1
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Angle ED, Cox PM. Multidisciplinary Insights into the Structure-Function Relationship of the CYP2B6 Active Site. Drug Metab Dispos 2023; 51:369-384. [PMID: 36418184 DOI: 10.1124/dmd.122.000853] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 11/27/2022] Open
Abstract
Cytochrome P450 2B6 (CYP2B6) is a highly polymorphic human enzyme involved in the metabolism of many clinically relevant drugs, environmental toxins, and endogenous molecules with disparate structures. Over the last 20-plus years, in silico and in vitro studies of CYP2B6 using various ligands have provided foundational information regarding the substrate specificity and structure-function relationship of this enzyme. Approaches such as homology modeling, X-ray crystallography, molecular docking, and kinetic activity assays coupled with CYP2B6 mutagenesis have done much to characterize this originally neglected monooxygenase. However, a complete understanding of the structural details that make new chemical entities substrates of CYP2B6 is still lacking. Surprisingly little in vitro data has been obtained about the structure-function relationship of amino acids identified to be in the CYP2B6 active site. Since much attention has already been devoted to elucidating the function of CYP2B6 allelic variants, here we review the salient findings of in silico and in vitro studies of the CYP2B6 structure-function relationship with a deliberate focus on the active site. In addition to summarizing these complementary approaches to studying structure-function relationships, we note gaps/challenges in existing data such as the need for more CYP2B6 crystal structures, molecular docking results with various ligands, and data coupling CYP2B6 active site mutagenesis with kinetic parameter measurement under standard expression conditions. Harnessing in silico and in vitro techniques in tandem to understand the CYP2B6 structure-function relationship will likely offer further insights into CYP2B6-mediated metabolism. SIGNIFICANCE STATEMENT: The apparent importance of cytochrome P450 2B6 (CYP2B6) in the metabolism of various xenobiotics and endogenous molecules has grown since its discovery with many in silico and in vitro studies offering a partial description of its structure-function relationship. Determining the structure-function relationship of CYP2B6 is difficult but may be aided by thorough biochemical investigations of the CYP2B6 active site that provide a more complete pharmacological understanding of this important enzyme.
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Affiliation(s)
- Ethan D Angle
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, Azusa Pacific University, Azusa, California (E.D.A., P.M.C.) and Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, Iowa (E.D.A.)
| | - Philip M Cox
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, Azusa Pacific University, Azusa, California (E.D.A., P.M.C.) and Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, Iowa (E.D.A.)
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2
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Zhang JM, Liu X, Wei Q, Ma C, Li D, Zou Y. Berberine bridge enzyme-like oxidase-catalysed double bond isomerization acts as the pathway switch in cytochalasin synthesis. Nat Commun 2022; 13:225. [PMID: 35017571 PMCID: PMC8752850 DOI: 10.1038/s41467-021-27931-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/10/2021] [Indexed: 11/09/2022] Open
Abstract
Cytochalasans (CYTs), as well as their polycyclic (pcCYTs) and polymerized (meCYTs) derivatives, constitute one of the largest families of fungal polyketide-nonribosomal peptide (PK-NRP) hybrid natural products. However, the mechanism of chemical conversion from mono-CYTs (moCYTs) to both pcCYTs and meCYTs remains unknown. Here, we show the first successful example of the reconstitution of the CYT core backbone as well as the whole pathway in a heterologous host. Importantly, we also describe the berberine bridge enzyme (BBE)-like oxidase AspoA, which uses Glu538 as a general acid biocatalyst to catalyse an unusual protonation-driven double bond isomerization reaction and acts as a switch to alter the native (for moCYTs) and nonenzymatic (for pcCYTs and meCYTs) pathways to synthesize aspochalasin family compounds. Our results present an unprecedented function of BBE-like enzymes and highly suggest that the isolated pcCYTs and meCYTs are most likely artificially derived products.
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Affiliation(s)
- Jin-Mei Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Xuan Liu
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Qian Wei
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Chuanteng Ma
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China.
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3
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Tao H, Mori T, Chen H, Lyu S, Nonoyama A, Lee S, Abe I. Molecular insights into the unusually promiscuous and catalytically versatile Fe(II)/α-ketoglutarate-dependent oxygenase SptF. Nat Commun 2022; 13:95. [PMID: 35013177 PMCID: PMC8748661 DOI: 10.1038/s41467-021-27636-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/01/2021] [Indexed: 11/23/2022] Open
Abstract
Non-heme iron and α-ketoglutarate-dependent (Fe/αKG) oxygenases catalyze various oxidative biotransformations. Due to their catalytic flexibility and high efficiency, Fe/αKG oxygenases have attracted keen attention for their application as biocatalysts. Here, we report the biochemical and structural characterizations of the unusually promiscuous and catalytically versatile Fe/αKG oxygenase SptF, involved in the biosynthesis of fungal meroterpenoid emervaridones. The in vitro analysis revealed that SptF catalyzes several continuous oxidation reactions, including hydroxylation, desaturation, epoxidation, and skeletal rearrangement. SptF exhibits extremely broad substrate specificity toward various meroterpenoids, and efficiently produced unique cyclopropane-ring-fused 5/3/5/5/6/6 and 5/3/6/6/6 scaffolds from terretonins. Moreover, SptF also hydroxylates steroids, including androsterone, testosterone, and progesterone, with different regiospecificities. Crystallographic and structure-based mutagenesis studies of SptF revealed the molecular basis of the enzyme reactions, and suggested that the malleability of the loop region contributes to the remarkable substrate promiscuity. SptF exhibits great potential as a promising biocatalyst for oxidation reactions.
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Affiliation(s)
- Hui Tao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
| | - Heping Chen
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shuang Lyu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Shoukou Lee
- Sumitomo Dainippon Pharma Co., Ltd, Osaka, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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4
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Izaguirre-Carbonell J, Christiansen L, Burns R, Schmitz J, Li C, Mokry RL, Bluemn T, Zheng Y, Shen J, Carlson KS, Rao S, Wang D, Zhu N. Critical role of Jumonji domain of JMJD1C in MLL-rearranged leukemia. Blood Adv 2019; 3:1499-1511. [PMID: 31076406 PMCID: PMC6517669 DOI: 10.1182/bloodadvances.2018026054] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 03/31/2019] [Indexed: 12/30/2022] Open
Abstract
JMJD1C, a member of the lysine demethylase 3 family, is aberrantly expressed in mixed lineage leukemia (MLL) gene-rearranged (MLLr) leukemias. We have shown previously that JMJD1C is required for self-renewal of acute myeloid leukemia (AML) leukemia stem cells (LSCs) but not normal hematopoietic stem cells. However, the domains within JMJD1C that promote LSC self-renewal are unknown. Here, we used clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease (Cas9) negative-selection screening and identified a requirement for the catalytic Jumonji (JmjC) domain and zinc finger domain for leukemia cell survival in vitro and in vivo. In addition, we found that histone H3 lysine 36 methylation (H3K36me) is a marker for JMJD1C activity at gene loci. Moreover, we performed single cell transcriptome analysis of mouse leukemia cells harboring a single guide RNA (sgRNA) against the JmjC domain and identified increased activation of RAS/MAPK and the JAK-STAT pathway in cells harboring the JmjC sgRNA. We discovered that upregulation of interleukin 3 (IL-3) receptor genes mediates increased activation of IL-3 signaling upon JMJD1C loss or mutation. Along these lines, we observed resistance to JMJD1C loss in MLLr AML bearing activating RAS mutations, suggesting that RAS pathway activation confers resistance to JMJD1C loss. Overall, we discovered the functional importance of the JMJD1C JmjC domain in AML leukemogenesis and a novel interplay between JMJD1C and the IL-3 signaling pathway as a potential resistance mechanism to targeting JMJD1C catalytic activity.
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MESH Headings
- Animals
- CRISPR-Cas Systems/genetics
- Cell Line, Tumor
- Gene Editing
- Histone-Lysine N-Methyltransferase/genetics
- Histones/metabolism
- Humans
- Interleukin-3/metabolism
- Jumonji Domain-Containing Histone Demethylases/chemistry
- Jumonji Domain-Containing Histone Demethylases/genetics
- Jumonji Domain-Containing Histone Demethylases/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred C57BL
- Myeloid-Lymphoid Leukemia Protein/genetics
- Oxidoreductases, N-Demethylating/chemistry
- Oxidoreductases, N-Demethylating/genetics
- Oxidoreductases, N-Demethylating/metabolism
- Protein Domains
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Signal Transduction
- Transplantation, Heterologous
- Zinc Fingers/genetics
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Affiliation(s)
| | - Luke Christiansen
- Blood Research Institute, Versiti, Milwaukee, WI; and
- Department of Cell Biology, Neurobiology, and Anatomy
| | - Robert Burns
- Blood Research Institute, Versiti, Milwaukee, WI; and
| | - Jesse Schmitz
- Blood Research Institute, Versiti, Milwaukee, WI; and
| | - Chenxuan Li
- Blood Research Institute, Versiti, Milwaukee, WI; and
| | | | - Theresa Bluemn
- Blood Research Institute, Versiti, Milwaukee, WI; and
- Department of Cell Biology, Neurobiology, and Anatomy
| | - Yongwei Zheng
- Blood Research Institute, Versiti, Milwaukee, WI; and
| | - Jian Shen
- Department of Microbiology and Immunology
| | - Karen-Sue Carlson
- Blood Research Institute, Versiti, Milwaukee, WI; and
- Department of Internal Medicine, and
| | - Sridhar Rao
- Blood Research Institute, Versiti, Milwaukee, WI; and
- Department of Cell Biology, Neurobiology, and Anatomy
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Demin Wang
- Blood Research Institute, Versiti, Milwaukee, WI; and
- Department of Microbiology and Immunology
| | - Nan Zhu
- Blood Research Institute, Versiti, Milwaukee, WI; and
- Department of Cell Biology, Neurobiology, and Anatomy
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5
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Abstract
Jumonji C (JmjC) domain-containing proteins have been shown to regulate cellular processes by hydroxylating or demethylating histone and non-histone targets. JMJD8 belongs to the JmjC domain-only family that was recently shown to be involved in angiogenesis and TNF-induced NF-κB signaling. Here, we employed bioinformatic analysis and immunofluorescence microscopy to examine the physiological properties of JMJD8. We demonstrated that JMJD8 localizes to the lumen of endoplasmic reticulum and that JMJD8 forms dimers or oligomers in vivo. Furthermore, we identified potential JMJD8-interacting proteins that are known to regulate protein complex assembly and protein folding. Taken together, this work demonstrates that JMJD8 is the first JmjC domain-containing protein found in the lumen of the endoplasmic reticulum that may function in protein complex assembly and protein folding.
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Affiliation(s)
- Kok Siong Yeo
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ming Cheang Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yat-Yuen Lim
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Chee-Kwee Ea
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9148, United States.
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6
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Schuller DJ, Reisch CR, Moran MA, Whitman WB, Lanzilotta WN. Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique. Protein Sci 2012; 21:289-98. [PMID: 22162093 PMCID: PMC3324773 DOI: 10.1002/pro.2015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 11/29/2011] [Indexed: 02/01/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is a ubiquitous algal metabolite and common carbon and sulfur source for marine bacteria. DMSP is a precursor for the climatically active gas dimethylsulfide that is readily oxidized to sulfate, sulfur dioxide, methanesulfonic acid, and other products that act as cloud condensation nuclei. Although the environmental importance of DMSP metabolism has been known for some time, the enzyme responsible for DMSP demethylation by marine bacterioplankton, dimethylsufoniopropionate-dependent demethylase A (DmdA, EC 2.1.1.B5), has only recently been identified and biochemically characterized. In this work, we report the structure for the apoenzyme DmdA from Pelagibacter ubique (2.1 Å), as well as for DmdA co-crystals soaked with substrate DMSP (1.6 Å) or the cofactor tetrahydrofolate (THF) (1.6 Å). Surprisingly, the overall fold of the DmdA is not similar to other enzymes that typically utilize the reduced form of THF and in fact is a triple domain structure similar to what has been observed for the glycine cleavage T protein or sarcosine oxidase. Specifically, while the THF binding fold appears conserved, previous biochemical studies have shown that all enzymes with a similar fold produce 5,10-methylene-THF, while DmdA catalyzes a redox-neutral methyl transfer reaction to produce 5-methyl-THF. On the basis of the findings presented herein and the available biochemical data, we outline a mechanism for a redox-neutral methyl transfer reaction that is novel to this conserved THF binding domain.
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Affiliation(s)
- David J Schuller
- Cornell High Energy Synchrotron Source, Cornell UniversityIthaca, New York 14853
| | - Chris R Reisch
- Department of Microbiology, University of GeorgiaAthens, Georgia 30602
| | - Mary Ann Moran
- Department of Marine Sciences, University of GeorgiaAthens, Georgia 30602
| | - William B Whitman
- Department of Microbiology, University of GeorgiaAthens, Georgia 30602
| | - William N Lanzilotta
- Department of Biochemistry and Molecular Biology and The Center for Metalloenzyme Studies, University of GeorgiaAthens, Georgia 30602
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7
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Lu F, Li G, Cui X, Liu C, Wang XJ, Cao X. Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J Integr Plant Biol 2008; 50:886-96. [PMID: 18713399 DOI: 10.1111/j.1744-7909.2008.00692.x] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Histone methylation homeostasis is achieved by controlling the balance between methylation and demethylation to maintain chromatin function and developmental regulation. In animals, a conserved Jumonji C (JmjC) domain was found in a large group of histone demethylases. However, it is still unclear whether plants also contain the JmjC domain-containing active histone demethylases. Here we performed genome-wide screen and phylogenetic analysis of JmjC domain-containing proteins in the dicot plant, Arabidopsis, and monocot plant rice, and found 21 and 20 JmjC domain-containing, respectively. We also examined the expression of JmjC domain-containing proteins and compared them to human JmjC counterparts for potential enzymatic activity. The spatial expression patterns of the Arabidopsis JmjC domain-containing genes revealed that they are all actively transcribed genes. These active plant JmjC domain-containing genes could possibly function in epigenetic regulation to antagonize the activity of the large number of putative SET domain-containing histone methyltransferase activity to dynamically regulate histone methylation homeostasis.
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Affiliation(s)
- Falong Lu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China
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8
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Koehler C, Bishop S, Dowler EF, Schmieder P, Diehl A, Oschkinat H, Ball LJ. Backbone and sidechain 1H, 13C and 15N resonance assignments of the Bright/ARID domain from the human JARID1C (SMCX) protein. Biomol NMR Assign 2008; 2:9-11. [PMID: 19636912 DOI: 10.1007/s12104-007-9071-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 11/24/2007] [Indexed: 05/28/2023]
Abstract
We have assigned 1H, 13C and 15N resonances of the Bright/ARID DNA-binding domain from the human JARID1C protein, a newly discovered histone demethylase belonging to the JmjC domain-containing protein family.
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Affiliation(s)
- Christian Koehler
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
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9
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Arrese EL, Rivera L, Hamada M, Mirza S, Hartson SD, Weintraub S, Soulages JL. Function and structure of lipid storage droplet protein 1 studied in lipoprotein complexes. Arch Biochem Biophys 2008; 473:42-7. [PMID: 18342616 DOI: 10.1016/j.abb.2008.02.036] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 02/25/2008] [Accepted: 02/26/2008] [Indexed: 11/18/2022]
Abstract
Triglycerides (TG) stored in lipid droplets (LDs) are the main energy reserve in all animals. The mechanism by which animals mobilize TG is complex and not fully understood. Several proteins surrounding the LDs have been implicated in TG homeostasis such as mammalian perilipin A and insect lipid storage proteins (Lsd). Most of the knowledge on LD-associated proteins comes from studies using cells or LDs leaving biochemical properties of these proteins uncharacterized. Here we describe the purification of recombinant Lsd1 and its reconstitution with lipids to form lipoprotein complexes suitable for functional and structural studies. Lsd1 in the lipid bound state is a predominately alpha-helical protein. Using lipoprotein complexes containing triolein it is shown that PKA mediated phosphorylation of Lsd1 promoted a 1.7-fold activation of the main fat body lipase demonstrating the direct link between Lsd1 phosphorylation and activation of lipolysis. Serine 20 was identified as the Lsd1-phosphorylation site triggering this effect.
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Affiliation(s)
- Estela L Arrese
- Department of Biochemistry and Molecular Biology, Oklahoma State University, 246 Noble Research Center, Stillwater, OK 74078, USA.
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10
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Mimasu S, Sengoku T, Fukuzawa S, Umehara T, Yokoyama S. Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A. Biochem Biophys Res Commun 2007; 366:15-22. [PMID: 18039463 DOI: 10.1016/j.bbrc.2007.11.066] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 11/07/2007] [Indexed: 11/17/2022]
Abstract
Transcriptional activity and chromatin structure accessibility are correlated with the methylation of specific histone residues. Lysine-specific demethylase 1 (LSD1) is the first discovered histone demethylase, which demethylates Lys4 or Lys9 of histone H3, using FAD. Among the known monoamine oxidase inhibitors, tranylcypromine (Parnate) showed the most potent inhibitory effect on LSD1. Recently, the crystal structure of LSD1 and tranylcypromine was solved at 2.75 A, revealing a five-membered ring fused to the flavin of LSD1. In this study, we refined the crystal structure of the LSD1-tranylcypromine complex to 2.25 A. The five-membered ring model did not fit completely with the electron density, giving R(work)/R(free) values of 0.226/0.254. On the other hand, the N(5) adduct gave the lowest R(work)/R(free) values of 0.218/0.248, among the tested models. These results imply that the LSD1-tranylcypromine complex is not completely composed of the five-membered adduct, but partially contains an intermediate, such as the N(5) adduct.
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Affiliation(s)
- Shinya Mimasu
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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11
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12
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Lin HL, Myshkin E, Waskell L, Hollenberg PF. Peroxynitrite inactivation of human cytochrome P450s 2B6 and 2E1: heme modification and site-specific nitrotyrosine formation. Chem Res Toxicol 2007; 20:1612-22. [PMID: 17907788 DOI: 10.1021/tx700220e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study examined the reaction of peroxynitrite (PN) with two human cytochrome P450s, P450 2B6 (2B6) and P450 2E1 (2E1). After the reaction with PN, the NADPH/reductase-supported 7-ethoxy-4-(trifluoromethyl)coumarin (EFC) deethylation activity of both P450s was decreased in a concentration-dependent manner. HPLC analysis revealed that the prosthetic heme group of 2B6 was modified but to a lesser extent than the decrease in enzymatic activity. In contrast, the heme moiety of 2E1 was not altered. These results suggest that protein modification by PN contributed to the loss in enzymatic activity of 2B6 and 2E1 but to different extents. After trypsin digestion of the control and PN-inactivated P450s, tyrosine nitration was used as a biomarker for protein modification and the addition of the nitro group was determined using electrospray ionization-liquid chromatography-tandem mass spectrometry, allowing site-specific assignment of the tyrosine residues nitrated. Tyrosine residues 354, 244, 268, and 380 in 2B6 and tyrosine residues 317, 422, 69, and 380 in 2E1 were found to be nitrated. Tyrosine 354 is the primary site of nitration in 2B6, and tyrosine residues 422 and 317 are the primary targets for nitration in 2E1. After PN exposure, the EFC catalytic activity of 2E1 supported by tert-butylhydroperoxide was not affected, and the activity of 2B6 supported by tert-butylhydroperoxide was decreased to a lesser extent than that supported by NADPH/reductase. Following exposure to PN, the levels of the reduced-CO complex were less than the content of native heme remaining. These results suggest that PN-mediated protein modification has no effect on substrate binding but may impair the interaction of the reductase with P450s, thereby inhibiting electron transfer. Homology modeling shows that Tyr422 of 2E1 is in close proximity to the FMN domain of reductase, suggesting that Tyr422 may be involved in transferring electrons from the reductase to the heme and thus may play a critical structural and functional role in the extensive activity loss following PN exposure.
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Affiliation(s)
- Hsia-Lien Lin
- Department of Pharmacology, University of Michigan and VA Medical Center, Ann Arbor, Michigan 48109, USA
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13
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Abstract
The discovery of histone-demethylating enzymes has revealed yet another reversible histone modification mark. In this review, we describe the structural and chemical insights that we have now derived underlying the activity of these enzymes. The recent co-crystal structures of LSD1 bound to a proparylamine-derivatized histone H3 peptide and JHDM structures bound to two different methylated histone H3 peptides illustrate the steric requirements and structural basis for substrate specificity.
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Affiliation(s)
- Ruchi Anand
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, USA
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14
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Abstract
Chromatin is a highly dynamic structure that undergoes a variety of chemical modifications. These modifications mediate alterations of the chromatin architecture, generate binding platforms that are recognized by other proteins, and are important elements of epigenetic gene regulation. An array of antagonizing histone modifying enzymes that catalyze the attachment and removal of a number of chemical groups has been described and their biologic role has been an intense area of research. With the recent discovery of the first histone demethylase, lysine-specific demethylase-1, a dynamic view of histone methylation was born. As a deeper understanding of their involvement in transcriptional regulation is gained, histone demethylases are becoming increasingly interesting targets for drug development.
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Affiliation(s)
- Pete Stavropoulos
- The Rockefeller University, Laboratory of Cell Biology, 1230 York Avenue, New York, NY 10021, USA
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15
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Tsukada Y. [Histone methylation and demethylation--focusing on demethylation--]. Seikagaku 2007; 79:691-7. [PMID: 17763704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- Yuichi Tsukada
- Department of Molecular and Cellular Biology, Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
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16
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Abstract
Histone demethylase LSD1 regulates transcription by demethylating Lys(4) of histone H3. The crystal structure of the enzyme in complex with CoREST and a substrate-like peptide inhibitor highlights an intricate network of interactions and a folded conformation of the bound peptide. The core of the peptide structure is formed by Arg(2), Gln(5), and Ser(10), which are engaged in specific intramolecular H-bonds. Several charged side chains on the surface of the substrate-binding pocket establish electrostatic interactions with the peptide. The three-dimensional structure predicts that methylated Lys(4) binds in a solvent inaccessible position in front of the flavin cofactor. This geometry is fully consistent with the demethylation reaction being catalyzed through a flavin-mediated oxidation of the substrate amino-methyl group. These features dictate the exquisite substrate specificity of LSD1 and provide a structural framework to explain the fine tuning of its catalytic activity and the active role of CoREST in substrate recognition.
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Affiliation(s)
- Federico Forneris
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
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17
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Couture JF, Collazo E, Ortiz-Tello PA, Brunzelle JS, Trievel RC. Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Nat Struct Mol Biol 2007; 14:689-95. [PMID: 17589523 DOI: 10.1038/nsmb1273] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Accepted: 06/15/2007] [Indexed: 12/25/2022]
Abstract
JMJD2A is a JmjC histone demethylase (HDM) that catalyzes the demethylation of di- and trimethylated Lys9 and Lys36 in histone H3 (H3K9me2/3 and H3K36me2/3). Here we present the crystal structures of the JMJD2A catalytic domain in complex with H3K9me3, H3K36me2 and H3K36me3 peptides. The structures reveal that histone substrates are recognized through a network of backbone hydrogen bonds and hydrophobic interactions that deposit the trimethyllysine into the active site. The trimethylated epsilon-ammonium cation is coordinated within a methylammonium-binding pocket through carbon-oxygen (CH...O) hydrogen bonds that position one of the zeta-methyl groups adjacent to the Fe(II) center for hydroxylation and demethylation. Mutations of the residues comprising this pocket abrogate demethylation by JMJD2A, with the exception of an S288A substitution, which augments activity, particularly toward H3K9me2. We propose that this residue modulates the methylation-state specificities of JMJD2 enzymes and other trimethyllysine-specific JmjC HDMs.
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Affiliation(s)
- Jean-François Couture
- Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109-0606, USA
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18
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Ng SS, Kavanagh KL, McDonough MA, Butler D, Pilka ES, Lienard BMR, Bray JE, Savitsky P, Gileadi O, von Delft F, Rose NR, Offer J, Scheinost JC, Borowski T, Sundstrom M, Schofield CJ, Oppermann U. Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature 2007; 448:87-91. [PMID: 17589501 DOI: 10.1038/nature05971] [Citation(s) in RCA: 257] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 06/04/2007] [Indexed: 11/09/2022]
Abstract
Post-translational histone modification has a fundamental role in chromatin biology and is proposed to constitute a 'histone code' in epigenetic regulation. Differential methylation of histone H3 and H4 lysyl residues regulates processes including heterochromatin formation, X-chromosome inactivation, genome imprinting, DNA repair and transcriptional regulation. The discovery of lysyl demethylases using flavin (amine oxidases) or Fe(II) and 2-oxoglutarate as cofactors (2OG oxygenases) has changed the view of methylation as a stable epigenetic marker. However, little is known about how the demethylases are selective for particular lysyl-containing sequences in specific methylation states, a key to understanding their functions. Here we reveal how human JMJD2A (jumonji domain containing 2A), which is selective towards tri- and dimethylated histone H3 lysyl residues 9 and 36 (H3K9me3/me2 and H3K36me3/me2), discriminates between methylation states and achieves sequence selectivity for H3K9. We report structures of JMJD2A-Ni(II)-Zn(II) inhibitor complexes bound to tri-, di- and monomethyl forms of H3K9 and the trimethyl form of H3K36. The structures reveal a lysyl-binding pocket in which substrates are bound in distinct bent conformations involving the Zn-binding site. We propose a mechanism for achieving methylation state selectivity involving the orientation of the substrate methyl groups towards a ferryl intermediate. The results suggest distinct recognition mechanisms in different demethylase subfamilies and provide a starting point to develop chemical tools for drug discovery and to study and dissect the complexity of reversible histone methylation and its role in chromatin biology.
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Affiliation(s)
- Stanley S Ng
- Structural Genomics Consortium, Botnar Research Center, University of Oxford, Oxford OX3 7LD, UK
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19
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Yang M, Culhane JC, Szewczuk LM, Jalili P, Ball HL, Machius M, Cole PA, Yu H. Structural Basis for the Inhibition of the LSD1 Histone Demethylase by the Antidepressant trans-2-Phenylcyclopropylamine,. Biochemistry 2007; 46:8058-65. [PMID: 17569509 DOI: 10.1021/bi700664y] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Histone modifications, such as acetylation and methylation, are important epigenetic marks that regulate diverse biological processes that use chromatin as the template, including transcription. Dysregulation of histone acetylation and methylation leads to the silencing of tumor suppressor genes and contributes to cancer progression. Inhibitors of enzymes that catalyze the addition and removal of these epigenetic marks thus have therapeutic potential for treating cancer. Lysine-specific demethylase 1 (LSD1) is the first discovered histone lysine demethylase and, with the help of its cofactor CoREST, specifically demethylates mono- and dimethylated histone H3 lysine 4 (H3-K4), thus repressing transcription. Because LSD1 belongs to the family of flavin adenine dinucleotide (FAD)-dependent amine oxidases, certain inhibitors of monoamine oxidases (MAOs), including the clinically used antidepressant trans-2-phenylcyclopropylamine (PCPA; tranylcypromine; Parnate), are also capable of inhibiting LSD1. In this study, we have further measured the kinetic parameters of the inhibition of LSD1 by PCPA and determined the crystal structure of LSD1-CoREST in the presence of PCPA. Our structural and mass spectrometry analyses are consistent with PCPA forming a covalent adduct with FAD in LSD1 that is distinct from the FAD-PCPA adduct of MAO B. The structure also reveals that the phenyl ring of the FAD-PCPA adduct in LSD1 does not form extensive interactions with active-site residues. This study thus provides the basis for designing more potent inhibitors of LSD1 that contain substitutions on the phenyl ring of PCPA to fully engage neighboring residues.
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Affiliation(s)
- Maojun Yang
- Departments of Pharmacology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390, USA
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20
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Winkler A, Kutchan TM, Macheroux P. 6-S-cysteinylation of bi-covalently attached FAD in berberine bridge enzyme tunes the redox potential for optimal activity. J Biol Chem 2007; 282:24437-43. [PMID: 17573342 DOI: 10.1074/jbc.m703642200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A mutagenic analysis of the amino acid residues His-104 and Cys-166, which are involved in the bi-covalent attachment of FAD to berberine bridge enzyme, was performed. Here we present a detailed biochemical characterization of the cysteine link to FAD observed in this recently discovered group of flavoproteins. The C166A mutant protein still has residual activity, but reduced to approximately 6% of the turnover rate observed for wild-type berberine bridge enzyme. A more detailed analysis of single reaction steps by stopped-flow spectrophotometry showed that the reductive half-reaction is greatly influenced by the lack of the 6-S-cysteinyl linkage, resulting in a 370-fold decrease in the rate of flavin reduction. Determination of the redox potentials for both wild type and the C166A mutein revealed that the difference in the redox potential observed can fully account for the change in the kinetic properties. The wild-type protein exhibits a midpoint potential of +132 mV, which is the highest redox potential determined for any flavoenzyme so far. Removal of the cysteine linkage to FAD in the C166A mutein leads to a redox potential of +53 mV, which is in the expected range for flavoproteins with a single covalent attachment of FAD to a His residue via its 8-alpha position. We also show that the biochemical properties of the mutein resemble that of typical flavoprotein oxidases and that deviations from this behavior observed for the wild type are due to the FAD-6-S-cysteinyl bond. In addition, rapid reaction stopped-flow experiments give no indication for a radical mechanism supporting the direct transfer of a hydride from the substrate to the cofactor.
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Affiliation(s)
- Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria
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21
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Chen Z, Zang J, Kappler J, Hong X, Crawford F, Wang Q, Lan F, Jiang C, Whetstine J, Dai S, Hansen K, Shi Y, Zhang G. Structural basis of the recognition of a methylated histone tail by JMJD2A. Proc Natl Acad Sci U S A 2007; 104:10818-23. [PMID: 17567753 PMCID: PMC1891149 DOI: 10.1073/pnas.0704525104] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Jumonji C domain is a catalytic motif that mediates histone lysine demethylation. The Jumonji C-containing oxygenase JMJD2A specifically demethylates tri- and dimethylated lysine-9 and lysine-36 of histone 3 (H3K9/36 me3/2). Here we present structures of the JMJD2A catalytic core complexed with methylated H3K36 peptide substrates in the presence of Fe(II) and N-oxalylglycine. We found that the interaction between JMJD2A and peptides largely involves the main chains of the enzyme and the peptide. The peptide-binding specificity is primarily determined by the primary structure of the peptide, which explains the specificity of JMJD2A for methylated H3K9 and H3K36 instead of other methylated residues such as H3K27. The specificity for a particular methyl group, however, is affected by multiple factors, such as space and the electrostatic environment in the catalytic center of the enzyme. These results provide insights into the mechanisms and specificity of histone demethylation.
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Affiliation(s)
- Zhongzhou Chen
- *Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Jianye Zang
- *Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206
| | - John Kappler
- *Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206
- Howard Hughes Medical Institute, National Jewish Medical and Research Center, Denver, CO 80206
- To whom correspondence may be addressed at:
Howard Hughes Medical Institute, Integrated Department of Immunology, National Jewish Medical and Research Center, 1400 Jackson Street, Denver, CO 80206. E-mail:
| | - Xia Hong
- *Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206
| | - Frances Crawford
- *Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206
- Howard Hughes Medical Institute, National Jewish Medical and Research Center, Denver, CO 80206
| | - Qin Wang
- *Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206
| | - Fei Lan
- Department of Pathology, Harvard Medical School, Boston, MA 02115
| | - Chengyu Jiang
- National Key Laboratory of Medical Molecular Biology, Peking Union Medical College, Tsinghua University and Chinese Academy of Medical Sciences, Beijing 100084, China; and
| | | | - Shaodong Dai
- *Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206
- Howard Hughes Medical Institute, National Jewish Medical and Research Center, Denver, CO 80206
| | - Kirk Hansen
- **Department of Pharmacology and Cancer Center, School of Medicine, University of Colorado Health Sciences Center, Aurora, CO 80045
| | - Yang Shi
- Department of Pathology, Harvard Medical School, Boston, MA 02115
| | - Gongyi Zhang
- *Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206
- **Department of Pharmacology and Cancer Center, School of Medicine, University of Colorado Health Sciences Center, Aurora, CO 80045
- To whom correspondence may be addressed at:
Integrated Department of Immunology, National Jewish Medical and Research Center, 1400 Jackson Street, Denver, CO 80206. E-mail:
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22
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Ralph EC, Hirschi JS, Anderson MA, Cleland WW, Singleton DA, Fitzpatrick PF. Insights into the mechanism of flavoprotein-catalyzed amine oxidation from nitrogen isotope effects on the reaction of N-methyltryptophan oxidase. Biochemistry 2007; 46:7655-64. [PMID: 17542620 PMCID: PMC2041825 DOI: 10.1021/bi700482h] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism of N-methyltryptophan oxidase, a flavin-dependent amine oxidase from Escherichia coli, was studied using a combination of kinetic isotope effects and theoretical calculations. The 15(kcat/Km) kinetic isotope effect for sarcosine oxidation is pH-dependent with a limiting value of 0.994-0.995 at high pH. Density functional theory calculations on model systems were used to interpret these isotope effects. The isotope effects are inconsistent with proposed mechanisms involving covalent amine-flavin adducts but cannot by themselves conclusively distinguish between some discrete electron-transfer mechanisms and a direct hydride-transfer mechanism, although the latter mechanism is more consistent with the energetics of the reaction.
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Affiliation(s)
- Erik C. Ralph
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX 77843-2128
| | - Jennifer S. Hirschi
- Department of Chemistry, Texas A&M University, College Station TX 77843-2128
| | - Mark A. Anderson
- Institute for Enzyme Research and Department of Biochemistry University of Wisconsin, Madison, WI
| | - W. Wallace Cleland
- Institute for Enzyme Research and Department of Biochemistry University of Wisconsin, Madison, WI
| | - Daniel A. Singleton
- Department of Chemistry, Texas A&M University, College Station TX 77843-2128
- *Corresponding authors. D.A.S.: phone, 979-845-9166; fax 979-845-0653; e-mail, . P.F.F.: phone, 979-845-5487; fax 979-845-4946; e-mail,
| | - Paul F. Fitzpatrick
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX 77843-2128
- Department of Chemistry, Texas A&M University, College Station TX 77843-2128
- *Corresponding authors. D.A.S.: phone, 979-845-9166; fax 979-845-0653; e-mail, . P.F.F.: phone, 979-845-5487; fax 979-845-4946; e-mail,
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23
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Abstract
Lysine-specific demethylase 1 (LSD1) is a transcriptional repressor and a flavin-dependent amine oxidase that is responsible for the removal of methyl from lysine 4 of histone H3. In this study, we characterize the mechanism and scope of LSD1 inhibition by a propargylamine-derivatized histone H3 substrate (1). Unlike aziridinyl and cyclopropylamine-derivatized histone H3 peptide substrate analogues, compound 1 appears to covalently modify and irreversibly inactivate LSD1 with high potency. Accompanying this inactivation is a spectroscopic change, which shifts the absorbance maximum to 392 nm. Spectral changes associated with the 1-LSD1 complex and reactivity to decreased pH and sodium borohydride treatment were suggestive of a structure involving a flavin-linked inhibitor conjugate between N5 of the flavin and the terminal carbon of the inhibitor. Using a 13C-labeled inhibitor, NMR analysis of the 1-flavin conjugate was consistent with this structural assignment. Kinetic analysis of the spectroscopic shift induced by 1 showed that the flavin adduct formed in a reaction with kinetic constants similar to those of the LSD1 inactivation process. Taken together, these data support a mechanism of LSD1 inactivation by 1 involving amine oxidation followed by Michael addition to the propargylic imine. We further examined the potential for a biotinylated analogue of 1 (1-Btn) to be used as a tool in affinity pulldown experiments. Using 1-Btn, it was feasible to selectively pull down spiked and endogenous LSD1 from HeLa cell nuclear extracts, setting the stage for activity-based demethylase proteomics.
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Affiliation(s)
- Lawrence M. Szewczuk
- Dept. of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jeffrey C. Culhane
- Dept. of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Maojun Yang
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, MD 21210
| | - Hongtao Yu
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390
| | - Philip A. Cole
- Dept. of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- To whom correspondence should be addressed. . Telephone: (410) 614-8849. Fax: (410) 614-7717
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24
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Abstract
Histone methylation plays important roles in the regulation of chromatin dynamics and transcription. Steady-state levels of histone lysine methylation are regulated by a balance between enzymes that catalyze either the addition or removal of methyl groups. Using an activity-based biochemical approach, we recently uncovered the JmjC domain as an evolutionarily conserved signature motif for histone demethylases. Furthermore, we demonstrated that Jhd1, a JmjC domain-containing protein in Saccharomyces cerevisiae, is an H3K36-specific demethylase. Here we report further characterization of Jhd1. Similar to its mammalian homolog, Jhd1-catalyzed histone demethylation requires iron and alpha-ketoglutarate as cofactors. Mutation and deletion studies indicate that the JmjC domain and adjacent sequences are critical for Jhd1 enzymatic activity, while the N-terminal PHD domain is dispensable. Overexpression of JHD1 results in a global reduction of H3K36 methylation in vivo. Finally, chromatin immunoprecipitation-coupled microarray studies reveal subtle changes in the distribution of H3K36me2 upon overexpression or deletion of JHD1. Our studies establish Jhd1 as a histone demethylase in budding yeast and suggest that Jhd1 functions to maintain the fidelity of histone methylation patterns along transcription units.
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Affiliation(s)
- Jia Fang
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, NC 27599, USA
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25
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Abstract
The catalytic domain of the flavin-dependent human histone demethylase lysine-specific demethylase 1 (LSD1) belongs to the family of amine oxidases including polyamine oxidase and monoamine oxidase (MAO). We previously assessed monoamine oxidase inhibitors (MAOIs) for their ability to inhibit the reaction catalyzed by LSD1 [Lee, M. G., et al. (2006) Chem. Biol. 13, 563-567], demonstrating that trans-2-phenylcyclopropylamine (2-PCPA, tranylcypromine, Parnate) was the most potent with respect to LSD1. Here we show that 2-PCPA is a time-dependent, mechanism-based irreversible inhibitor of LSD1 with a KI of 242 microM and a kinact of 0.0106 s-1. 2-PCPA shows limited selectivity for human MAOs versus LSD1, with kinact/KI values only 16-fold and 2.4-fold higher for MAO B and MAO A, respectively. Profiles of LSD1 activity and inactivation by 2-PCPA as a function of pH are consistent with a mechanism of inactivation dependent upon enzyme catalysis. Mass spectrometry supports a role for FAD as the site of covalent modification by 2-PCPA. These results will provide a foundation for the design of cyclopropylamine-based inhibitors that are selective for LSD1 to probe its role in vivo.
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Affiliation(s)
- Dawn M Z Schmidt
- Department of Chemistry, B120 Levine Science Research Center, Box 90317, Duke University, Durham, North Carolina 27708, USA
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26
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Abstract
Histone methylation has important roles in regulating transcription, genome integrity and epigenetic inheritance. Historically, methylated histone arginine and lysine residues have been considered static modifications because of the low levels of methyl-group turnover in chromatin. The recent identification of enzymes that antagonize or remove histone methylation has changed this view and now the dynamic nature of these modifications is being appreciated. Here, we examine the enzymatic and structural basis for the mechanisms that these enzymes use to counteract histone methylation and provide insights into their substrate specificity and biological function.
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Affiliation(s)
- Robert J Klose
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295, USA
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27
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Christensen J, Agger K, Cloos PAC, Pasini D, Rose S, Sennels L, Rappsilber J, Hansen KH, Salcini AE, Helin K. RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell 2007; 128:1063-76. [PMID: 17320161 DOI: 10.1016/j.cell.2007.02.003] [Citation(s) in RCA: 414] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 12/14/2006] [Accepted: 02/02/2007] [Indexed: 12/12/2022]
Abstract
Methylation of histones has been regarded as a stable modification defining the epigenetic program of the cell, which regulates chromatin structure and transcription. However, the recent discovery of histone demethylases has challenged the stable nature of histone methylation. Here we demonstrate that the JARID1 proteins RBP2, PLU1, and SMCX are histone demethylases specific for di- and trimethylated histone 3 lysine 4 (H3K4). Consistent with a role for the JARID1 Drosophila homolog Lid in regulating expression of homeotic genes during development, we show that RBP2 is displaced from Hox genes during embryonic stem (ES) cell differentiation correlating with an increase of their H3K4me3 levels and expression. Furthermore, we show that mutation or RNAi depletion of the C. elegans JARID1 homolog rbr-2 leads to increased levels of H3K4me3 during larval development and defects in vulva formation. Taken together, these results suggest that H3K4me3/me2 demethylation regulated by the JARID1 family plays an important role during development.
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28
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Abstract
During the past few years, there have been exciting developments in the field of flavoenzymology. New flavoenzymes have been discovered that are implicated in a variety of biological processes, including cell signaling, chromatin remodeling and cell development. The structures of several of these new flavoenzymes have been described, as exemplified by crystallographic analyses of MICAL, histone demethylase LSD1 and tryptophan dehalogenase. In addition, new structural information has revealed the evolutionary and mechanistic complexity of the enzymes of the riboflavin biosynthetic pathway. The integration of the enzymology data with crystallographic studies at atomic resolution is resulting in unprecedented insight into the chemical and geometric properties underlying flavoenzyme function.
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Affiliation(s)
- Luigi De Colibus
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
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29
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Abstract
Histone methylation has important roles in regulating gene expression and forms part of the epigenetic memory system that regulates cell fate and identity. Enzymes that directly remove methyl marks from histones have recently been identified, revealing a new level of plasticity within this epigenetic modification system. Here we analyse the evolutionary relationship between Jumonji C (JmjC)-domain-containing proteins and discuss their cellular functions in relation to their potential enzymatic activities.
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Affiliation(s)
- Robert J Klose
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7295, USA
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30
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Forneris F, Binda C, Dall'Aglio A, Fraaije MW, Battaglioli E, Mattevi A. A highly specific mechanism of histone H3-K4 recognition by histone demethylase LSD1. J Biol Chem 2006; 281:35289-95. [PMID: 16987819 DOI: 10.1074/jbc.m607411200] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human lysine-specific demethylase (LSD1) is a chromatin-modifying enzyme that specifically removes methyl groups from mono- and dimethylated Lys4 of histone H3 (H3-K4). We used a combination of in vivo and in vitro experiments to characterize the substrate specificity and recognition by LSD1. Biochemical assays on histone peptides show that essentially all epigenetic modifications on the 21 N-terminal amino acids of histone H3 cause a significant reduction in enzymatic activity. Replacement of Lys4 with Arg greatly enhances binding affinity, and a histone peptide incorporating this mutation has a strong inhibitory power. Conversely, a peptide bearing a trimethylated Lys4 is only a weak inhibitor of the enzyme. Rapid kinetics measurements evidence that the enzyme is efficiently reoxidized by molecular oxygen with a second-order rate constant of 9.6x10(3) M-1 s-1, and that the presence of the reaction product does not greatly influence the rate of flavin reoxidation. In vivo experiments provide a correlation between the in vitro inhibitory properties of the tested peptides and their ability of affecting endogenous LSD1 activity. Our results show that epigenetic modifications on histone H3 need to be removed before Lys4 demethylation can efficiently occur. The complex formed by LSD1 with histone deacetylases 1/2 may function as a "double-blade razor" that first eliminates the acetyl groups from acetylated Lys residues and then removes the methyl group from Lys4. We suggest that after H3-K4 demethylation, LSD1 recruits the forthcoming chromatin remodelers leading to the introduction of gene repression marks.
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Affiliation(s)
- Federico Forneris
- Dipartimento di Genetica e Microbiologia, Università di Pavia, via Ferrata 1, 27100 Pavia, Italy
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31
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Chen Y, Yang Y, Wang F, Wan K, Yamane K, Zhang Y, Lei M. Crystal structure of human histone lysine-specific demethylase 1 (LSD1). Proc Natl Acad Sci U S A 2006; 103:13956-61. [PMID: 16956976 PMCID: PMC1599895 DOI: 10.1073/pnas.0606381103] [Citation(s) in RCA: 206] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Indexed: 01/23/2023] Open
Abstract
Lysine-specific demethylase 1 (LSD1) was recently identified as the first histone demethylase that specifically demethylates monomethylated and dimethylated histone H3 at K4. It is a component of the CoREST and other corepressor complexes and plays an important role in silencing neuronal-specific genes in nonneuronal cells, but the molecular mechanisms of its action remain unclear. The 2.8-A-resolution crystal structure of the human LSD1 reveals that LSD1 defines a new subfamily of FAD-dependent oxidases. The active center of LSD1 is characterized by a remarkable 1,245-A3 substrate-binding cavity with a highly negative electrostatic potential. Although the protein core of LSD1 resembles other flavoenzymes, its enzymatic activity and functions require two additional structural modules: an N-terminal SWIRM domain important for protein stability and a large insertion in the catalytic domain indispensable both for the demethylase activity and the interaction with CoREST. These results provide a framework for further probing the catalytic mechanism and the functional roles of LSD1.
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Affiliation(s)
- Yong Chen
- *Department of Biological Chemistry, University of Michigan Medical School, 5413 Medical Science I, 1301 Catherine Road, Ann Arbor, MI 48109-0606; and
| | - Yuting Yang
- *Department of Biological Chemistry, University of Michigan Medical School, 5413 Medical Science I, 1301 Catherine Road, Ann Arbor, MI 48109-0606; and
| | - Feng Wang
- *Department of Biological Chemistry, University of Michigan Medical School, 5413 Medical Science I, 1301 Catherine Road, Ann Arbor, MI 48109-0606; and
| | - Ke Wan
- *Department of Biological Chemistry, University of Michigan Medical School, 5413 Medical Science I, 1301 Catherine Road, Ann Arbor, MI 48109-0606; and
| | - Kenichi Yamane
- Howard Hughes Medical Institute and Department of Radiation Oncology, University of North Carolina, Box 7512, 101 Manning Drive, Chapel Hill, NC 27514
| | - Yi Zhang
- Howard Hughes Medical Institute and Department of Radiation Oncology, University of North Carolina, Box 7512, 101 Manning Drive, Chapel Hill, NC 27514
| | - Ming Lei
- *Department of Biological Chemistry, University of Michigan Medical School, 5413 Medical Science I, 1301 Catherine Road, Ann Arbor, MI 48109-0606; and
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32
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Lewis DFV, Ito Y, Goldfarb PS. Investigating human P450s involved in drug metabolism via homology with high-resolution P450 crystal structures of the CYP2C subfamily. Curr Drug Metab 2006; 7:589-98. [PMID: 16918314 DOI: 10.2174/138920006778017812] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The important role of high-resolution crystal structures of cytochrome P450 (CYP) enzymes for the generation of P450 models by homology is discussed. The main focus is on human P450 enzymes involved in drug metabolism, where the role of homology modelling has been emphasized in the recent literature. Report of the first human P450 crystal structure has provided an opportunity for comparison between those modelled from other crystallographic templates, and the recent substrate-bound rabbit CYP2C5 structure exemplifies the relevance of high-resolution template structures to generating 3-D models of P450s where the homology is relatively high. In particular, the homology models of human CYP1 and CYP2 family enzymes are presented, where good agreement with experiment findings are apparent.
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Affiliation(s)
- David F V Lewis
- School of Biomedical and Molecular Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK.
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33
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Tochio N, Umehara T, Koshiba S, Inoue M, Yabuki T, Aoki M, Seki E, Watanabe S, Tomo Y, Hanada M, Ikari M, Sato M, Terada T, Nagase T, Ohara O, Shirouzu M, Tanaka A, Kigawa T, Yokoyama S. Solution structure of the SWIRM domain of human histone demethylase LSD1. Structure 2006; 14:457-68. [PMID: 16531230 DOI: 10.1016/j.str.2005.12.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Revised: 11/06/2005] [Accepted: 12/15/2005] [Indexed: 11/21/2022]
Abstract
SWIRM is an evolutionarily conserved domain involved in several chromatin-modifying complexes. Recently, the LSD1 protein, which bears a SWIRM domain, was found to be a demethylase for Lys4-methylated histone H3. Here, we report a solution structure of the SWIRM domain of human LSD1. It forms a compact fold composed of 6 alpha helices, in which a 20 amino acid long helix (alpha4) is surrounded by 5 other short helices. The SWIRM domain structure could be divided into the N-terminal part (alpha1-alpha3) and the C-terminal part (alpha4-alpha6), which are connected to each other by a salt bridge. While the N-terminal part forms a SWIRM-specific structure, the C-terminal part adopts a helix-turn-helix (HTH)-related fold. We discuss a model in which the SWIRM domain acts as an anchor site for a histone tail.
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Affiliation(s)
- Naoya Tochio
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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34
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Yang M, Gocke CB, Luo X, Borek D, Tomchick DR, Machius M, Otwinowski Z, Yu H. Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase. Mol Cell 2006; 23:377-87. [PMID: 16885027 DOI: 10.1016/j.molcel.2006.07.012] [Citation(s) in RCA: 244] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Revised: 06/24/2006] [Accepted: 07/18/2006] [Indexed: 01/10/2023]
Abstract
Histone methylation regulates diverse chromatin-templated processes, including transcription. Many transcriptional corepressor complexes contain lysine-specific demethylase 1 (LSD1) and CoREST that collaborate to demethylate mono- and dimethylated H3-K4 of nucleosomes. Here, we report the crystal structure of the LSD1-CoREST complex. LSD1-CoREST forms an elongated structure with a long stalk connecting the catalytic domain of LSD1 and the CoREST SANT2 domain. LSD1 recognizes a large segment of the H3 tail through a deep, negatively charged pocket at the active site and possibly a shallow groove on its surface. CoREST SANT2 interacts with DNA. Disruption of the SANT2-DNA interaction diminishes CoREST-dependent demethylation of nucleosomes by LSD1. The shape and dimension of LSD1-CoREST suggest its bivalent binding to nucleosomes, allowing efficient H3-K4 demethylation. This spatially separated, multivalent nucleosome binding mode may apply to other chromatin-modifying enzymes that generally contain multiple nucleosome binding modules.
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Affiliation(s)
- Maojun Yang
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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35
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Zhao Y, Halpert JR. Structure-function analysis of cytochromes P450 2B. Biochim Biophys Acta Gen Subj 2006; 1770:402-12. [PMID: 16935426 DOI: 10.1016/j.bbagen.2006.07.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 07/14/2006] [Accepted: 07/18/2006] [Indexed: 01/11/2023]
Abstract
In the last 4 years, breakthroughs were made in the field of P450 2B (CYP2B) structure-function through determination of one ligand-free and two inhibitor-bound X-ray crystal structures of CYP2B4, which revealed many of the structural features required for binding ligands of different size and shape. Large conformational changes of several plastic regions of CYP2B4 can dramatically reshape the active site of the enzyme to fit the size and shape of the bound ligand without perturbing the overall P450 fold. Solution biophysical studies using isothermal titration calorimetry (ITC) have revealed the large difference in the thermodynamic parameters of CYP2B4 in binding inhibitors of different ring chemistry and side chains. Other studies have revealed that the effects of site-specific mutations on steady-state kinetic parameters and mechanism-based inactivation are often substrate dependent. These findings agree with the structural data that the enzymes adopt different conformations to bind various ligands. Thus, the substrate specificity of an individual enzyme is determined not only by active site residues but also non-active site residues that modulate conformational changes that are important for substrate access and rearrangement of the active site to accommodate the bound substrate.
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Affiliation(s)
- Yonghong Zhao
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX 77555-1031, USA.
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36
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Stavropoulos P, Blobel G, Hoelz A. Crystal structure and mechanism of human lysine-specific demethylase-1. Nat Struct Mol Biol 2006; 13:626-32. [PMID: 16799558 DOI: 10.1038/nsmb1113] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2006] [Accepted: 05/22/2006] [Indexed: 11/09/2022]
Abstract
The reversible methylation of specific lysine residues in histone tails is crucial in epigenetic gene regulation. LSD1, the first known lysine-specific demethylase, selectively removes monomethyl and dimethyl, but not trimethyl modifications of Lys4 or Lys9 of histone-3. Here, we present the crystal structure of LSD1 at 2.9-A resolution. LSD1 forms a highly asymmetric, closely packed domain structure from which a long helical 'tower' domain protrudes. The active site cavity is spacious enough to accommodate several residues of the histone tail substrate, but does not appear capable of recognizing the different methylation states of the substrate lysine. This supports the hypothesis that trimethylated lysine is chemically rather than sterically discriminated. We present a biochemical analysis of LSD1 mutants that identifies crucial residues in the active site cavity and shows the importance of the SWIRM and tower domains for catalysis.
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Affiliation(s)
- Pete Stavropoulos
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
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37
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Winkler A, Hartner F, Kutchan TM, Glieder A, Macheroux P. Biochemical evidence that berberine bridge enzyme belongs to a novel family of flavoproteins containing a bi-covalently attached FAD cofactor. J Biol Chem 2006; 281:21276-21285. [PMID: 16728404 DOI: 10.1074/jbc.m603267200] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Berberine bridge enzyme (BBE) is involved in the transformation of (S)-reticuline to (S)-scoulerine in benzophenanthridine alkaloid biosynthesis of plants. In this report, we describe the high level expression of BBE encoded by the gene from Eschscholzia californica (California poppy) in the methylotrophic yeast Pichia pastoris employing the secretory pathway of the host organism. Using a two-step chromatographic purification protocol, 120 mg of BBE could be obtained from 1 liter of fermentation culture. The purified protein exhibits a turnover number for substrate conversion of 8.2 s(-1). The recombinant enzyme is glycosylated and carries a covalently attached FAD cofactor. In addition to the previously known covalent attachment of the 8alpha-position of the flavin ring system to a histidine (His-104), we could also demonstrate that a covalent linkage between the 6-position and a thiol group of a cysteine residue (Cys-166) is present in BBE. The major evidence for the occurrence of a bi-covalently attached FAD cofactor is provided by N-terminal amino acid sequencing and mass spectrometric analysis of the isolated flavin-containing peptide. Furthermore, it could be shown that anaerobic photoirradiation leads to cleavage of the linkage between the 6-cysteinyl group yielding 6-mercaptoflavin and a peptide with the cysteine residue replaced by alanine due to breakage of the C-S bond. Overall, BBE is shown to exhibit typical flavoprotein oxidase properties as exemplified by the occurrence of an anionic flavin semiquinone species and formation of a flavin N(5)-sulfite adduct.
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Affiliation(s)
- Andreas Winkler
- Graz University of Technology, Institute of Biochemistry, Petersgasse 12/II, A-8010 Graz, Austria
| | - Franz Hartner
- Research Centre Applied Biocatalysis, c/o Graz University of Technology, Institute of Molecular Biotechnology, A-8010 Graz, Austria
| | - Toni M Kutchan
- Abteilung Naturstoff-Biotechnologie, Leibniz-Institut für Pflanzenbiochemie, D-06120 Halle/Saale, Germany
| | - Anton Glieder
- Research Centre Applied Biocatalysis, c/o Graz University of Technology, Institute of Molecular Biotechnology, A-8010 Graz, Austria
| | - Peter Macheroux
- Graz University of Technology, Institute of Biochemistry, Petersgasse 12/II, A-8010 Graz, Austria.
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Genest O, Seduk F, Ilbert M, Méjean V, Iobbi-Nivol C. Signal peptide protection by specific chaperone. Biochem Biophys Res Commun 2006; 339:991-5. [PMID: 16337610 DOI: 10.1016/j.bbrc.2005.11.107] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Accepted: 11/18/2005] [Indexed: 10/25/2022]
Abstract
TorD is the private chaperone of TorA, a periplasmic respiratory molybdoenzyme of Escherichia coli. In this study, it is demonstrated that TorD is required to maintain the integrity of the twin-arginine signal sequence of the cytoplasmic TorA precursors. In the absence of TorD, 35 out of the 39 amino acid residues of the signal peptide were lost and the proteolysis of the N-terminal extremity of TorA precursors was not prevented by the molybdenum cofactor insertion. We thus propose that one of the main roles of TorD is to protect the TorA signal peptide to allow translocation of the enzyme by the TAT system.
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Affiliation(s)
- Olivier Genest
- Laboratoire de Chimie Bactérienne, Institut de Biologie Structurale et Microbiologie, Centre National de la Recherche Scientifique Marseille, France
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39
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Tsukada YI, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, Zhang Y. Histone demethylation by a family of JmjC domain-containing proteins. Nature 2005; 439:811-6. [PMID: 16362057 DOI: 10.1038/nature04433] [Citation(s) in RCA: 1546] [Impact Index Per Article: 81.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Accepted: 11/15/2005] [Indexed: 12/13/2022]
Abstract
Covalent modification of histones has an important role in regulating chromatin dynamics and transcription. Whereas most covalent histone modifications are reversible, until recently it was unknown whether methyl groups could be actively removed from histones. Using a biochemical assay coupled with chromatography, we have purified a novel JmjC domain-containing protein, JHDM1 (JmjC domain-containing histone demethylase 1), that specifically demethylates histone H3 at lysine 36 (H3-K36). In the presence of Fe(ii) and alpha-ketoglutarate, JHDM1 demethylates H3-methyl-K36 and generates formaldehyde and succinate. Overexpression of JHDM1 reduced the level of dimethyl-H3-K36 (H3K36me2) in vivo. The demethylase activity of the JmjC domain-containing proteins is conserved, as a JHDM1 homologue in Saccharomyces cerevisiae also has H3-K36 demethylase activity. Thus, we identify the JmjC domain as a novel demethylase signature motif and uncover a protein demethylation mechanism that is conserved from yeast to human.
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Affiliation(s)
- Yu-ichi Tsukada
- Howard Hughes Medical Institute, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295, USA
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40
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Holbert MA, Marmorstein R. Structure and activity of enzymes that remove histone modifications. Curr Opin Struct Biol 2005; 15:673-80. [PMID: 16263263 DOI: 10.1016/j.sbi.2005.10.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2005] [Revised: 08/17/2005] [Accepted: 10/20/2005] [Indexed: 01/16/2023]
Abstract
The post-translational modification of histones plays an important role in chromatin regulation, a process that insures the fidelity of gene expression and other DNA transactions. Equally important as the enzymes that generate these modifications are the enzymes that remove them. Recent studies have identified some of the enzymes that remove histone modifications and have characterized their activities. In addition, structural and biochemical studies of these enzymes have focused on the histone lysine deacetylases HDAC8 and sirtuins, and on the arginine and lysine demethylases PAD and BHC110/LSD1, respectively. These new findings may be used as a context to present new information that contributes to our understanding of chromatin regulation, and to pose remaining questions pertaining to the activities of these enzymes and the roles they play in chromatin regulation.
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Affiliation(s)
- Marc A Holbert
- The Wistar Institute and The Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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41
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Abstract
The effect of temperature on the rates of monoxygenase reactions was studied with microsomes prepared from phenobarbital pretreated rats. The rates of the N-demethylation of ethylmorphine, benzphethamine, aminopyrine, and p-nitroanisole were studied. Breaks at temperatures around 24 degrees C were observed in the Arrhenius plots of all these reactions. The energy of activation of these reactions has values of 10-12 and 19-21 kcal per mol at temperature ranges above and below the break temperature, respectively. The break, however, was not observed if 30% glycerol was added to the microsomes. The Arrhenius plot of the microsomal NADPH-cytochrome c reductase activity also did not show any break. The implications of these observations in relationship to the fluidity of the membrane, the translational mobility of membrane enzymes, and the rate of monoxygenase reactions are discussed.
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Affiliation(s)
- C S Yang
- Department of Biochemistry, New Jersey Medical School, CMDNJ Newark, NJ 07103, USA
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42
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Mitsuda M, Iwasaki M. Improvement in the expression of CYP2B6 by co-expression with molecular chaperones GroES/EL in Escherichia coli. Protein Expr Purif 2005; 46:401-5. [PMID: 16310378 DOI: 10.1016/j.pep.2005.10.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Revised: 09/24/2005] [Accepted: 10/18/2005] [Indexed: 10/25/2022]
Abstract
Improvement of CYP2B6 expression was examined by co-expression with molecular chaperones GroES/EL. Although a CO-reduced difference spectrum was not detected in Escherichia coli transformed only by the CYP2B6-expressing vector, co-expression of GroES/EL resulted in high-level expression which reached over 2000 nmol P450/L. CYP2B6 was purified from the E. coli membrane with a high yield. Purified CYP2B6 showed 7-ethoxy-4-trifluoromethylcoumarin O-deethylase activity in a reconstitution system. This expression system would be useful for the production of large amounts of active CYP2B6 and for the detailed analysis of the enzyme.
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Affiliation(s)
- Maori Mitsuda
- Department of Biology, Graduate School of Science, Osaka University, 2-17-85, Jusohonmachi, Osaka 532-8686, Japan
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43
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Toogood HS, van Thiel A, Scrutton NS, Leys D. Stabilization of Non-productive Conformations Underpins Rapid Electron Transfer to Electron-transferring Flavoprotein. J Biol Chem 2005; 280:30361-6. [PMID: 15975918 DOI: 10.1074/jbc.m505562200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Crystal structures of protein complexes with electron-transferring flavoprotein (ETF) have revealed a dual protein-protein interface with one region serving as anchor while the ETF FAD domain samples available space within the complex. We show that mutation of the conserved Glu-165beta in human ETF leads to drastically modulated rates of interprotein electron transfer with both medium chain acyl-CoA dehydrogenase and dimethylglycine dehydrogenase. The crystal structure of free E165betaA ETF is essentially identical to that of wild-type ETF, but the crystal structure of the E165betaA ETF.medium chain acyl-CoA dehydrogenase complex reveals clear electron density for the FAD domain in a position optimal for fast interprotein electron transfer. Based on our observations, we present a dynamic multistate model for conformational sampling that for the wild-type ETF. medium chain acyl-CoA dehydrogenase complex involves random motion between three distinct positions for the ETF FAD domain. ETF Glu-165beta plays a key role in stabilizing positions incompatible with fast interprotein electron transfer, thus ensuring high rates of complex dissociation.
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Affiliation(s)
- Helen S Toogood
- Department of Biochemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, LE1 7RH, Leicester United Kingdom
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44
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Ida K, Moriguchi T, Suzuki H. Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96. Biochem Biophys Res Commun 2005; 333:359-66. [PMID: 15946648 DOI: 10.1016/j.bbrc.2005.05.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Accepted: 05/19/2005] [Indexed: 11/23/2022]
Abstract
Sarcosine oxidase from Corynebacterium sp. U-96 is a heterotetrameric enzyme. Here we report the crystal structures of the enzyme in complex with dimethylglycine and folinic acid. The alpha subunit is composed of two domains, contains NAD(+), and binds folinic acid. The beta subunit contains dimethylglycine, FAD, and FMN, and these flavins are approximately 10A apart. The gamma subunit is in contact with two domains of alpha subunit and has possibly a folate-binding structure. The delta subunit contains a single atom of zinc and has a Cys(3)His zinc finger structure. Based on the structures determined and on the previous works, the structure-function relationship on the heterotetrameric sarcosine oxidase is discussed.
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Affiliation(s)
- Koh Ida
- Department of Biosciences, School of Science, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555, Japan.
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45
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Abstract
N-Methyltryptophan oxidase (MTOX), a flavoenzyme from Escherichia coli, catalyzes the oxidative demethylation of secondary amino acids such as N-methyltryptophan or N-methylglycine (sarcosine). MTOX is one of several flavin-dependent amine oxidases whose chemical mechanism is still debated. The kinetic properties of MTOX with the slow substrate sarcosine were determined. Initial rate data are well-described by the equation for a ping-pong kinetic mechanism, in that the V/K(O)()2 value is independent of the sarcosine concentration at all accessible concentrations of oxygen. The k(cat)/K(sarc) pH profile is bell-shaped, with pK(a) values of 8.8 and about 10; the latter value matches the pK(a) value of the substrate nitrogen. The k(cat) pH profile exhibits a single pK(a) value of 9.1 for a group that must be unprotonated for catalysis. There is no significant solvent isotope effect on the k(cat)/K(sarc) value. With N-methyl-(2)H(3)-glycine as the substrate, there is a pH-independent kinetic isotope effect on k(cat), k(cat)/K(sarc), and the rate constant for flavin reduction, with an average value of 7.2. Stopped-flow spectroscopy with both the protiated and deuterated substrate failed to detect any intermediates between the enzyme-substrate complex and the fully reduced enzyme. These results are used to evaluate proposed chemical mechanisms.
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Affiliation(s)
- Erik C Ralph
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
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46
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Brizio C, Brandsch R, Bufano D, Pochini L, Indiveri C, Barile M. Over-expression in Escherichia coli, functional characterization and refolding of rat dimethylglycine dehydrogenase. Protein Expr Purif 2005; 37:434-42. [PMID: 15358367 DOI: 10.1016/j.pep.2004.06.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Revised: 06/08/2004] [Indexed: 11/17/2022]
Abstract
Dimethylglycine dehydrogenase (Me(2)GlyDH) is a mitochondrial enzyme that catalyzes the oxidative demethylation of dimethylglycine to sarcosine. The enzyme requires flavin adenine dinucleotide (FAD), which is covalently bound to the apoprotein via a histidyl(N3)-(8alpha)FAD linkage. In the present study, the mature form of rat Me(2)GlyDH has been over-expressed in Escherichia coli as an N-terminally 6-His-tagged fusion protein. The over-expressed protein distributed almost equally between the soluble and insoluble (inclusion bodies) cell fraction. By applying the soluble cell lysate to a nickel-chelating column, two fractions were eluted, both containing a nearly homogeneous protein with a molecular mass of 93 kDa, on SDS-PAGE. The first protein fraction was identified by Western blotting analysis as the covalently flavinylated Me(2)GlyDH. It showed optical properties and specific activity (240 nmol/min/mg protein) similar to those of the native holoenzyme. The second fraction was identified as an underflavinylated (apo-) form of Me(2)GlyDH, with a 70% lower specific activity. The recombinant holoenzyme exhibited optimal activity at pH 8.5, an activation energy of about 80 kJ/mol, and two KM values for N,N-dimethylglycine (KM1 = 0.05 mM and KM2 = 9.4 mM), as described for the native holoenzyme. Starting from the inclusion bodies, the unfolded flavinylated enzyme was solubilized by SDS treatment and refolded by an 80-fold dilution step, with a reactivation yield of 50-60%.
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Affiliation(s)
- Carmen Brizio
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Bari, Via Orabona 4, 70126 Bari, Italy
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47
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Limburg J, Mure M, Klinman JP. Cloning and characterization of histamine dehydrogenase from Nocardioides simplex. Arch Biochem Biophys 2005; 436:8-22. [PMID: 15752704 DOI: 10.1016/j.abb.2004.11.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2004] [Revised: 11/24/2004] [Indexed: 11/16/2022]
Abstract
Histamine dehydrogenase (NSHADH) can be isolated from cultures of Nocardioides simplex grown with histamine as the sole nitrogen source. A previous report suggested that NSHADH might contain the quinone cofactor tryptophan tryptophyl quinone (TTQ). Here, the hdh gene encoding NSHADH is cloned from the genomic DNA of N. simplex, and the isolated enzyme is subjected to a full spectroscopic characterization. Protein sequence alignment shows NSHADH to be related to trimethylamine dehydrogenase (TMADH: EC 1.5.99.7), where the latter contains a bacterial ferredoxin-type [4Fe-4S] cluster and 6-S-cysteinyl FMN cofactor. NSHADH has no sequence similarity to any TTQ containing amine dehydrogenases. NSHADH contains 3.6+/-0.3 mol Fe and 3.7+/-0.2 mol acid labile S per subunit. A comparison of the UV/vis spectra of NSHADH and TMADH shows significant similarity. The EPR spectrum of histamine reduced NSHADH also supports the presence of the flavin and [4Fe-4S] cofactors. Importantly, we show that NSHADH has a narrow substrate specificity, oxidizing only histamine (K(m)=31+/-11 microM, k(cat)/K(m)=2.1 (+/-0.4)x10(5)M(-1)s(-1)), agmatine (K(m)=37+/-6 microM, k(cat)/K(m)=6.0 (+/-0.6)x10(4)M(-1)s(-1)), and putrescine (K(m)=1280+/-240 microM, k(cat)/K(m)=1500+/-200 M(-1)s(-1)). A kinetic characterization of the oxidative deamination of histamine by NSHADH is presented that includes the pH dependence of k(cat)/K(m) (histamine) and the measurement of a substrate deuterium isotope effect, (D)(k(cat)/K(m) (histamine))=7.0+/-1.8 at pH 8.5. k(cat) is also pH dependent and has a reduced substrate deuterium isotope of (D)(k(cat))=1.3+/-0.2.
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Affiliation(s)
- Julian Limburg
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA.
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48
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Leys D, Basran J, Talfournier F, Chohan KK, Munro AW, Sutcliffe MJ, Scrutton NS. Flavin radicals, conformational sampling and robust design principles in interprotein electron transfer: the trimethylamine dehydrogenase-electron-transferring flavoprotein complex. Biochem Soc Symp 2005:1-14. [PMID: 15777008 DOI: 10.1042/bss0710001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
TMADH (trimethylamine dehydrogenase) is a complex iron-sulphur flavoprotein that forms a soluble electron-transfer complex with ETF (electron-transferring flavoprotein). The mechanism of electron transfer between TMADH and ETF has been studied using stopped-flow kinetic and mutagenesis methods, and more recently by X-ray crystallography. Potentiometric methods have also been used to identify key residues involved in the stabilization of the flavin radical semiquinone species in ETF. These studies have demonstrated a key role for 'conformational sampling' in the electron-transfer complex, facilitated by two-site contact of ETF with TMADH. Exploration of three-dimensional space in the complex allows the FAD of ETF to find conformations compatible with enhanced electronic coupling with the 4Fe-4S centre of TMADH. This mechanism of electron transfer provides for a more robust and accessible design principle for interprotein electron transfer compared with simpler models that invoke the collision of redox partners followed by electron transfer. The structure of the TMADH-ETF complex confirms the role of key residues in electron transfer and molecular assembly, originally suggested from detailed kinetic studies in wild-type and mutant complexes, and from molecular modelling.
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Affiliation(s)
- David Leys
- Department of Biochemistry, University of Leicester, University Road, Leicester LEI 7RH, UK
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49
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Lomtev AS, Bobrov AG, Vekshin NL. [The release of flavin adenine dinucleotide upon local conformational transition in electron-transferring flavoprotein induced by trimethylamine dehydrogenase]. Bioorg Khim 2005; 30:247-53. [PMID: 15344654 DOI: 10.1023/b:rubi.0000030128.70128.07] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The electron-transferring proteins, trimethylamine dehydrogenase (TMAD) and electron-transferring flavoprotein (ETF) from the bacterium Methylophilius methylotrophus, were studied in vitro by fluorescence spectroscopy. Flavin adenine dinucleotide (FAD) was found to be capable of a slow and spontaneous release from ETF, which is accompanied by an increase in flavin fluorescence. At a rather high ionic strength (0.1 M NaCl or 50 mM phosphate), the FAD release is sharply activated by TMAD preparations that induce a local conformational transition in ETF. The values of tryptophan fluorescence polarization and lifetime and the use of the Levshin-Perrin equation helped show that the size of protein particles remain unchanged upon the TMAD and ETF mixing; i.e., these proteins themselves do not form a stable complex with each other. The protein mixture did not release flavin from ETF in the presence of trimethylamine and formaldehyde. In this case, a stable complex between the proteins appeared to be formed under the action of formaldehyde. Upon a short-term incubation of ETF with ferricyanide, FAD was hydrolyzed to flavin mononucleotide (FMN) and AMP. This fact explains the previous detection of AMP in ETF preparations by some researches. A fluorescence method was proposed for distinguishing FAD from FMN in solution using ethylene glycol. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 3; see also http://www.maik.ru.
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Zukunft J, Lang T, Richter T, Hirsch-Ernst KI, Nussler AK, Klein K, Schwab M, Eichelbaum M, Zanger UM. A natural CYP2B6 TATA box polymorphism (-82T--> C) leading to enhanced transcription and relocation of the transcriptional start site. Mol Pharmacol 2005; 67:1772-82. [PMID: 15722458 DOI: 10.1124/mol.104.008086] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We investigated the impact of promoter polymorphisms on transcription of the human CYP2B6 gene. In total, 98 DNA samples from white persons from a previously characterized liver bank were sequenced throughout 2.3 kilobases of upstream sequence and haplotype structures were determined using additional coding sequence information. HepG2 cells and primary rat and human hepatocytes were transfected with luciferase reporter gene constructs driven by 2033 base pairs (bp) of the most frequent promoter variants. The novel haplotype *22 (-1848C--> A, -801G--> T, -750T--> C, and -82T--> C) showed 3- to 9-fold enhanced transcriptional activity in all transfected cells. Constructs containing single mutations surprisingly revealed -82T--> C, predicted to disrupt a putative TATA box, to be alone responsible for this effect. In silico analysis and electrophoretic mobility shift assay demonstrated conversion of the putative TATA box into a functional CCAAT/enhancer-binding protein binding site. Analysis of transcriptional start sites showed the mutant promoter to be transcribed from a start site located approximately 30 bp downstream of the wild-type start site, consistent with the use of a noncanonical TATA box at -55 bp. Median CYP2B6 mRNA expression and bupropion hydroxylase activity as a selective marker of CYP2B6 catalytic activity were approximately 2-fold higher in livers genotyped -82TC as in those genotyped -82TT (20.4 versus 9.8 arbitrary units, p = 0.007, and 201.8 versus 106.7 pmol/mg/min, p = 0.042, respectively). This promoter polymorphism thus contributes to CYP2B6 functional variability and represents a novel mechanism by which mutations can enhance transcription. Furthermore, a detailed interspecies comparison of CYP2B promoters and transcriptional start sites provided novel insights into evolutionary relationships.
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Affiliation(s)
- Jörg Zukunft
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
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