailed base-by-base view, however, there exist many intermediate states. The average single-base-pair hybridization and dehybridization rates in a duplex DNA formation have been determined to be on the order of a millisecond. Meanwhile, accurate information on the early stages of hybridization, such as the dynamics of nucleation, is still lacking. The investigation of spontaneous flipping of a single base in a mismatched base pair in a duplex DNA, although very important, has only recently been initiated because of the earlier lack of suitable probing tools. In sum, the study of DNA hybridization offers a rich range of research opportunities; recent progress is highlighting areas that are ripe for more detailed investigation.
Collapse
Affiliation(s)
- Yandong Yin
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China
| |
Collapse
|
147
|
Pastore C, Topalidou I, Forouhar F, Yan AC, Levy M, Hunt JF. Crystal structure and RNA binding properties of the RNA recognition motif (RRM) and AlkB domains in human AlkB homolog 8 (ABH8), an enzyme catalyzing tRNA hypermodification. J Biol Chem 2011; 287:2130-43. [PMID: 22065580 DOI: 10.1074/jbc.m111.286187] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Humans express nine paralogs of the bacterial DNA repair enzyme AlkB, an iron/2-oxoglutarate-dependent dioxygenase that reverses alkylation damage to nucleobases. The biochemical and physiological roles of these paralogs remain largely uncharacterized, hampering insight into the evolutionary expansion of the AlkB family. However, AlkB homolog 8 (ABH8), which contains RNA recognition motif (RRM) and methyltransferase domains flanking its AlkB domain, recently was demonstrated to hypermodify the anticodon loops in some tRNAs. To deepen understanding of this activity, we performed physiological and biophysical studies of ABH8. Using GFP fusions, we demonstrate that expression of the Caenorhabditis elegans ABH8 ortholog is widespread in larvae but restricted to a small number of neurons in adults, suggesting that its function becomes more specialized during development. In vitro RNA binding studies on several human ABH8 constructs indicate that binding affinity is enhanced by a basic α-helix at the N terminus of the RRM domain. The 3.0-Å-resolution crystal structure of a construct comprising the RRM and AlkB domains shows disordered loops flanking the active site in the AlkB domain and a unique structural Zn(II)-binding site at its C terminus. Although the catalytic iron center is exposed to solvent, the 2-oxoglutarate co-substrate likely adopts an inactive conformation in the absence of tRNA substrate, which probably inhibits uncoupled free radical generation. A conformational change in the active site coupled to a disorder-to-order transition in the flanking protein segments likely controls ABH8 catalytic activity and tRNA binding specificity. These results provide insight into the functional and structural adaptations underlying evolutionary diversification of AlkB domains.
Collapse
Affiliation(s)
- Chiara Pastore
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | | | | | | | | | | |
Collapse
|
148
|
Law S, Feig M. Base-flipping mechanism in postmismatch recognition by MutS. Biophys J 2011; 101:2223-31. [PMID: 22067162 PMCID: PMC3207177 DOI: 10.1016/j.bpj.2011.09.045] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Revised: 09/12/2011] [Accepted: 09/13/2011] [Indexed: 11/15/2022] Open
Abstract
DNA mismatch recognition and repair is vital for preserving the fidelity of the genome. Conserved across prokaryotes and eukaryotes, MutS is the primary protein that is responsible for recognizing a variety of DNA mismatches. From molecular dynamics simulations of the Escherichia coli MutS-DNA complex, we describe significant conformational dynamics in the DNA surrounding a G·T mismatch that involves weakening of the basepair hydrogen bonding in the basepair adjacent to the mismatch and, in one simulation, complete base opening via the major groove. The energetics of base flipping was further examined with Hamiltonian replica exchange free energy calculations revealing a stable flipped-out state with an initial barrier of ~2 kcal/mol. Furthermore, we observe changes in the local DNA structure as well as in the MutS structure that appear to be correlated with base flipping. Our results suggest a role of base flipping as part of the repair initiation mechanism most likely leading to sliding-clamp formation.
Collapse
Affiliation(s)
- Sean M. Law
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Michael Feig
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan
- Department of Chemistry, Michigan State University, East Lansing, Michigan
| |
Collapse
|
149
|
Shankaracharya, Das S, Vidyarthi AS. Homology modeling and function prediction of hABH1, involving in repair of alkylation damaged DNA. Interdiscip Sci 2011; 3:175-81. [DOI: 10.1007/s12539-011-0087-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/13/2010] [Accepted: 08/20/2010] [Indexed: 10/17/2022]
|
150
|
Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ. Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions. Structure 2011; 19:821-32. [PMID: 21645853 DOI: 10.1016/j.str.2011.03.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 03/16/2011] [Accepted: 03/22/2011] [Indexed: 01/23/2023]
Abstract
DNA is susceptible to alkylation damage by a number of environmental agents that modify the Watson-Crick edge of the bases. Such lesions, if not repaired, may be bypassed by Y-family DNA polymerases. The bypass polymerase Dpo4 is strongly inhibited by 1-methylguanine (m1G) and 3-methylcytosine (m3C), with nucleotide incorporation opposite these lesions being predominantly mutagenic. Further, extension after insertion of both correct and incorrect bases, introduces additional base substitution and deletion errors. Crystal structures of the Dpo4 ternary extension complexes with correct and mismatched 3'-terminal primer bases opposite the lesions reveal that both m1G and m3C remain positioned within the DNA template/primer helix. However, both correct and incorrect pairing partners exhibit pronounced primer terminal nucleotide distortion, being primarily evicted from the DNA helix when opposite m1G or misaligned when pairing with m3C. Our studies provide insights into mechanisms related to hindered and mutagenic bypass of methylated lesions and models associated with damage recognition by repair demethylases.
Collapse
Affiliation(s)
- Olga Rechkoblit
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
| | | | | | | |
Collapse
|