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Kim DS, Jang K, Kim WS, Ryu M, Park JH, Kim YJ. Crystal Structure of H227A Mutant of Arginine Kinase in Daphnia magna Suggests the Importance of Its Stability. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030884. [PMID: 35164149 PMCID: PMC8839106 DOI: 10.3390/molecules27030884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022]
Abstract
Arginine kinase (AK) plays a crucial role in the survival of Daphnia magna, a water flea and a common planktonic invertebrate sensitive to water pollution, owing to the production of bioenergy. AK from D. magna (DmAK) has four highly conserved histidine residues, namely, H90, H227, H284, and H315 in the amino acid sequence. In contrast to DmAK WT (wild type), the enzyme activity of the H227A mutant decreases by 18%. To identify the structure-function relationship of this H227A mutant enzyme, the crystal 3D X-ray structure has been determined and an unfolding assay using anilino-1-naphthalenesulfonic acid (ANS) fluorescence has been undertaken. The results revealed that when compared to the DmAK WT, the hydrogen bonding between H227 and A135 was broken in the H227A crystal structure. This suggests that H227 residue, closed to the arginine binding site, plays an important role in maintaining the structural stability and maximizing the enzyme activity through hydrogen bonding with the backbone oxygen of A135.
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Affiliation(s)
- Da Som Kim
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea; (D.S.K.); (W.S.K.); (M.R.)
| | - Kiyoung Jang
- Department of Lifestyle Medicine, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan 54596, Korea;
| | - Wan Seo Kim
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea; (D.S.K.); (W.S.K.); (M.R.)
| | - Moonhee Ryu
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea; (D.S.K.); (W.S.K.); (M.R.)
| | - Jung Hee Park
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea; (D.S.K.); (W.S.K.); (M.R.)
- Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
- Correspondence: (J.H.P.); (Y.J.K.)
| | - Yong Ju Kim
- Department of Lifestyle Medicine, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan 54596, Korea;
- Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
- Department of Oriental Medicine Resources, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan 54596, Korea
- Correspondence: (J.H.P.); (Y.J.K.)
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Rao Z, Kim SY, Li X, Kim DS, Kim YJ, Park JH. Insight into Structural Aspects of Histidine 284 of Daphnia magna Arginine Kinase. Mol Cells 2020; 43:784-792. [PMID: 32863281 PMCID: PMC7528679 DOI: 10.14348/molcells.2020.0136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/29/2020] [Accepted: 08/10/2020] [Indexed: 11/27/2022] Open
Abstract
Arginine kinase (AK), a bioenergy-related enzyme, is distributed widely in invertebrates. The role of highly conserved histidines in AKs is still unascertained. In this study, the highly conserved histidine 284 (H284) in AK of Daphnia magna (DmAK) was replaced with alanine to elucidate the role of H284. We examined the alteration of catalytic activity and structural changes of H284A in DmAK. The catalytic activity of H284A was reduced dramatically compared to that in wild type (WT). Thus the crystal structure of H284A displayed several structural changes, including the alteration of D324, a hydrogen-bonding network around H284, and the disruption of π-stacking between the imidazole group of the H284 residue and the adenine ring of ATP. These findings suggest that such alterations might affect a conformational change of the specific loop consisting of G310-V322 at the antiparallel β-sheet region. Thus, we speculated that the H284 residue might play an important role in the conformational change of the specific loop when ATP binds to the substrate-binding site of DmAK.
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Affiliation(s)
- Zhili Rao
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
- These authors contributed equally to this work
| | - So Young Kim
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
- These authors contributed equally to this work
| | - Xiaotong Li
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
| | - Da Som Kim
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
| | - Yong Ju Kim
- Department of Herbal Medicine Resources, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan 54596, Korea
- Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
| | - Jung Hee Park
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
- Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
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Qi XL, Su XF, Lu GQ, Liu CX, Liang GM, Cheng HM. The effect of silencing arginine kinase by RNAi on the larval development of Helicoverpa armigera. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:555-565. [PMID: 26138927 DOI: 10.1017/s0007485315000450] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Arginine kinase (AK) is an important regulation factor of energy metabolism in invertebrate. An arginine kinase gene, named HaAK, was identified to be differentially expressed between Cry1Ac-susceptible (96S) and Cry1Ac-resistant (Bt-R) Helicoverpa armigera larvae using cDNA-amplification fragment length polymorphism analysis. The full-length open reading frame sequence of HaAK gene with 1068 bp was isolated from H. armigera. Quantitative reverse transcription polymerase chain reaction assay revealed that HaAK gene is specifically expressed in multiple tissues and at larval developmental stages. The peak expression level of HaAK was detected in the midgut of the fifth-instar larvae. Moreover, the expression of HaAK was obviously down-regulated in Bt-R larvae. We further constructed a dsRNA vector directly targeting HaAK and employed RNAi technology to control the larvae. The feeding bioassays showed that minute quantities of dsRNA could greatly increase the larval mortality and delay the larval pupation. Silencing of HaAK significantly retarded the larval development, indicating that HaAK is a potential target for RNA interference-based pest management.
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Affiliation(s)
- X-L Qi
- Biotechnology Research Institute,Chinese Academy of Agricultural Sciences,Beijing 100081,China
| | - X-F Su
- Biotechnology Research Institute,Chinese Academy of Agricultural Sciences,Beijing 100081,China
| | - G-Q Lu
- Biotechnology Research Institute,Chinese Academy of Agricultural Sciences,Beijing 100081,China
| | - C-X Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests,Institute of Plant Protection,Chinese Academy of Agricultural Sciences,Beijing 100193,China
| | - G-M Liang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests,Institute of Plant Protection,Chinese Academy of Agricultural Sciences,Beijing 100193,China
| | - H-M Cheng
- Biotechnology Research Institute,Chinese Academy of Agricultural Sciences,Beijing 100081,China
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Wu QY, Guo HY, Geng HL, Ru BM, Cao J, Chen C, Zeng LY, Wang XY, Li F, Xu KL. T273 plays an important role in the activity and structural stability of arginine kinase. Int J Biol Macromol 2013; 63:21-8. [PMID: 24157705 DOI: 10.1016/j.ijbiomac.2013.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022]
Abstract
Arginine kinase (AK) is a key enzyme for cellular energy metabolism, catalyzing the reversible phosphoryl transfer from phosphoarginine to ADP in invertebrates. The amino acid residue C271 is involved in keeping AK's activity and constraining the orientation of the substrate arginine. However, the roles of the C271 interaction amino acid residues in AK's substrate synergism, activity and structural stability are still unclear. The crystal structure of AK implied that the amino acid residue T273 interacted with the residue C271 and might play vital roles in keeping AK's activity, substrate synergism and structural stability. The mutations T273G and T273A led to significantly loss of activity, obviously decreased of substrate synergism and structural stability. Furthermore, spectroscopic experiments indicated that mutations T273G and T273A impaired the structure of AK and led them to a partially unfolded state. The inability to fold to the functional state made the mutations prone to aggregate under environmental stresses. Moreover, the mutations T273S and T273D almost had no effects on AK's activity and structural stability. This study herein indicated that the residue T273 played key roles in AK's activity, substrate synergism and structural stability.
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Affiliation(s)
- Qing-Yun Wu
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China; Laboratory of Transplantation and Immunology, Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Hua-Yan Guo
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Hong-Li Geng
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Bian-Mei Ru
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Jiang Cao
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Chong Chen
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Ling-Yu Zeng
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China; Laboratory of Transplantation and Immunology, Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Xiao-Yun Wang
- College of Life Sciences, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
| | - Feng Li
- Department of Neurobiology, Xuzhou Medical College, 221002 Xuzhou, People's Republic of China.
| | - Kai-Lin Xu
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China.
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Liu T, Wang X. Zinc induces unfolding and aggregation of dimeric arginine kinase by trapping reversible unfolding intermediate. Acta Biochim Biophys Sin (Shanghai) 2010; 42:779-86. [PMID: 20929927 DOI: 10.1093/abbs/gmq092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Arginine kinase plays an important role in the cellular energy metabolism of invertebrates. Dimeric arginine kinase (dAK) is unique in some marine invertebrates. The effects of Zn²(+) on the unfolding and aggregation of dAK from the sea cucumber Stichopus japonicus were investigated. Our results indicated that Zn²(+) caused dAK inactivation accompanied by conformational unfolding, the exposure of hydrophobic surface, and aggregation. Kinetic studies showed the inactivation and unfolding of dAK followed biphasic kinetic courses. Zn²(+) can affect unfolding and refolding of dAK by trapping the reversible intermediate. Our study provides important information regarding the effect of Zn²(+) on metabolic enzymes in marine invertebrates.
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Effects of N-terminal deletion mutation on arginine kinase from the sea cucumber Stichopus japonicus. Int J Biol Macromol 2008; 42:68-74. [DOI: 10.1016/j.ijbiomac.2007.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Revised: 09/21/2007] [Accepted: 09/21/2007] [Indexed: 11/23/2022]
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Zhu WJ, Li M, Wang XY. Chemical modification studies on arginine kinase: Essential cysteine and arginine residues at the active site. Int J Biol Macromol 2007; 41:564-71. [PMID: 17765964 DOI: 10.1016/j.ijbiomac.2007.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 07/17/2007] [Accepted: 07/17/2007] [Indexed: 11/23/2022]
Abstract
Chemical modification was used to elucidate the essential amino acids in the catalytic activity of arginine kinase (AK) from Migratoria manilensis. Among six cysteine (Cys) residues only one Cys residue was determined to be essential in the active site by Tsou's method. Furthermore, the AK modified by DTNB can be fully reactivated by dithiothreitol (DTT) in a monophasic kinetic course. At the same time, this reactivation can be slowed down in the presence of ATP, suggesting that the essential Cys is located near the ATP binding site. The ionizing groups at the AK active site were studied and the standard dissociation enthalpy (DeltaH degrees ) was 12.38kcal/mol, showing that the dissociation group may be the guanidino of arginine (Arg). Using the specific chemical modifier phenylglyoxal (PG) demonstrated that only one Arg, located near the ATP binding site, is essential for the activity of AK.
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Affiliation(s)
- Wen-Jing Zhu
- College of Life Science, Shandong Agricultural University, Shandong Taian 271018, People's Republic of China
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Zeng J, Dunlop R, Rodgers K, Davies M. Evidence for inactivation of cysteine proteases by reactive carbonyls via glycation of active site thiols. Biochem J 2006; 398:197-206. [PMID: 16671891 PMCID: PMC1550308 DOI: 10.1042/bj20060019] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Hyperglycaemia, triose phosphate decomposition and oxidation reactions generate reactive aldehydes in vivo. These compounds react non-enzymatically with protein side chains and N-terminal amino groups to give adducts and cross-links, and hence modified proteins. Previous studies have shown that free or protein-bound carbonyls inactivate glyceraldehyde-3-phosphate dehydrogenase with concomitant loss of thiol groups [Morgan, Dean and Davies (2002) Arch. Biochem. Biophys. 403, 259-269]. It was therefore hypothesized that modification of lysosomal cysteine proteases (and the structurally related enzyme papain) by free and protein-bound carbonyls may modulate the activity of these components of the cellular proteolytic machinery responsible for the removal of modified proteins and thereby contribute to a decreased removal of modified proteins from cells. It is shown that MGX (methylglyoxal), GO (glyoxal) and glycolaldehyde, but not hydroxyacetone and glucose, inhibit catB (cathepsin B), catL (cathepsin L) and catS (cathepsin S) activity in macrophage cell lysates, in a concentration-dependent manner. Protein-bound carbonyls produced similar inhibition with both cell lysates and intact macrophage cells. Inhibition was also observed with papain, with this paralleled by loss of the active site cysteine residue and formation of the adduct species S-carboxymethylcysteine, from GO, in a concentration-dependent manner. Inhibition of autolysis of papain by MGX, along with cross-link formation, was detected by SDS/PAGE. Treatment of papain and catS with the dialdehyde o-phthalaldehyde resulted in enzyme inactivation and an intra-molecular active site cysteine-lysine cross-link. These results demonstrate that reactive aldehydes inhibit cysteine proteases by modification of the active site cysteine residue. This process may contribute to the accumulation of modified proteins in tissues of people with diabetes and age-related pathologies, including atherosclerosis, cataract and Alzheimer's disease.
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Affiliation(s)
- Jingmin Zeng
- *The Heart Research Institute, 145 Missenden Road, Sydney, NSW 2050, Australia
| | - Rachael A. Dunlop
- *The Heart Research Institute, 145 Missenden Road, Sydney, NSW 2050, Australia
| | - Kenneth J. Rodgers
- *The Heart Research Institute, 145 Missenden Road, Sydney, NSW 2050, Australia
| | - Michael J. Davies
- *The Heart Research Institute, 145 Missenden Road, Sydney, NSW 2050, Australia
- †Faculty of Medicine, University of Sydney, Sydney, NSW 2006, Australia
- To whom correspondence should be addressed (email )
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Feng Z, Qin G, Xicheng W. The kinetic study of arginine kinase from the sea cucumber Stichopus japonicus with 5,5'-dithiobis-(2-nitrobenzoic acid). Int J Biol Macromol 2005; 36:184-90. [PMID: 16038973 DOI: 10.1016/j.ijbiomac.2005.06.001] [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] [Received: 03/15/2005] [Revised: 05/03/2005] [Accepted: 06/02/2005] [Indexed: 12/25/2022]
Abstract
The Stichopus japonicus arginine kinase (AK) is a significant dimeric enzyme. Its modification and inactivation course with 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB) and the reactivation course of DTNB-modified AK by dithiothreitol were investigated on the basis of the kinetic theory of the substrate reaction during the modification of enzyme activity. The results show that the modification is a biphasic course while the inactivation is monophasic, with one essential reactive cysteine per subunit. The Cys274 (numbering from the Stichopus sequence) is exposed to DTNB and is near the ATP binding site. The modified AK can be reactivated by an excess concentration of dithiothreitol in a monophasic kinetic course. The presence of ATP or the transition-state analog markedly slows the apparent reactivation rate constant. The analog components, arginine-ADP-Mg2+ can induce conformational changes of the modified enzyme, but adding NO3- cannot induce further changes that occur with the native enzyme. The reactive cysteines' location and its role in the catalysis of AK are discussed. The results suggest that the cysteine may be located in the hinge area of the two domains of AK. The reactive cysteine of AK, which was proposed to be Cys274, may play an important role not in the binding of the transition-state analog but in the conformational changes caused by the transition-state analog.
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Affiliation(s)
- Zhao Feng
- Department of Biological Science and Biotechnology, School of Life Science and Engineering, Tsinghua University, Beijing 100084, China
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