1
|
Nielipinski M, Pietrzyk-Brzezinska AJ, Wlodawer A, Sekula B. Structural analysis and molecular substrate recognition properties of Arabidopsis thaliana ornithine transcarbamylase, the molecular target of phaseolotoxin produced by Pseudomonas syringae. FRONTIERS IN PLANT SCIENCE 2023; 14:1297956. [PMID: 38179474 PMCID: PMC10765591 DOI: 10.3389/fpls.2023.1297956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/17/2023] [Indexed: 01/06/2024]
Abstract
Halo blight is a plant disease that leads to a significant decrease in the yield of common bean crops and kiwi fruits. The infection is caused by Pseudomonas syringae pathovars that produce phaseolotoxin, an antimetabolite which targets arginine metabolism, particularly by inhibition of ornithine transcarbamylase (OTC). OTC is responsible for production of citrulline from ornithine and carbamoyl phosphate. Here we present the first crystal structures of the plant OTC from Arabidopsis thaliana (AtOTC). Structural analysis of AtOTC complexed with ornithine and carbamoyl phosphate reveals that OTC undergoes a significant structural transition when ornithine enters the active site, from the opened to the closed state. In this study we discuss the mode of OTC inhibition by phaseolotoxin, which seems to be able to act only on the fully opened active site. Once the toxin is proteolytically cleaved, it mimics the reaction transition state analogue to fit inside the fully closed active site of OTC. Additionally, we indicate the differences around the gate loop region which rationally explain the resistance of some bacterial OTCs to phaseolotoxin.
Collapse
Affiliation(s)
- Maciej Nielipinski
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Agnieszka J. Pietrzyk-Brzezinska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD, United States
| | - Bartosz Sekula
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| |
Collapse
|
2
|
Barnsley KK, Ondrechen MJ. Enzyme active sites: Identification and prediction of function using computational chemistry. Curr Opin Struct Biol 2022; 74:102384. [DOI: 10.1016/j.sbi.2022.102384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/20/2022] [Accepted: 03/28/2022] [Indexed: 11/03/2022]
|
3
|
Zhu YY, Niu Y, Niu YN, Yang SD. Recent advances in the synthesis and applications of phosphoramides. Org Biomol Chem 2021; 19:10296-10313. [PMID: 34812834 DOI: 10.1039/d1ob01566d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Phosphoramide, as an important framework of many biologically active molecules, has attracted widespread attention in recent decades. It is not only widely used in pharmaceuticals because of its excellent biological activities, but it also shows good performance in organic dyes, flame retardants and extractors. Thus, it is of great significance to develop effective and convenient methods for the synthesis of phosphoramides. In this review, the recent advancements made in the synthesis routes and applications of phosphoramides are discussed. The synthetic strategies of phosphoramides can be separated into five categories: phosphorus halides as the substrate, phosphates as the substrate, phosphorus hydrogen as the substrate, azides as the substrate and other methods. The latest examples of these methods are provided and some representative mechanisms are also described.
Collapse
Affiliation(s)
- Yuan-Yuan Zhu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
| | - Yuan Niu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
| | - Yan-Ning Niu
- Department of Teaching and Research, Nanjing Forestry University, Huaian 223003, P. R. China
| | - Shang-Dong Yang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
| |
Collapse
|
4
|
Couchet M, Breuillard C, Corne C, Rendu J, Morio B, Schlattner U, Moinard C. Ornithine Transcarbamylase - From Structure to Metabolism: An Update. Front Physiol 2021; 12:748249. [PMID: 34658931 PMCID: PMC8517447 DOI: 10.3389/fphys.2021.748249] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/07/2021] [Indexed: 12/30/2022] Open
Abstract
Ornithine transcarbamylase (OTC; EC 2.1.3.3) is a ubiquitous enzyme found in almost all organisms, including vertebrates, microorganisms, and plants. Anabolic, mostly trimeric OTCs catalyze the production of L-citrulline from L-ornithine which is a part of the urea cycle. In eukaryotes, such OTC localizes to the mitochondrial matrix, partially bound to the mitochondrial inner membrane and part of channeling multi-enzyme assemblies. In mammals, mainly two organs express OTC: the liver, where it is an integral part of the urea cycle, and the intestine, where it synthesizes citrulline for export and plays a major role in amino acid homeostasis, particularly of L-glutamine and L-arginine. Here, we give an overview on OTC genes and proteins, their tissue distribution, regulation, and physiological function, emphasizing the importance of OTC and urea cycle enzymes for metabolic regulation in human health and disease. Finally, we summarize the current knowledge of OTC deficiency, a rare X-linked human genetic disorder, and its emerging role in various chronic pathologies.
Collapse
Affiliation(s)
- Morgane Couchet
- Université Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | - Charlotte Breuillard
- Université Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | | | - John Rendu
- Centre Hospitalier Université Grenoble Alpes, Grenoble, France
| | - Béatrice Morio
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Lyon, France
| | - Uwe Schlattner
- Université Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France.,Institut Universitaire de France, Paris, France
| | - Christophe Moinard
- Université Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| |
Collapse
|
5
|
Ornithine carbamoyltransferase from psychrophiles to thermophiles: structural evolution of catalytic fold to accommodate physiological diversity. Extremophiles 2020; 25:15-24. [PMID: 33084979 DOI: 10.1007/s00792-020-01208-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/07/2020] [Indexed: 10/23/2022]
Abstract
Here, we have analyzed the enzyme ornithine carbamoyltransferase (OCTase) in different classes of microorganisms belonging to psychrophiles, mesophiles and thermophiles. This OCTase catalyzes the formation of citrulline from carbamoyl phosphate (CP) and ornithine (ORN) in arginine biosynthesis pathway and has certain unique adaptations to regulate metabolic pathways in extreme conditions. The tertiary structure of OCTase showed two binding domains, the CP domain and ORN-binding domain at N and C terminals, respectively. We propose general acid-base catalysis in Pseudomonas gessardii between His259 and Asp220 in which later may act as a recipient of proton in the process. The comparative docking analysis showed that substrate-binding loops have been evolved to accommodate their lifestyles across the physiological temperature range where two substrates bind on two distinct loops in psychrophiles and mesophiles, whereas both the substrates bind on a single-substrate-binding loop in thermophiles and bring down the flexibility of the active site pocket to improve its evolutionary fitness.
Collapse
|
6
|
Yan Y, Liu N, Tang Y. Recent developments in self-resistance gene directed natural product discovery. Nat Prod Rep 2020; 37:879-892. [PMID: 31912842 PMCID: PMC7340575 DOI: 10.1039/c9np00050j] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: 2000 to 2019Natural products (NPs) are important sources of human therapeutic agents and pesticides. To prevent self-harm from bioactive NPs, some microbial producers employ self-resistance genes to protect themselves. One effective strategy is to employ a self-resistance enzyme (SRE), which is a slightly mutated version of the original metabolic enzyme, and is resistant to the toxic NP but is still functional. The presence of a SRE in a gene cluster can serve as a predictive window to the biological activity of the NPs synthesized by the pathway. In this highlight, we summarize representative examples of NP biosynthetic pathways that utilize self-resistance genes for protection. Recent discoveries based on self-resistance gene identification have helped in bridging the gap between activity-guided and genome-driven approaches for NP discovery and functional assignment.
Collapse
Affiliation(s)
- Yan Yan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
| | | | | |
Collapse
|
7
|
Ngu L, Winters JN, Nguyen K, Ramos KE, DeLateur NA, Makowski L, Whitford PC, Ondrechen MJ, Beuning PJ. Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase. PLoS One 2020; 15:e0228487. [PMID: 32027716 PMCID: PMC7004355 DOI: 10.1371/journal.pone.0228487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 01/16/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding how enzymes achieve their tremendous catalytic power is a major question in biochemistry. Greater understanding is also needed for enzyme engineering applications. In many cases, enzyme efficiency and specificity depend on residues not in direct contact with the substrate, termed remote residues. This work focuses on Escherichia coli ornithine transcarbamoylase (OTC), which plays a central role in amino acid metabolism. OTC has been reported to undergo an induced-fit conformational change upon binding its first substrate, carbamoyl phosphate (CP), and several residues important for activity have been identified. Using computational methods based on the computed chemical properties from theoretical titration curves, sequence-based scores derived from evolutionary history, and protein surface topology, residues important for catalytic activity were predicted. The roles of these residues in OTC activity were tested by constructing mutations at predicted positions, followed by steady-state kinetics assays and substrate binding studies with the variants. First-layer mutations R57A and D231A, second-layer mutation H272L, and third-layer mutation E299Q, result in 57- to 450-fold reductions in kcat/KM with respect to CP and 44- to 580-fold reductions with respect to ornithine. Second-layer mutations D140N and Y160S also reduce activity with respect to ornithine. Most variants had decreased stability relative to wild-type OTC, with variants H272L, H272N, and E299Q having the greatest decreases. Variants H272L, E299Q, and R57A also show compromised CP binding. In addition to direct effects on catalytic activity, effects on overall protein stability and substrate binding were observed that reveal the intricacies of how these residues contribute to catalysis.
Collapse
Affiliation(s)
- Lisa Ngu
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, United States of America
| | - Jenifer N. Winters
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, United States of America
| | - Kien Nguyen
- Department of Physics, Northeastern University, Boston, MA, United States of America
| | - Kevin E. Ramos
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, United States of America
| | - Nicholas A. DeLateur
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, United States of America
| | - Lee Makowski
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, United States of America
- Department of Bioengineering, Northeastern University, Boston, MA, United States of America
| | - Paul C. Whitford
- Department of Physics, Northeastern University, Boston, MA, United States of America
| | - Mary Jo Ondrechen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, United States of America
- * E-mail: (MJO); (PJB)
| | - Penny J. Beuning
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, United States of America
- * E-mail: (MJO); (PJB)
| |
Collapse
|
8
|
Tan M, Zheng W, Yang L, Zhou L, Zeng Q. I
2
‐Catalyzed Oxidative N−P Cross‐Coupling of Diarylphosphine Oxides and Sulfoximines. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900476] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Mingchao Tan
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection College of Materials, Chemistry & Chemical EngineeringChengdu University of Technology Chengdu 610059 P. R. China
| | - Wenting Zheng
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection College of Materials, Chemistry & Chemical EngineeringChengdu University of Technology Chengdu 610059 P. R. China
| | - Lu Yang
- Department of Chemistry Graduate School of ScienceTohoku University 6-3 Azaaoba Aramaki, Aoba-ku Sendai 980-8578 Japan
| | - Lihong Zhou
- College of Environment and EcologyChengdu University of Technology Chengdu 610059 P. R. China
| | - Qingle Zeng
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection College of Materials, Chemistry & Chemical EngineeringChengdu University of Technology Chengdu 610059 P. R. China
| |
Collapse
|
9
|
O'Neill EC, Schorn M, Larson CB, Millán-Aguiñaga N. Targeted antibiotic discovery through biosynthesis-associated resistance determinants: target directed genome mining. Crit Rev Microbiol 2019; 45:255-277. [PMID: 30985219 DOI: 10.1080/1040841x.2019.1590307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Intense competition between microbes in the environment has directed the evolution of antibiotic production in bacteria. Humans have harnessed these natural molecules for medicinal purposes, magnifying them from environmental concentrations to industrial scale. This increased exposure to antibiotics has amplified antibiotic resistance across bacteria, spurring a global antimicrobial crisis and a search for antibiotics with new modes of action. Genetic insights into these antibiotic-producing microbes reveal that they have evolved several resistance strategies to avoid self-toxicity, including product modification, substrate transport and binding, and target duplication or modification. Of these mechanisms, target duplication or modification will be highlighted in this review, as it uniquely links an antibiotic to its mode of action. We will further discuss and propose a strategy to mine microbial genomes for these genes and their associated biosynthetic gene clusters to discover novel antibiotics using target directed genome mining.
Collapse
Affiliation(s)
- Ellis C O'Neill
- a Department of Plant Sciences, University of Oxford , Oxford , Oxfordshire , UK
| | - Michelle Schorn
- b Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego , CA , USA
| | - Charles B Larson
- b Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego , CA , USA
| | - Natalie Millán-Aguiñaga
- c Universidad Autónoma de Baja California, Facultad de Ciencias Marinas , Ensenada , Baja California , México
| |
Collapse
|
10
|
Aguilera S, Alvarez-Morales A, Murillo J, Hernández-Flores JL, Bravo J, De la Torre-Zavala S. Temperature-mediated biosynthesis of the phytotoxin phaseolotoxin by Pseudomonas syringae pv. phaseolicola depends on the autoregulated expression of the phtABC genes. PLoS One 2017; 12:e0178441. [PMID: 28570637 PMCID: PMC5453526 DOI: 10.1371/journal.pone.0178441] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/12/2017] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas syringae pv. phaseolicola produces phaseolotoxin in a temperature dependent manner, being optimally synthesized between 18°C and 20°C, while no detectable amounts are present above 28°C. The Pht cluster, involved in the biosynthesis of phaseolotoxin, contains 23 genes that are organized in five transcriptional units. The function of most of the genes from the Pht cluster is still unknown and little information about the regulatory circuitry leading to expression of these genes has been reported. The purpose of the present study was to investigate the participation of pht genes in the regulation of the operons coded into the Pht cluster. We conducted Northern blot, uidA fusions and reverse transcription-PCR assays of pht genes in several mutants unable to produce phaseolotoxin. This allowed us to determine that, in P. syringae pv. phaseolicola NPS3121, genes phtABC are essential to prevent their own expression at 28°C, a temperature at which no detectable amounts of the toxin are present. We obtained evidence that the phtABC genes also participate in the regulation of the phtD, phtM and phtL operons. According to our results, we propose that PhtABC and other Pht product activities could be involved in the synthesis of the sulfodiaminophosphinyl moiety of phaseolotoxin, which indirectly could be involved in the transcriptional regulation of the phtA operon.
Collapse
Affiliation(s)
- Selene Aguilera
- Laboratorio Integral de Investigación en Alimentos. CONACYT-Instituto Tecnológico de Tepic, Tepic, Nayarit, México
- * E-mail:
| | - Ariel Alvarez-Morales
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, México
| | - Jesús Murillo
- Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Spain
| | - José Luis Hernández-Flores
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, México
| | - Jaime Bravo
- Laboratorio Integral de Investigación en Alimentos. Instituto Tecnológico de Tepic, Tepic, Nayarit, México
| | - Susana De la Torre-Zavala
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| |
Collapse
|
11
|
Li M, Chen L, Deng Z, Zhao C. Characterization of AmtA, an amidinotransferase involved in the biosynthesis of phaseolotoxins. FEBS Open Bio 2016; 6:603-9. [PMID: 27419063 PMCID: PMC4887976 DOI: 10.1002/2211-5463.12071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/05/2016] [Accepted: 04/14/2016] [Indexed: 11/18/2022] Open
Abstract
Phaseolotoxins (PHTs), which are produced by Pseudomonas, belong to a family of phosphoramidate natural products. Two nonproteinogenic amino acid precursors, Nδ(N′‐sulfo‐diaminophosphinyl)‐ornithine (PSOrn) and homoarginine (hArg), are involved in biosynthesis of PHTs. Amidinotransferase AmtA catalyses the formation of hArg, with arginine and lysine as substrates. AmtA was overexpressed and purified in an Escherichia coli system. An in vitro enzyme assay showed that it has stricter substrate specificity than certain other amidinotransferases. Site‐directed mutagenesis experiments showed that the mutation AmtA Met243His244 is an alternative while Met246 is essential for the transamidination activity.
Collapse
Affiliation(s)
- Mi Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University China
| | - Li Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University China
| | - Changming Zhao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University China
| |
Collapse
|
12
|
Shi D, Allewell NM, Tuchman M. From Genome to Structure and Back Again: A Family Portrait of the Transcarbamylases. Int J Mol Sci 2015; 16:18836-64. [PMID: 26274952 PMCID: PMC4581275 DOI: 10.3390/ijms160818836] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 11/18/2022] Open
Abstract
Enzymes in the transcarbamylase family catalyze the transfer of a carbamyl group from carbamyl phosphate (CP) to an amino group of a second substrate. The two best-characterized members, aspartate transcarbamylase (ATCase) and ornithine transcarbamylase (OTCase), are present in most organisms from bacteria to humans. Recently, structures of four new transcarbamylase members, N-acetyl-l-ornithine transcarbamylase (AOTCase), N-succinyl-l-ornithine transcarbamylase (SOTCase), ygeW encoded transcarbamylase (YTCase) and putrescine transcarbamylase (PTCase) have also been determined. Crystal structures of these enzymes have shown that they have a common overall fold with a trimer as their basic biological unit. The monomer structures share a common CP binding site in their N-terminal domain, but have different second substrate binding sites in their C-terminal domain. The discovery of three new transcarbamylases, l-2,3-diaminopropionate transcarbamylase (DPTCase), l-2,4-diaminobutyrate transcarbamylase (DBTCase) and ureidoglycine transcarbamylase (UGTCase), demonstrates that our knowledge and understanding of the spectrum of the transcarbamylase family is still incomplete. In this review, we summarize studies on the structures and function of transcarbamylases demonstrating how structural information helps to define biological function and how small structural differences govern enzyme specificity. Such information is important for correctly annotating transcarbamylase sequences in the genome databases and for identifying new members of the transcarbamylase family.
Collapse
Affiliation(s)
- Dashuang Shi
- Center for Genetic Medicine Research, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
- Department of Integrative Systems Biology, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
| | - Norma M Allewell
- Department of Cell Biology and Molecular Genetics, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, MD 20742, USA.
- Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, MD 20742, USA.
| | - Mendel Tuchman
- Center for Genetic Medicine Research, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
- Department of Integrative Systems Biology, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
| |
Collapse
|
13
|
Ornithine Transcarbamylase ArgK Plays a Dual role for the Self-defense of Phaseolotoxin Producing Pseudomonas syringae pv. phaseolicola. Sci Rep 2015; 5:12892. [PMID: 26256666 PMCID: PMC4530439 DOI: 10.1038/srep12892] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 07/14/2015] [Indexed: 12/19/2022] Open
Abstract
Pseudomonas syringae is a phytopathogenic bacterium widely spread on terrestrial plants. Sulfodiaminophosphinyl tripeptide Phaseolotoxins (PHTs), produced by P. syringae pv. phaseolicola and P. syringae pv. actinidiae, represent a kind of antimetabolic phytotoxins. PHTs inhibit host cell Ornithine transcarbamylase (OTCase) activity and induce Arginine auxotrophic phenotype. The biosynthesis of PHT is temperature dependent, being optically produced at around 18 °C, while blocked above 28 °C. PHT resistant OTCase ArgK acts as a functional replacement of housekeeping OTCase ArgF, which is the acting target of PHT, to confer PHT producers with self-resistance. It was postulated that argK might be regulated directly by a PHT biosynthetic precursor and indirectly by temperature with an unknown manner. Neither transcriptional regulator nor thermal regulation related protein encoding gene was detected from PHT biosynthetic gene cluster. The tripeptide, Cit-Ala-hArg, was identified to be a by-product of PHT biosynthetic pathway in this report. Formation of Cit-Ala-hArg was catalyzed by ArgK with tripeptide Orn-Ala-hArg and carbamyl phosphate as substrates. It showed that ArgK not only provided alternative Arginine source as reported previously, but also controlled the production of PHTs by converting PHT biosynthetic precursors to nontoxic Cit-Ala-hArg reservoir for producers’ self-defense.
Collapse
|
14
|
Fang RS, Dong YC, Xu TY, He GQ, Chen QH. Ethyl carbamate formation regulated by ornithine transcarbamylase and urea metabolism in the processing of Chinese yellow rice wine. Int J Food Sci Technol 2013. [DOI: 10.1111/ijfs.12248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ruo-Si Fang
- Department of Food Science and Nutrition; Zhejiang University; Hangzhou 310058 China
| | - Ya-Chen Dong
- Department of Food Science and Nutrition; Zhejiang University; Hangzhou 310058 China
| | - Teng-Yang Xu
- Department of Food Science and Nutrition; Zhejiang University; Hangzhou 310058 China
| | - Guo-Qing He
- Department of Food Science and Nutrition; Zhejiang University; Hangzhou 310058 China
| | - Qi-He Chen
- Department of Food Science and Nutrition; Zhejiang University; Hangzhou 310058 China
- Food Microbiology Research Key Laboratory of Zhejiang Province; Hangzhou 310058 China
| |
Collapse
|
15
|
Gallego P, Planell R, Benach J, Querol E, Perez-Pons JA, Reverter D. Structural characterization of the enzymes composing the arginine deiminase pathway in Mycoplasma penetrans. PLoS One 2012; 7:e47886. [PMID: 23082227 PMCID: PMC3474736 DOI: 10.1371/journal.pone.0047886] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 09/24/2012] [Indexed: 11/19/2022] Open
Abstract
The metabolism of arginine towards ATP synthesis has been considered a major source of energy for microorganisms such as Mycoplasma penetrans in anaerobic conditions. Additionally, this pathway has also been implicated in pathogenic and virulence mechanism of certain microorganisms, i.e. protection from acidic stress during infection. In this work we present the crystal structures of the three enzymes composing the gene cluster of the arginine deiminase pathway from M. penetrans: arginine deiminase (ADI), ornithine carbamoyltransferase (OTC) and carbamate kinase (CK). The arginine deiminase (ADI) structure has been refined to 2.3 Å resolution in its apo-form, displaying an "open" conformation of the active site of the enzyme in comparison to previous complex structures with substrate intermediates. The active site pocket of ADI is empty, with some of the catalytic and binding residues far from their active positions, suggesting major conformational changes upon substrate binding. Ornithine carbamoyltransferase (OTC) has been refined in two crystal forms at 2.5 Å and 2.6 Å resolution, respectively, both displaying an identical dodecameric structure with a 23-point symmetry. The dodecameric structure of OTC represents the highest level of organization in this protein family and in M.penetrans it is constituted by a novel interface between the four catalytic homotrimers. Carbamate kinase (CK) has been refined to 2.5 Å resolution and its structure is characterized by the presence of two ion sulfates in the active site, one in the carbamoyl phosphate binding site and the other in the β-phosphate ADP binding pocket of the enzyme. The CK structure also shows variations in some of the elements that regulate the catalytic activity of the enzyme. The relatively low number of metabolic pathways and the relevance in human pathogenesis of Mycoplasma penetrans places the arginine deiminase pathway enzymes as potential targets to design specific inhibitors against this human parasite.
Collapse
Affiliation(s)
- Pablo Gallego
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Raquel Planell
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Benach
- Experiments Division, ALBA Synchrotron Light Source, Barcelona, Spain
| | - Enrique Querol
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep A. Perez-Pons
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| |
Collapse
|
16
|
Shabalin IG, Porebski PJ, Cooper DR, Grabowski M, Onopriyenko O, Grimshaw S, Savchenko A, Chruszcz M, Minor W. Structure of anabolic ornithine carbamoyltransferase from Campylobacter jejuni at 2.7 Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1018-24. [PMID: 22949186 PMCID: PMC3433189 DOI: 10.1107/s1744309112031259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 07/09/2012] [Indexed: 11/10/2022]
Abstract
Anabolic ornithine transcarbamoylase (aOTC) catalyzes the reaction between carbamoyl phosphate (CP) and L-ornithine (ORN) to form L-citrulline and phosphate in the urea cycle and L-arginine biosynthesis. The crystal structure of unliganded aOTC from Campylobacter jejuni (Cje aOTC) was determined at 2.7 Å resolution and refined to an R(work) of 20.3% and an R(free) of 24.0%. Cje aOTC is a trimer that forms a head-to-head pseudohexamer in the asymmetric unit. Each monomer is composed of an N-terminal CP-binding domain and a C-terminal ORN-binding domain joined by two interdomain helices. The Cje aOTC structure presents an open conformation of the enzyme with a relatively flexible orientation of the ORN-binding domain respective to the CP-binding domain. The conformation of the B2-H3 loop (residues 68-78), which is involved in binding CP in an adjacent subunit of the trimer, differs from that seen in homologous proteins with CP bound. The loop containing the ORN-binding motif (DxxxSMG, residues 223-230) has a conformation that is different from those observed in unliganded OTC structures from other species, but is similar to those in structures with bound ORN analogs. The major differences in tertiary structure between Cje aOTC and human aOTC are described.
Collapse
Affiliation(s)
- I. G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases, USA
| | - P. J. Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases, USA
| | - D. R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases, USA
| | - M. Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases, USA
| | - O. Onopriyenko
- Center for Structural Genomics of Infectious Diseases, USA
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON M5G 1L6, Canada
| | - S. Grimshaw
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - A. Savchenko
- Center for Structural Genomics of Infectious Diseases, USA
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON M5G 1L6, Canada
| | - M. Chruszcz
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases, USA
| | - W. Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases, USA
| |
Collapse
|
17
|
Shi D, Yu X, Zhao G, Ho J, Lu S, Allewell NM, Tuchman M. Crystal structure and biochemical properties of putrescine carbamoyltransferase from Enterococcus faecalis: Assembly, active site, and allosteric regulation. Proteins 2012; 80:1436-47. [PMID: 22328207 DOI: 10.1002/prot.24042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 01/03/2012] [Accepted: 01/11/2012] [Indexed: 11/09/2022]
Abstract
Putrescine carbamoyltransferase (PTCase) catalyzes the conversion of carbamoylputrescine to putrescine and carbamoyl phosphate (CP), a substrate of carbamate kinase (CK). The crystal structure of PTCase has been determined and refined at 3.2 Å resolution. The trimeric molecular structure of PTCase is similar to other carbamoyltransferases, including the catalytic subunit of aspartate carbamoyltransferase (ATCase) and ornithine carbamoyltransferase (OTCase). However, in contrast to other trimeric carbamoyltransferases, PTCase binds both CP and putrescine with Hill coefficients at saturating concentrations of the other substrate of 1.53 ± 0.03 and 1.80 ± 0.06, respectively. PTCase also has a unique structural feature: a long C-terminal helix that interacts with the adjacent subunit to enhance intersubunit interactions in the molecular trimer. The C-terminal helix appears to be essential for both formation of the functional trimer and catalytic activity, since truncated PTCase without the C-terminal helix aggregates and has only 3% of native catalytic activity. The active sites of PTCase and OTCase are similar, with the exception of the 240's loop. PTCase lacks the proline-rich sequence found in knotted carbamoyltransferases and is unknotted. A Blast search of all available genomes indicates that 35 bacteria, most of which are Gram-positive, have an agcB gene encoding PTCase located near the genes that encode agmatine deiminase and CK, consistent with the catabolic role of PTCase in the agmatine degradation pathway. Sequence comparisons indicate that the C-terminal helix identified in this PTCase structure will be found in all other PTCases identified, suggesting that it is the signature feature of the PTCase family of enzymes.
Collapse
Affiliation(s)
- Dashuang Shi
- Center for Genetic Medicine Research and Department of Integrative Systems Biology, Children's National Medical Center, The George Washington University, Washington, District of Columbia 20010, USA.
| | | | | | | | | | | | | |
Collapse
|
18
|
Huang SY, Zou X. Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function. J Chem Inf Model 2011; 51:2097-106. [PMID: 21830787 DOI: 10.1021/ci2000727] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Based on a statistical mechanics-based iterative method, we have extracted a set of distance-dependent, all-atom pairwise potentials for protein-ligand interactions from the crystal structures of 1300 protein-ligand complexes. The iterative method circumvents the long-standing reference state problem in knowledge-based scoring functions. The resulted scoring function, referred to as ITScore 2.0, has been tested with the CSAR (Community Structure-Activity Resource, 2009 release) benchmark of 345 diverse protein-ligand complexes. ITScore 2.0 achieved a Pearson correlation of R(2) = 0.54 in binding affinity prediction. A comparative analysis has been done on the scoring performances of ITScore 2.0, the van der Waals (VDW) scoring function, the VDW with heavy atoms only, and the force field (FF) scoring function of DOCK which consists of a VDW term and an electrostatic term. The results reveal several important factors that affect the scoring performances, which could be helpful for the improvement of scoring functions.
Collapse
Affiliation(s)
- Sheng-You Huang
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | | |
Collapse
|
19
|
Li Y, Yu X, Ho J, Fushman D, Allewell NM, Tuchman M, Shi D. Reversible post-translational carboxylation modulates the enzymatic activity of N-acetyl-L-ornithine transcarbamylase. Biochemistry 2010; 49:6887-95. [PMID: 20695527 DOI: 10.1021/bi1007386] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-Acetyl-l-ornithine transcarbamylase (AOTCase), rather than ornithine transcarbamylase (OTCase), is the essential carbamylase enzyme in the arginine biosynthesis of several plant and human pathogens. The specificity of this unique enzyme provides a potential target for controlling the spread of these pathogens. Recently, several crystal structures of AOTCase from Xanthomonas campestris (xc) have been determined. In these structures, an unexplained electron density at the tip of the Lys302 side chain was observed. Using (13)C NMR spectroscopy, we show herein that Lys302 is post-translationally carboxylated. The structure of wild-type AOTCase in a complex with the bisubstrate analogue N(delta)-(phosphonoacetyl)-N(alpha)-acetyl-l-ornithine (PALAO) indicates that the carboxyl group on Lys302 forms a strong hydrogen bonding network with surrounding active site residues, Lys252, Ser253, His293, and Glu92 from the adjacent subunit either directly or via a water molecule. Furthermore, the carboxyl group is involved in binding N-acetyl-l-ornithine via a water molecule. Activity assays with the wild-type enzyme and several mutants demonstrate that the post-translational modification of lysine 302 has an important role in catalysis.
Collapse
Affiliation(s)
- Yongdong Li
- Research Center for Genetic Medicine and Department of Integrative Systems Biology, Children's National Medical Center, The George Washington University, Washington, DC 20010, USA
| | | | | | | | | | | | | |
Collapse
|
20
|
Islam Sikdar S, Kim JS. Characterization of a gene encoding ornithine carbamoyltransferase from rice. ACTA ACUST UNITED AC 2009. [DOI: 10.5010/jpb.2009.36.4.397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
21
|
Crystal structure of the hexameric catabolic ornithine transcarbamylase from Lactobacillus hilgardii: Structural insights into the oligomeric assembly and metal binding. J Mol Biol 2009; 393:425-34. [PMID: 19666033 DOI: 10.1016/j.jmb.2009.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/30/2009] [Accepted: 08/01/2009] [Indexed: 11/22/2022]
Abstract
Catabolic ornithine transcarbamylase (cOTC; EC 2.1.3.3) catalyzes the formation of ornithine (ORN) and carbamoyl phosphate from citrulline, which constitutes the second step of the degradation of arginine via the arginine deiminase pathway. Here, we report the crystal structure of cOTC from the lactic acid bacteria Lactobacillus hilgardii (Lh-cOTC) refined to 2.1 A resolution. The structure reveals that Lh-cOTC forms a hexameric assembly, which was also confirmed by gel-filtration chromatography and analytical ultracentrifugation. The homohexamer, with 32 point group symmetry, represents a new oligomeric state within the members of the ornithine transcarbamylase family that are typically homotrimeric or homododecameric. The C-terminal end from each subunit constitutes a key structural element for the stabilization of the hexameric assembly in solution. Additionally, the structure reveals, for the first time in the ornithine transcarbamylase family, a metal-binding site located at the 3-fold molecular symmetry axis of each trimer.
Collapse
|
22
|
Sankaranarayanan R, Cherney MM, Cherney LT, Garen CR, Moradian F, James MNG. The crystal structures of ornithine carbamoyltransferase from Mycobacterium tuberculosis and its ternary complex with carbamoyl phosphate and L-norvaline reveal the enzyme's catalytic mechanism. J Mol Biol 2007; 375:1052-63. [PMID: 18062991 DOI: 10.1016/j.jmb.2007.11.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 11/06/2007] [Accepted: 11/09/2007] [Indexed: 11/27/2022]
Abstract
Mycobacterium tuberculosis ornithine carbamoyltransferase (Mtb OTC) catalyzes the sixth step in arginine biosynthesis; it produces citrulline from carbamoyl phosphate (CP) and ornithine (ORN). Here, we report the crystal structures of Mtb OTC in orthorhombic (form I) and hexagonal (form II) space groups. The molecules in form II are complexed with CP and l-norvaline (NVA); the latter is a competitive inhibitor of OTC. The asymmetric unit in form I contains a pseudo hexamer with 32 point group symmetry. The CP and NVA in form II induce a remarkable conformational change in the 80s and the 240s loops with the displacement of these loops towards the active site. The displacement of these loops is strikingly different from that seen in other OTC structures. In addition, the ligands induce a domain closure of 4.4 degrees in form II. Sequence comparison of active-site residues of Mtb OTC with several other OTCs of known structure reveals that they are virtually identical. The interactions involving the active-site residues of Mtb OTC with CP and NVA and a modeling study of ORN in the form II structure strongly rule out an earlier proposed mechanistic role of Cys264 in catalysis and suggest a possible mechanism for OTC. Our results strongly support the view that ORN with an already deprotonated N(epsilon) atom is the species that binds to the enzyme and that one of the phosphate oxygen atoms of CP is likely to be involved in accepting a proton from the doubly protonated N(epsilon) atom of ORN. We have interpreted this deprotonation as part of the collapse of the transition state of the reaction.
Collapse
Affiliation(s)
- Ramasamy Sankaranarayanan
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | | | | | | | | |
Collapse
|
23
|
Aguilera S, López-López K, Nieto Y, Garcidueñas-Piña R, Hernández-Guzmán G, Hernández-Flores JL, Murillo J, Alvarez-Morales A. Functional characterization of the gene cluster from Pseudomonas syringae pv. phaseolicola NPS3121 involved in synthesis of phaseolotoxin. J Bacteriol 2007; 189:2834-43. [PMID: 17237165 PMCID: PMC1855804 DOI: 10.1128/jb.01845-06] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas syringae pv. phaseolicola is the causal agent of halo blight disease of beans (Phaseolus vulgaris L.), which is characterized by water-soaked lesions surrounded by a chlorotic halo resulting from the action of a non-host-specific toxin known as phaseolotoxin. This phytotoxin inhibits the enzyme ornithine carbamoyltransferase involved in arginine biosynthesis. Different evidence suggested that genes involved in phaseolotoxin production were clustered. Two genes had been previously identified in our laboratory within this cluster: argK, which is involved in the immunity of the bacterium to its own toxin, and amtA, which is involved in the synthesis of homoarginine. We sequenced the region around argK and amtA in P. syringae pv. phaseolicola NPS3121 to determine the limits of the putative phaseolotoxin gene cluster and to determine the transcriptional pattern of the genes comprising it. We report that the phaseolotoxin cluster (Pht cluster) is composed of 23 genes and is flanked by insertion sequences and transposases. The mutation of 14 of the genes within the cluster lead to a Tox(-) phenotype for 11 of them, while three mutants exhibited low levels of toxin production. The analysis of fusions of selected DNA fragments to uidA, Northern probing, and reverse transcription-PCR indicate the presence of five transcriptional units, two monocistronic and three polycistronic; one is internal to a larger operon. The site for transcription initiation has been determined for each promoter, and the putative promoter regions were identified. Preliminary results also indicate that the gene product of phtL is involved in the regulation of the synthesis of phaseolotoxin.
Collapse
Affiliation(s)
- Selene Aguilera
- Cinvestav, IPN Unidad Irapuato, Departamento de Ingeniería Genética, Irapuato, Gto., Apdo. Postal 629, CP 36500 Mexico
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Affiliation(s)
- W Wallace Cleland
- Institute for Enzyme Research and Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.
| | | |
Collapse
|
25
|
Shi D, Yu X, Roth L, Morizono H, Tuchman M, Allewell NM. Structures ofN-acetylornithine transcarbamoylase fromXanthomonas campestriscomplexed with substrates and substrate analogs imply mechanisms for substrate binding and catalysis. Proteins 2006; 64:532-42. [PMID: 16741992 DOI: 10.1002/prot.21013] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
N-acetyl-L-ornithine transcarbamoylase (AOTCase) is a new member of the transcarbamoylase superfamily that is essential for arginine biosynthesis in several eubacteria. We report here crystal structures of the binary complexes of AOTCase with its substrates, carbamoyl phosphate (CP) or N-acetyl-L-ornithine (AORN), and the ternary complex with CP and N-acetyl-L-norvaline. Comparison of these structures demonstrates that the substrate-binding mechanism of this novel transcarbamoylase is different from those of aspartate and ornithine transcarbamoylases, both of which show ordered substrate binding with large domain movements. CP and AORN bind to AOTCase independently, and the main conformational change upon substrate binding is ordering of the 80's loop, with a small domain closure around the active site and little movement of the 240's loop. The structures of the complexes provide insight into the mode of substrate binding and the mechanism of the transcarbamoylation reaction.
Collapse
Affiliation(s)
- Dashuang Shi
- Children's National Medical Center, Washington, DC 20010-2970, USA.
| | | | | | | | | | | |
Collapse
|
26
|
Bachmann AS, Xu R, Ratnapala L, Patil SS. Inhibitory effects of phaseolotoxin on proliferation of leukemia cells HL-60, K-562 and L1210 and pancreatic cells RIN-m5F. Leuk Res 2004; 28:301-6. [PMID: 14687626 DOI: 10.1016/j.leukres.2003.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phaseolotoxin (PT) is a non-host specific phytotoxin produced by the plant pathogenic bacterium Pseudomonas syringae (P.s.) pv. phaseolicola. In the present study, the inhibitory effect of PT on the proliferation of leukemia cells was studied. After 4 days of treatment, PT decreased cell growth of leukemia cell lines HL-60, K-562 and L1210 in a dose-dependent manner. In addition, PT also reduced cell growth of the insulinoma pancreatic cell line RIN-m5F. IC50 values were 2.1 +/- 1.0 microM (HL-60), 13.3 +/- 3.7 microM (K-562), 2.5 +/- 0.4 microM (L1210) and 5.5 +/- 0.3 microM (RIN-m5F). Although the exact mechanism by which PT inhibits cell growth in these cells is currently not known, we present first evidence that PT may in part be active via inhibition of ornithine decarboxylase (ODC). Based on our findings, PT presents a lead compound with potential for further development into a new anti-cancer agent.
Collapse
Affiliation(s)
- André S Bachmann
- Pacific Biomedical Research Center and Biotechnology Program, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
| | | | | | | |
Collapse
|
27
|
López-López K, Hernández-Flores JL, Cruz-Aguilar M, Alvarez-Morales A. In Pseudomonas syringae pv. phaseolicola, expression of the argK gene, encoding the phaseolotoxin-resistant ornithine carbamoyltransferase, is regulated indirectly by temperature and directly by a precursor resembling carbamoylphosphate. J Bacteriol 2004; 186:146-53. [PMID: 14679234 PMCID: PMC303443 DOI: 10.1128/jb.186.1.146-153.2004] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2003] [Accepted: 10/08/2003] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas syringae pv. phaseolicola synthesizes a non-host-specific toxin, phaseolotoxin, and also synthesizes a phaseolotoxin-resistant ornithine carbamoyltransferase (ROCT) to protect itself from its own toxin. ROCT is encoded by argK, which is expressed coordinately with phaseolotoxin synthesis at 18 degrees C. To investigate the regulatory mechanisms of this system, null mutants were constructed for argK, argF (encoding the phaseolotoxin-sensitive OCTase [SOCT]), and amtA (encoding an amidinotransferase involved in phaseolotoxin synthesis). The argF mutant did not exhibit arginine auxotrophy when grown in M9 medium at 28 degrees C, because under this condition SOCT was replaced by ROCT. This loss of thermoregulation of argK was apparently caused by accumulation of carbamoylphosphate, one of the substrates of SOCT. Carbamoylphosphate, which has a structure similar to that of the inorganic moiety of phaseolotoxin, was used in induction assays with wild-type P. syringae pv. phaseolicola and was shown to be able to induce argK expression in M9 medium at 28 degrees C. These results indicate that argK expression is independent of temperature and is regulated directly by a compound resembling the inorganic moiety of phaseolotoxin.
Collapse
Affiliation(s)
- Karina López-López
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV) del Instituto Politecnico Nacional (IPN), Unidad Irapuato, Irapuato, Guanajuato, C.P. 36500, Mexico
| | | | | | | |
Collapse
|
28
|
Haworth NL, Bacskay GB. The structure of N δ -( N ′-sulfodiaminophosphinyl)- l -ornithine and its binding to ornithine transcarbamoylase: A quantum chemical study. MOLECULAR SIMULATION 2002. [DOI: 10.1080/0892702021000002485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
29
|
Shi D, Gallegos R, DePonte J, Morizono H, Yu X, Allewell NM, Malamy M, Tuchman M. Crystal structure of a transcarbamylase-like protein from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution. J Mol Biol 2002; 320:899-908. [PMID: 12095263 DOI: 10.1016/s0022-2836(02)00539-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A transcarbamylase-like protein essential for arginine biosynthesis in the anaerobic bacterium Bacteroides fragilis has been purified and crystallized in space group P4(3)2(1)2 (a=b=153.4 A, c=94.8 A). The structure was solved using a single isomorphous replacement with anomalous scattering (SIRAS) and was refined at 2.0 A resolution to an R-factor of 20.6% (R-free=25.2%). The molecular model is trimeric and comprises 960 amino acid residues, two phosphate groups and 422 water molecules. The monomer has the consensus transcarbamylase fold with two structural domains linked by two long interdomain helices: the putative carbamoyl phosphate-binding domain and a binding domain for the second substrate. Each domain has a central parallel beta-sheet surrounded by alpha-helices and loops with alpha/beta topology. The putative carbamoyl phosphate-binding site is similar to those in ornithine transcarbamylases (OTCases) and aspartate transcarbamylases (ATCases); however, the second substrate-binding site is strikingly different. This site has several insertions and deletions, and residues critical to substrate binding and catalysis in other known transcarbamylases are not conserved. The three-dimensional structure and the fact that this protein is essential for arginine biosynthesis suggest strongly that it is a new member of the transcarbamylase family. A similar protein has been found in Xylella fastidiosa, a bacterium that infects grapes, citrus and other plants.
Collapse
Affiliation(s)
- Dashuang Shi
- Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue N.W., Washington, DC 20010-2970, USA.
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Metzler DE, Metzler CM, Sauke DJ. The Metabolism of Nitrogen and Amino Acids. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|