1
|
Hagedoorn PL, Pabst M, Hanefeld U. The metal cofactor: stationary or mobile? Appl Microbiol Biotechnol 2024; 108:391. [PMID: 38910188 PMCID: PMC11194214 DOI: 10.1007/s00253-024-13206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/25/2024]
Abstract
Metal cofactors are essential for catalysis and enable countless conversions in nature. Interestingly, the metal cofactor is not always static but mobile with movements of more than 4 Å. These movements of the metal can have different functions. In the case of the xylose isomerase and medium-chain dehydrogenases, it clearly serves a catalytic purpose. The metal cofactor moves during substrate activation and even during the catalytic turnover. On the other hand, in class II aldolases, the enzymes display resting states and active states depending on the movement of the catalytic metal cofactor. This movement is caused by substrate docking, causing the metal cofactor to take the position essential for catalysis. As these metal movements are found in structurally and mechanistically unrelated enzymes, it has to be expected that this metal movement is more common than currently perceived. KEY POINTS: • Metal ions are essential cofactors that can move during catalysis. • In class II aldolases, the metal cofactors can reside in a resting state and an active state. • In MDR, the movement of the metal cofactor is essential for substrate docking.
Collapse
Affiliation(s)
- Peter-Leon Hagedoorn
- Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Martin Pabst
- Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Ulf Hanefeld
- Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands.
| |
Collapse
|
2
|
Stewart C, Mamori M, Arman H, Musie GT. Synthesis, Characterization and Spectroscopic Investigation of Novel Tetra‐Iron(III) Complexes and D‐Glucose under Redox Conditions. ChemistrySelect 2021. [DOI: 10.1002/slct.202102315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Christopher Stewart
- Department of Chemistry The University of Texas at San Antonio San Antonio TX 78249 United States
| | - Myles Mamori
- Department of Chemistry The University of Texas at San Antonio San Antonio TX 78249 United States
| | - Hadi Arman
- Department of Chemistry The University of Texas at San Antonio San Antonio TX 78249 United States
| | - Ghezai T. Musie
- Department of Chemistry The University of Texas at San Antonio San Antonio TX 78249 United States
| |
Collapse
|
3
|
Protein Dynamics and Time Resolved Protein Crystallography at Synchrotron Radiation Sources: Past, Present and Future. CRYSTALS 2021. [DOI: 10.3390/cryst11050521] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The ultrabright and ultrashort pulses produced at X-ray free electron lasers (XFELs) has enabled studies of crystallized molecular machines at work under ‘native’ conditions at room temperature by the so-called time-resolved serial femtosecond crystallography (TR-SFX) technique. Since early TR-SFX experiments were conducted at XFELs, it has been largely reported in the literature that time-resolved X-ray experiments at synchrotrons are no longer feasible or are impractical due to the severe technical limitations of these radiation sources. The transfer of the serial crystallography approach to newest synchrotrons upgraded for higher flux density and with beamlines using sophisticated focusing optics, submicron beam diameters and fast low-noise photon-counting detectors offers a way to overcome these difficulties opening new and exciting possibilities. In fact, there is an increasing amount of publications reporting new findings in structural dynamics of protein macromolecules by using time resolved crystallography from microcrystals at synchrotron sources. This review gathers information to provide an overview of the recent work and the advances made in this filed in the past years, as well as outlines future perspectives at the next generation of synchrotron sources and the upcoming compact pulsed X-ray sources.
Collapse
|
4
|
Identification of a Novel Cobamide Remodeling Enzyme in the Beneficial Human Gut Bacterium Akkermansia muciniphila. mBio 2020; 11:mBio.02507-20. [PMID: 33293380 PMCID: PMC7733943 DOI: 10.1128/mbio.02507-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cobamides, comprising the vitamin B12 family of cobalt-containing cofactors, are required for metabolism in all domains of life, including most bacteria. Cobamides have structural variability in the lower ligand, and selectivity for particular cobamides has been observed in most organisms studied to date. The beneficial human gut bacterium Akkermansia muciniphila provides metabolites to other members of the gut microbiota by breaking down host mucin, but most of its other metabolic functions have not been investigated. A. muciniphila strain MucT is known to use cobamides, the vitamin B12 family of cofactors with structural diversity in the lower ligand. However, A. muciniphila MucT is unable to synthesize cobamides de novo, and the specific forms that can be used by A. muciniphila have not been examined. We found that the levels of growth of A. muciniphila MucT were nearly identical with each of seven cobamides tested, in contrast to nearly all bacteria that had been studied previously. Unexpectedly, this promiscuity is due to cobamide remodeling—the removal and replacement of the lower ligand—despite the absence of the canonical remodeling enzyme CbiZ in A. muciniphila. We identified a novel enzyme, CbiR, that is capable of initiating the remodeling process by hydrolyzing the phosphoribosyl bond in the nucleotide loop of cobamides. CbiR does not share similarity with other cobamide remodeling enzymes or B12-binding domains and is instead a member of the apurinic/apyrimidinic (AP) endonuclease 2 enzyme superfamily. We speculate that CbiR enables bacteria to repurpose cobamides that they cannot otherwise use in order to grow under cobamide-requiring conditions; this function was confirmed by heterologous expression of cbiR in Escherichia coli. Homologs of CbiR are found in over 200 microbial taxa across 22 phyla, suggesting that many bacteria may use CbiR to gain access to the diverse cobamides present in their environment.
Collapse
|
5
|
Mehrabi P, Schulz EC, Agthe M, Horrell S, Bourenkov G, von Stetten D, Leimkohl JP, Schikora H, Schneider TR, Pearson AR, Tellkamp F, Miller RJD. Liquid application method for time-resolved analyses by serial synchrotron crystallography. Nat Methods 2019; 16:979-982. [DOI: 10.1038/s41592-019-0553-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/06/2019] [Indexed: 01/01/2023]
|
6
|
Taberman H, Bury CS, van der Woerd MJ, Snell EH, Garman EF. Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:931-944. [PMID: 31274415 PMCID: PMC6613113 DOI: 10.1107/s1600577519005599] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 04/23/2019] [Indexed: 05/29/2023]
Abstract
Xylose isomerase (XI) is an industrially important metalloprotein studied for decades. Its reaction mechanism has been postulated to involve movement of the catalytic metal cofactor to several different conformations. Here, a dose-dependent approach was used to investigate the radiation damage effects on XI and their potential influence on the reaction mechanism interpreted from the X-ray derived structures. Radiation damage is still one of the major challenges for X-ray diffraction experiments and causes both global and site-specific damage. In this study, consecutive high-resolution data sets from a single XI crystal from the same wedge were collected at 100 K and the progression of radiation damage was tracked over increasing dose (0.13-3.88 MGy). The catalytic metal and its surrounding amino acid environment experience a build-up of free radicals, and the results show radiation-damage-induced structural perturbations ranging from an absolute metal positional shift to specific residue motions in the active site. The apparent metal movement is an artefact of global damage and the resulting unit-cell expansion, but residue motion appears to be driven by the dose. Understanding and identifying radiation-induced damage is an important factor in accurately interpreting the biological conclusions being drawn.
Collapse
Affiliation(s)
- Helena Taberman
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein Straße 15, 12489 Berlin, Germany
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Charles S. Bury
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark J. van der Woerd
- Department of Enterprise Technology Services, 2001 Capitol Avenue, Cheyenne, WY 82001, USA
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Materials Design and Innovation, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| |
Collapse
|
7
|
Abstract
Protein crystallization is a powerful purification tool. It is the first step for crystallographic structural investigations, and can be preparatory for biotechnological applications. However, crystallizing proteins is challenging and methods to control the crystallization process are needed. Ionic-liquid hydrogel composite membranes (IL-HCMs) have been used here as material capable of supporting protein crystallization and hosting grown crystals. We found that IL-HCMs affect the selection mechanism of glucose isomerase (GI) polymorphs and make GI crystals grow completely immersed into the hydrogel layer. X-ray diffraction studies show that IL ions do not bind to the protein, likely because IL molecules are constrained in the polymeric framework. Our GI crystal structures have been compared with many existing GI crystal structures using multivariate analysis tools, allowing a comprehensive overview of factors determining structural similarities, i.e., temperature variations and external stresses exerted during or after crystal growth, such as dehydration or presence of hydrogel of a different nature. GI crystals grown on IL-HCM fit perfectly in this framework, showing typical features induced by external forces. Overall, protein crystallization by IL-HCMs show potential for biotechnological applications, as it could constitute a natural means for containing crystallized enzymes in working conditions.
Collapse
|
8
|
Crystallization of Liganded Phosphatases in the HAD Superfamily. Methods Enzymol 2018; 607:157-184. [PMID: 30149857 DOI: 10.1016/bs.mie.2018.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phosphotransferases catalyze reactions on chemically diverse molecules in organisms from all domains of life. The haloalkanoate dehalogenase superfamily (HADSF) is a model system for phosphoryl transfer enzymes as members catalyze phosphoester hydrolase, phosphonate hydrolase, and phosphomutase reactions on sugars, lipids, nucleotides, and peptides. Because these reactions are fundamental to essential metabolic transformations, understanding the mechanism and determinants of substrate specificity in the HADSF is critical. Structure/function relationships in the superfamily have also been leveraged in the development of methodologies for the assignment of enzyme function. Enzyme complexes with substrate, product, and analogs of the ground state or intermediate/transition state can be studied via high-resolution macromolecular crystallography to provide insight to the relative location of residues and ligands, as well as associated enzyme conformational states. This knowledge can aid in inhibitor design for phosphohydrolase reactions and target-specific therapeutics. Here we describe experimental approaches to capture liganded X-ray crystallographic structures of HADSF members. A number of these methods can be employed generally, including other families of phosphohydrolases and enzymes catalyzing phosphoryl transfer.
Collapse
|
9
|
Wozniak PP, Vriend G, Kotulska M. Correlated mutations select misfolded from properly folded proteins. Bioinformatics 2017; 33:1497-1504. [PMID: 28203707 DOI: 10.1093/bioinformatics/btx013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/11/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- P P Wozniak
- Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wrocław University of Science and Technology, Wrocław, Poland
| | - G Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - M Kotulska
- Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wrocław University of Science and Technology, Wrocław, Poland
| |
Collapse
|
10
|
NMR studies on mechanism of isomerisation of fructose 6-phosphate to glucose 6-phosphate catalysed by phosphoglucose isomerase from Thermococcus kodakarensis. Bioorg Chem 2016; 66:41-5. [DOI: 10.1016/j.bioorg.2016.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 03/02/2016] [Accepted: 03/13/2016] [Indexed: 11/22/2022]
|
11
|
Touw WG, Joosten RP, Vriend G. New Biological Insights from Better Structure Models. J Mol Biol 2016; 428:1375-1393. [PMID: 26869101 DOI: 10.1016/j.jmb.2016.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 01/04/2016] [Accepted: 02/01/2016] [Indexed: 02/01/2023]
Abstract
Structure validation is a key component of all steps in the structure determination process, from structure building, refinement, deposition, and evaluation all the way to post-deposition optimisation of structures in the Protein Data Bank (PDB) by re-refinement and re-building. Today, many aspects of protein structures are understood better than 10years ago, and combined with improved software and more computing power, the automated PDB_REDO procedure can significantly improve about 85% of all X-ray structures ever deposited in the PDB. We review structure validation, structure improvement, and a series of validation resources and facilities that give access to improved PDB files and to reports on the quality of the original and the improved structures. Post-deposition optimisation generally leads to improved protein structures and a series of examples will illustrate how that, in turn, leads to improved or even novel biological insights.
Collapse
Affiliation(s)
- Wouter G Touw
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands.
| |
Collapse
|
12
|
Sugrue E, Hartley CJ, Scott C, Jackson CJ. The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes. Aust J Chem 2016. [DOI: 10.1071/ch16426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An increasing number of bacterial metalloenzymes have been shown to catalyse the breakdown of xenobiotics in the environment, while others exhibit a variety of promiscuous xenobiotic-degrading activities. Several different evolutionary processes have allowed these enzymes to gain or enhance xenobiotic-degrading activity. In this review, we have surveyed the range of xenobiotic-degrading metalloenzymes, and discuss the molecular and catalytic basis for the development of new activities. We also highlight how our increased understanding of the natural evolution of xenobiotic-degrading metalloenzymes can be been applied to laboratory enzyme design.
Collapse
|
13
|
Stewart CD, Arman H, Bawazir H, Musie GT. Synthesis, Characterization, and Spectroscopic Investigation of New Iron(III) and Copper(II) Complexes of a Carboxylate Rich Ligand and Their Interaction with Carbohydrates in Aqueous Solution. Inorg Chem 2014; 53:10974-88. [DOI: 10.1021/ic501351a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Christopher D. Stewart
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Hadi Arman
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Huda Bawazir
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Ghezai T. Musie
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| |
Collapse
|
14
|
L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study. Structure 2014; 22:1287-1300. [DOI: 10.1016/j.str.2014.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/19/2014] [Accepted: 07/01/2014] [Indexed: 11/22/2022]
|
15
|
Goldfeder M, Kanteev M, Isaschar-Ovdat S, Adir N, Fishman A. Determination of tyrosinase substrate-binding modes reveals mechanistic differences between type-3 copper proteins. Nat Commun 2014; 5:4505. [PMID: 25074014 DOI: 10.1038/ncomms5505] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/25/2014] [Indexed: 11/09/2022] Open
Abstract
Tyrosinase is responsible for the two initial enzymatic steps in the conversion of tyrosine to melanin. Many tyrosinase mutations are the leading cause of albinism in humans, and it is a prominent biotechnology and pharmaceutical industry target. Here we present crystal structures that show that both monophenol hydroxylation and diphenol oxidation occur at the same site. It is suggested that concurrent presence of a phenylalanine above the active site and a restricting thioether bond on the histidine coordinating CuA prevent hydroxylation of monophenols by catechol oxidases. Furthermore, a conserved water molecule activated by E195 and N205 is proposed to mediate deprotonation of the monophenol at the active site. Overall, the structures reveal precise steps in the enzymatic catalytic cycle as well as differences between tyrosinases and other type-3 copper enzymes.
Collapse
Affiliation(s)
- Mor Goldfeder
- 1] Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel [2]
| | - Margarita Kanteev
- 1] Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel [2]
| | - Sivan Isaschar-Ovdat
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| |
Collapse
|
16
|
Munshi P, Snell EH, van der Woerd MJ, Judge RA, Myles DAA, Ren Z, Meilleur F. Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant. ACTA ACUST UNITED AC 2014; 70:414-20. [DOI: 10.1107/s1399004713029684] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/28/2013] [Indexed: 11/10/2022]
Abstract
Ketol-isomerases catalyze the reversible isomerization between aldoses and ketoses. D-Xylose isomerase carries out the first reaction in the catabolism of D-xylose, but is also able to convert D-glucose to D-fructose. The first step of the reaction is an enzyme-catalyzed ring opening of the cyclic substrate. The active-site amino-acid acid/base pair involved in ring opening has long been investigated and several models have been proposed. Here, the structure of the xylose isomerase E186Q mutant with cyclic glucose bound at the active site, refined against joint X-ray and neutron diffraction data, is reported. Detailed analysis of the hydrogen-bond networks at the active site of the enzyme suggests that His54, which is doubly protonated, is poised to protonate the glucose O5 position, while Lys289, which is neutral, promotes deprotonation of the glucose O1H hydroxyl groupviaan activated water molecule. The structure also reveals an extended hydrogen-bonding network that connects the conserved residues Lys289 and Lys183 through three structurally conserved water molecules and residue 186, which is a glutamic acid to glutamine mutation.
Collapse
|
17
|
Cho JW, Han BG, Park SY, Kim SJ, Kim MD, Lee BI. Overexpression, crystallization and preliminary X-ray crystallographic analysis of a putative xylose isomerase from Bacteroides thetaiotaomicron. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1127-30. [PMID: 24100564 PMCID: PMC3792672 DOI: 10.1107/s1744309113023877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/25/2013] [Indexed: 11/10/2022]
Abstract
Bacteroides thetaiotaomicron BT0793, a putative xylose isomerase, was overexpressed in Escherichia coli, purified and crystallized using polyethylene glycol monomethyl ether 550 as the precipitant. X-ray diffraction data were collected to 2.10 Å resolution at 100 K using synchrotron X-rays. The crystal was found to belong to space group P1, with unit-cell parameters a=96.3, b=101.7, c=108.3 Å, α=82.8, β=68.2, γ=83.0°. The asymmetric unit contained eight subunits of xylose isomerase with a crystal volume per protein weight (VM) of 2.38 Å3 Da(-1) and a solvent content of 48.3%.
Collapse
Affiliation(s)
- Jea-Won Cho
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Republic of Korea
- Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Goyang, Gyeonggi 410-769, Republic of Korea
| | - Byeong-Gu Han
- Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Goyang, Gyeonggi 410-769, Republic of Korea
| | - Sang Youn Park
- School of Systems Biomedical Science, Soongsil University, Seoul 156-743, Republic of Korea
| | - Seung Jun Kim
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Republic of Korea
| | - Myoung-Dong Kim
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Byung Il Lee
- Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Goyang, Gyeonggi 410-769, Republic of Korea
| |
Collapse
|
18
|
Desai KK, Bingman CA, Phillips GN, Raines RT. Structures of the noncanonical RNA ligase RtcB reveal the mechanism of histidine guanylylation. Biochemistry 2013; 52:2518-25. [PMID: 23560983 DOI: 10.1021/bi4002375] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
RtcB is an atypical RNA ligase that joins either 2',3'-cyclic phosphate or 3'-phosphate termini to 5'-hydroxyl termini. In contrast to typical RNA ligases, which rely on ATP and Mg(II), catalysis by RtcB is dependent on GTP and Mn(II) with ligation proceeding through a covalent RtcB-histidine-GMP intermediate. Here, we present three structures of Pyrococcus horikoshii RtcB complexes that capture snapshots along the entire guanylylation pathway. These structures show that prior to binding GTP, a single manganese ion (Mn1) is bound to RtcB. To capture the step immediately preceding RtcB guanylylation, we determined a structure of RtcB in complex with Mn(II) and the unreactive GTP analogue guanosine 5'-(α-thio)triphosphate (GTPαS). This structure shows that Mn1 is poised to stabilize the pentavalent transition state of guanylylation while a second manganese ion (Mn2) is coordinated to a nonbridging oxygen of the γ-phosphoryl group. The pyrophosphate leaving group of GTPαS is oriented apically to His404 with the ε-nitrogen poised for in-line attack on the α-phosphorus atom. The structure of RtcB in complex with GTPαS also reveals the network of hydrogen bonds that recognize GTP and illuminates the significant conformational changes that accompany the binding of this cofactor. Finally, a structure of the enzymic histidine-GMP intermediate depicts the end of the guanylylation pathway. The ensuing molecular description of the RtcB guanylylation pathway shows that RtcB and classical ATP- and Mg(II)-dependent nucleic acid ligases have converged upon a similar two-metal mechanism for formation of the nucleotidylated enzyme intermediate.
Collapse
Affiliation(s)
- Kevin K Desai
- Department of Biochemistry, University of Wisconsin, Madison, Madison, Wisconsin 53706, USA
| | | | | | | |
Collapse
|
19
|
Ben-David M, Wieczorek G, Elias M, Silman I, Sussman JL, Tawfik DS. Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme. J Mol Biol 2013; 425:1028-38. [PMID: 23318950 DOI: 10.1016/j.jmb.2013.01.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 01/03/2013] [Accepted: 01/07/2013] [Indexed: 11/16/2022]
Abstract
Although largely deemed as structurally conserved, catalytic metal ion sites can rearrange, thereby contributing to enzyme evolvability. Here, we show that in paraoxonase-1, a lipo-lactonase, catalytic promiscuity and divergence into an organophosphate hydrolase are correlated with an alternative mode of the catalytic Ca(2+). We describe the crystal structures of active-site mutants bearing mutations at position 115. The histidine at this position acts as a base to activate the lactone-hydrolyzing water molecule. Mutations to Trp or Gln indeed diminish paraoxonase-1's lactonase activity; however, the promiscuous organophosphate hydrolase activity is enhanced. The structures reveal a 1.8-Å upward displacement towards the enzyme's surface of the catalytic Ca(2+) in the His115 mutants and configurational changes in the ligating side chains and water molecules, relative to the wild-type enzyme. Biochemical analysis and molecular dynamics simulations suggest that this alternative, upward metal mode mediates the promiscuous hydrolysis of organophosphates. The upward Ca(2+) mode observed in the His115 mutants also appears to mediate the wild type's paraoxonase activity. However, whereas the upward mode dominates in the Trp115 mutant, it is scarcely populated in wild type. Thus, the plasticity of active-site metal ions may permit alternative, latent, promiscuous activities and also provide the basis for the divergence of new enzymatic functions.
Collapse
Affiliation(s)
- Moshe Ben-David
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | | | | | | |
Collapse
|
20
|
Bera M, Curtiss ABS, Musie GT, Powell DR. New Dinuclear Cobalt(II) and Zinc(II) Complexes of a Carboxylate-Rich Dinucleating Ligand: Synthesis, Structure, Spectroscopic Characterization, and Their Interactions with Sugars. Inorg Chem 2012; 51:12093-101. [DOI: 10.1021/ic3004432] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manindranath Bera
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal 741235,
India
| | - Ashley B. S. Curtiss
- Department of Chemistry, The University of Texas at San Antonio, San Antonio,
Texas 78249, United States
| | - Ghezai T. Musie
- Department of Chemistry, The University of Texas at San Antonio, San Antonio,
Texas 78249, United States
| | - Douglas R. Powell
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United
States
| |
Collapse
|
21
|
Kovalevsky A, Hanson BL, Mason SA, Forsyth VT, Fisher Z, Mustyakimov M, Blakeley MP, Keen DA, Langan P. Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1201-6. [PMID: 22948921 PMCID: PMC3489103 DOI: 10.1107/s0907444912024808] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/30/2012] [Indexed: 11/10/2022]
Abstract
D-Xylose isomerase (XI) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of polyol binding to the XI active site, a 2.0 Å resolution room-temperature joint X-ray/neutron structure of XI in complex with Ni(2+) cofactors and sorbitol inhibitor at pH 5.9 and a room-temperature X-ray structure of XI containing Mg(2+) ions and xylitol at the physiological pH of 7.7 were obtained. The protonation of oxygen O5 of the inhibitor, which was found to be deprotonated and negatively charged in previous structures of XI complexed with linear glucose and xylulose, was directly observed. The Ni(2+) ions occupying the catalytic metal site (M2) were found at two locations, while Mg(2+) in M2 is very mobile and has a high B factor. Under acidic conditions sorbitol gains a water-mediated interaction that connects its O1 hydroxyl to Asp257. This contact is not found in structures at basic pH. The new interaction that is formed may improve the binding of the inhibitor, providing an explanation for the increased affinity of the polyols for XI at low pH.
Collapse
Affiliation(s)
- Andrey Kovalevsky
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Directed evolution of xylose isomerase for improved xylose catabolism and fermentation in the yeast Saccharomyces cerevisiae. Appl Environ Microbiol 2012; 78:5708-16. [PMID: 22685138 DOI: 10.1128/aem.01419-12] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The heterologous expression of a highly functional xylose isomerase pathway in Saccharomyces cerevisiae would have significant advantages for ethanol yield, since the pathway bypasses cofactor requirements found in the traditionally used oxidoreductase pathways. However, nearly all reported xylose isomerase-based pathways in S. cerevisiae suffer from poor ethanol productivity, low xylose consumption rates, and poor cell growth compared with an oxidoreductase pathway and, additionally, often require adaptive strain evolution. Here, we report on the directed evolution of the Piromyces sp. xylose isomerase (encoded by xylA) for use in yeast. After three rounds of mutagenesis and growth-based screening, we isolated a variant containing six mutations (E15D, E114G, E129D, T142S, A177T, and V433I) that exhibited a 77% increase in enzymatic activity. When expressed in a minimally engineered yeast host containing a gre3 knockout and tal1 and XKS1 overexpression, the strain expressing this mutant enzyme improved its aerobic growth rate by 61-fold and both ethanol production and xylose consumption rates by nearly 8-fold. Moreover, the mutant enzyme enabled ethanol production by these yeasts under oxygen-limited fermentation conditions, unlike the wild-type enzyme. Under microaerobic conditions, the ethanol production rates of the strain expressing the mutant xylose isomerase were considerably higher than previously reported values for yeast harboring a xylose isomerase pathway and were also comparable to those of the strains harboring an oxidoreductase pathway. Consequently, this study shows the potential to evolve a xylose isomerase pathway for more efficient xylose utilization.
Collapse
|
23
|
Weakly hydrated surfaces and the binding interactions of small biological solutes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:369-77. [DOI: 10.1007/s00249-011-0776-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 11/01/2011] [Accepted: 11/08/2011] [Indexed: 10/15/2022]
|
24
|
Toteva MM, Silvaggi NR, Allen KN, Richard JP. Binding energy and catalysis by D-xylose isomerase: kinetic, product, and X-ray crystallographic analysis of enzyme-catalyzed isomerization of (R)-glyceraldehyde. Biochemistry 2011; 50:10170-81. [PMID: 21995300 DOI: 10.1021/bi201378c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
D-Xylose isomerase (XI) and triosephosphate isomerase (TIM) catalyze the aldose-ketose isomerization reactions of D-xylose and d-glyceraldehyde 3-phosphate (DGAP), respectively. D-Glyceraldehyde (DGA) is the triose fragment common to the substrates for XI and TIM. The XI-catalyzed isomerization of DGA to give dihydroxyacetone (DHA) in D(2)O was monitored by (1)H nuclear magnetic resonance spectroscopy, and a k(cat)/K(m) of 0.034 M(-1) s(-1) was determined for this isomerization at pD 7.0. This is similar to the k(cat)/K(m) of 0.017 M(-1) s(-1) for the TIM-catalyzed carbon deprotonation reaction of DGA in D(2)O at pD 7.0 [Amyes, T. L., O'Donoghue, A. C., and Richard, J. P. (2001) J. Am. Chem. Soc. 123, 11325-11326]. The much larger activation barrier for XI-catalyzed isomerization of D-xylose (k(cat)/K(m) = 490 M(-1) s(-1)) versus that for the TIM-catalyzed isomerization of DGAP (k(cat)/K(m) = 9.6 × 10(6) M(-1) s(-1)) is due to (i) the barrier to conversion of cyclic d-xylose to the reactive linear sugar (5.4 kcal/mol) being larger than that for conversion of DGAP hydrate to the free aldehyde (1.7 kcal/mol) and (ii) the intrinsic binding energy [Jencks, W. P. (1975) Adv. Enzymol. Relat. Areas Mol. Biol. 43, 219-410] of the terminal ethylene glycol fragment of D-xylose (9.3 kcal/mol) being smaller than that of the phosphodianion group of DGAP (~12 kcal/mol). The XI-catalyzed isomerization of DGA in D(2)O at pD 7.0 gives a 90% yield of [1-(1)H]DHA and a 10% yield of [1-(2)H]DHA, the product of isomerization with incorporation of deuterium from solvent D(2)O. By comparison, the transfer of (3)H from the labeled hexose substrate to solvent is observed only once in every 10(9) turnovers for the XI-catalyzed isomerization of [2-(3)H]glucose in H(2)O [Allen, K. N., Lavie, A., Farber, G. K., Glasfeld, A., Petsko, G. A., and Ringe, D. (1994) Biochemistry 33, 1481-1487]. We propose that truncation of the terminal ethylene glycol fragment of d-xylose to give DGA results in a large decrease in the rate of XI-catalyzed isomerization with hydride transfer compared with that for proton transfer. An ultra-high-resolution (0.97 Å) X-ray crystal structure was determined for the complex obtained by soaking crystals of XI with 50 mM DGA. The triose binds to XI as the unreactive hydrate, but ligand binding induces metal cofactor movement and conformational changes in active site residues similar to those observed for XI·sugar complexes.
Collapse
Affiliation(s)
- Maria M Toteva
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, USA
| | | | | | | |
Collapse
|
25
|
Fenn TD, Schnieders MJ, Mustyakimov M, Wu C, Langan P, Pande VS, Brunger AT. Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration. Structure 2011; 19:523-33. [PMID: 21481775 PMCID: PMC3083928 DOI: 10.1016/j.str.2011.01.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 01/13/2011] [Accepted: 01/14/2011] [Indexed: 10/18/2022]
Abstract
Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms.
Collapse
Affiliation(s)
- Timothy D Fenn
- Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | | | | | | | | | | | | |
Collapse
|
26
|
Abstract
Molecular dynamics simulations employing a combined quantum mechanical and molecular mechanical potential have been carried out to elucidate the reaction mechanism of the hydrolysis of a cyclic nucleotide cAMP substrate by phosphodiesterase 4B (PDE4B). PDE4B is a member of the PDE superfamily of enzymes that play crucial roles in cellular signal transduction. We have determined a two-dimensional potential of mean force (PMF) for the coupled phosphoryl bond cleavage and proton transfer through a general acid catalysis mechanism in PDE4B. The results indicate that the ring-opening process takes place through an S(N)2 reaction mechanism, followed by a proton transfer to stabilize the leaving group. The computed free energy of activation for the PDE4B-catalyzed cAMP hydrolysis is about 13 kcal·mol(-1) and an overall reaction free energy is about -17 kcal·mol(-1), both in accord with experimental results. In comparison with the uncatalyzed reaction in water, the enzyme PDE4B provides a strong stabilization of the transition state, lowering the free energy barrier by 14 kcal·mol(-1). We found that the proton transfer from the general acid residue His234 to the O3' oxyanion of the ribosyl leaving group lags behind the nucleophilic attack, resulting in a shallow minimum on the free energy surface. A key contributing factor to transition state stabilization is the elongation of the distance between the divalent metal ions Zn(2+) and Mg(2+) in the active site as the reaction proceeds from the Michaelis complex to the transition state.
Collapse
Affiliation(s)
- Kin-Yiu Wong
- Department of Chemistry, Digital Technology Center, University of Minnesota, Minneapolis, MN 55455, USA.
| | | |
Collapse
|
27
|
Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study. Structure 2010; 18:688-99. [PMID: 20541506 DOI: 10.1016/j.str.2010.03.011] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 01/11/2010] [Accepted: 03/08/2010] [Indexed: 11/21/2022]
Abstract
Conversion of aldo to keto sugars by the metalloenzyme D-xylose isomerase (XI) is a multistep reaction that involves hydrogen transfer. We have determined the structure of this enzyme by neutron diffraction in order to locate H atoms (or their isotope D). Two studies are presented, one of XI containing cadmium and cyclic D-glucose (before sugar ring opening has occurred), and the other containing nickel and linear D-glucose (after ring opening has occurred but before isomerization). Previously we reported the neutron structures of ligand-free enzyme and enzyme with bound product. The data show that His54 is doubly protonated on the ring N in all four structures. Lys289 is neutral before ring opening and gains a proton after this; the catalytic metal-bound water is deprotonated to hydroxyl during isomerization and O5 is deprotonated. These results lead to new suggestions as to how changes might take place over the course of the reaction.
Collapse
|
28
|
|
29
|
Yoshida H, Yamaji M, Ishii T, Izumori K, Kamitori S. Catalytic reaction mechanism of Pseudomonas stutzeri l-rhamnose isomerase deduced from X-ray structures. FEBS J 2010; 277:1045-57. [DOI: 10.1111/j.1742-4658.2009.07548.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
30
|
Lv YK, Zhan CH, Feng YL. A chiral manganese–potassium heterometallic MOF with an unusual (3,7)-connected network. CrystEngComm 2010. [DOI: 10.1039/b925546j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
31
|
Wu R, Xie H, Mo Y, Cao Z. Broad Substrate Specificity and Catalytic Mechanism of Pseudomonas stutzeri l-Rhamnose Isomerase: Insights from QM/MM Molecular Dynamics Simulations. J Phys Chem A 2009; 113:11595-603. [DOI: 10.1021/jp901093g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ruibo Wu
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China, and Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008
| | - Hujun Xie
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China, and Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008
| | - Yirong Mo
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China, and Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008
| | - Zexing Cao
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China, and Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008
| |
Collapse
|
32
|
Ruiz-Pernía JJ, Garcia-Viloca M, Bhattacharyya S, Gao J, Truhlar DG, Tuñón I. Critical role of substrate conformational change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase. J Am Chem Soc 2009; 131:2687-98. [PMID: 19199636 PMCID: PMC2746755 DOI: 10.1021/ja8087423] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
4-Oxalocrotonate tautomerase enzyme (4-OT) catalyzes the isomerization of 2-oxo-4-hexenedioate to 2-oxo-3-hexenedioate. The chemical process involves two proton transfers, one from a carbon of the substrate to the nitrogen of Pro1 and another from this nitrogen atom to a different carbon of the substrate. In this paper the isomerization has been studied using the combined quantum mechanical and molecular mechanical method with a dual-level treatment of the quantum subsystem employing the MPW1BK density functional as the higher level. Exploration of the potential energy surface shows that the process is stepwise, with a stable intermediate state corresponding to the deprotonated substrate and a protonated proline. The rate constant of the overall process has been evaluated using ensemble-averaged variational transition state theory, including the quantized vibrational motion of a primary zone of active-site atoms and a transmission coefficient based on an ensemble of optimized reaction coordinates to account for recrossing trajectories and optimized multidimensional tunneling. The two proton-transfer steps have similar free energy barriers, but the transition state associated with the first proton transfer is found to be higher in energy. The calculations show that reaction progress is coupled to a conformational change of the substrate, so it is important that the simulation allows this flexibility. The coupled conformational change is promoted by changes in the electron distribution of the substrate that take place as the proton transfers occur.
Collapse
Affiliation(s)
| | - Mireia Garcia-Viloca
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona (SPAIN)
- Departament de Química, Universitat Autònoma de Barcelona , Barcelona (SPAIN)
| | - Sudeep Bhattacharyya
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minneasota 55455-0431
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minneasota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minneasota 55455-0431
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, València (SPAIN)
| |
Collapse
|
33
|
Burkhardt A, Spielberg E, Simon S, Görls H, Buchholz A, Plass W. Hydrogen Bonds as Structural Directive towards Unusual Polynuclear Complexes: Synthesis, Structure, and Magnetic Properties of Copper(II) and Nickel(II) Complexes with a 2-Aminoglucose Ligand. Chemistry 2008; 15:1261-71. [DOI: 10.1002/chem.200800670] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
34
|
Buchholz K, Seibel J. Industrial carbohydrate biotransformations. Carbohydr Res 2008; 343:1966-79. [DOI: 10.1016/j.carres.2008.02.007] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 02/04/2008] [Accepted: 02/06/2008] [Indexed: 11/16/2022]
|
35
|
Wu R, Xie H, Cao Z, Mo Y. Combined Quantum Mechanics/Molecular Mechanics Study on the Reversible Isomerization of Glucose and Fructose Catalyzed by Pyrococcus furiosus Phosphoglucose Isomerase. J Am Chem Soc 2008; 130:7022-31. [DOI: 10.1021/ja710633c] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ruibo Wu
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, 361005, China, and Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008
| | - Hujun Xie
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, 361005, China, and Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008
| | - Zexing Cao
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, 361005, China, and Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008
| | - Yirong Mo
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, 361005, China, and Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008
| |
Collapse
|
36
|
Liu C, Li D, Liang YH, Li LF, Su XD. Ring-Opening Mechanism Revealed by Crystal Structures of NagB and Its ES Intermediate Complex. J Mol Biol 2008; 379:73-81. [DOI: 10.1016/j.jmb.2008.03.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 03/12/2008] [Accepted: 03/17/2008] [Indexed: 11/26/2022]
|
37
|
Tan TC, Mijts BN, Swaminathan K, Patel BK, Divne C. Crystal Structure of the Polyextremophilic α-Amylase AmyB from Halothermothrix orenii: Details of a Productive Enzyme–Substrate Complex and an N Domain with a Role in Binding Raw Starch. J Mol Biol 2008; 378:852-70. [DOI: 10.1016/j.jmb.2008.02.041] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Revised: 02/15/2008] [Accepted: 02/19/2008] [Indexed: 11/15/2022]
|
38
|
Borgi MA, Rhimi M, Bejar S. Involvement of alanine 103 residue in kinetic and physicochemical properties of glucose isomerases fromStreptomyces species. Biotechnol J 2007; 2:254-9. [PMID: 17203501 DOI: 10.1002/biot.200600085] [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] [Indexed: 11/12/2022]
Abstract
The Ala103 to Gly mutation, introduced within the glucose isomerase from Streptomyces sp. SK (SKGI) decreased its catalytic efficiency (k(cat)/K(m)) toward D-glucose from 7.1 to 3 mM(-1) min(-1). The reverse counterpart replacement Gly103Ala introduced into the glucose isomerase of Streptomyces olivochromogenes (SOGI) considerably improved its catalytic efficiency to be 6.7 instead of 3.2 mM(-1) min(-1). This later mutation also increased the half-life time of the enzyme from 70 to 95 min at 80 degrees C and mainly modified its pH profile. These results provide evidence that the residue Ala103 plays an essential role in the kinetic and physicochemical properties of glucose isomerases from Streptomyces species.
Collapse
Affiliation(s)
- Mohamed Ali Borgi
- Laboratory of Prokaryotic Enzymes and Metabolites, Center of Biotechnology of Sfax, Sfax, Tunisia
| | | | | |
Collapse
|
39
|
Ding X, Rasmussen BF, Petsko GA, Ringe D. Direct crystallographic observation of an acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of a peptidyl ester substrate: Exploiting the "glass transition" in protein dynamics. Bioorg Chem 2006; 34:410-23. [PMID: 17083959 PMCID: PMC1751290 DOI: 10.1016/j.bioorg.2006.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 10/10/2006] [Accepted: 10/10/2006] [Indexed: 11/28/2022]
Abstract
The crystal structure of the acyl complex of porcine pancreatic elastase with its peptidyl ester substrate N-acetyl-ala-ala-ala-methyl ester (Ac(Ala)3OMe) has been determined at 2.5 A resolution. The complex was stabilized by exploiting the "glass transition" in protein dynamics that occurs at around -53 degrees C (220 K). Substrate was flowed into the crystal in a cryoprotective solvent above this temperature, and then the crystal was rapidly cooled to a temperature below the transition to trap the species that formed. The use of a flow cell makes the experiment a kinetic one and means that the species prior to the rate determining transition state has a chance to accumulate. The resulting crystal structure shows an acyl-enzyme intermediate in which the leaving group is absent and the carbonyl carbon of the C-terminal alanine residue is covalently bound to the gamma oxygen of the active site serine. The ester carbonyl shows no significant distortion from planarity, with the carbonyl oxygen forming one hydrogen bond with the oxyanion hole. The tripeptide is bound in an extended antiparallel beta-sheet with main chain residues of the enzyme. The geometry and interactions of this acyl-enzyme suggest that it represents a productive intermediate. To test this hypothesis, the same crystal was then warmed above the glass transition temperature and a second data set was collected. The resulting electron density map shows no sign of the substrate, indicating hydrolysis of the intermediate followed by product release. This experiment provides direct evidence for the importance of dynamic properties in catalysis and also provides a blueprint for the stabilization of other short-lived species for direct crystallographic observation.
Collapse
Affiliation(s)
| | | | | | - Dagmar Ringe
- *To whom correspondence should be addressed. Telephone: (781) 736-4902; FAX: (781) 736-2405; E-MAIL:
| |
Collapse
|
40
|
Burkhardt A, Buchholz A, Görls H, Plass W. Synthesis, Structure and Magnetic Properties of a Tetranuclear Copper(II) Complex on the Basis of a 2-Substituted Glucopyranoside Schiff Base Ligand. Eur J Inorg Chem 2006. [DOI: 10.1002/ejic.200600404] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
41
|
Häusler H, Weber H, Stütz* AE. D-XYLOSE (D-GLUCOSE) ISOMERASE (EC 5.3.1.5): OBSERVATIONS AND COMMENTS CONCERNING STRUCTURAL REQUIREMENTS OF SUBSTRATES AS WELL AS MECHANISTIC FEATURES. J Carbohydr Chem 2006. [DOI: 10.1081/car-100104860] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Herwig Häusler
- a Glycogroup, Institut für Organische Chemie, Technische Universität Graz , Stremayrgasse 16, Graz, A-8010, Austria
| | - Hansjörg Weber
- a Glycogroup, Institut für Organische Chemie, Technische Universität Graz , Stremayrgasse 16, Graz, A-8010, Austria
| | - Arnold E. Stütz*
- a Glycogroup, Institut für Organische Chemie, Technische Universität Graz , Stremayrgasse 16, Graz, A-8010, Austria
| |
Collapse
|
42
|
Gao J, Ma S, Major DT, Nam K, Pu J, Truhlar DG. Mechanisms and free energies of enzymatic reactions. Chem Rev 2006; 106:3188-209. [PMID: 16895324 PMCID: PMC4477011 DOI: 10.1021/cr050293k] [Citation(s) in RCA: 317] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiali Gao
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Shuhua Ma
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Dan T. Major
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Kwangho Nam
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jingzhi Pu
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| |
Collapse
|
43
|
Kato M, Sah AK, Tanase T, Mikuriya M. Tetranuclear Copper(II) Complexes Bridged by α-d-Glucose-1-Phosphate and Incorporation of Sugar Acids through the Cu4 Core Structural Changes. Inorg Chem 2006; 45:6646-60. [PMID: 16903719 DOI: 10.1021/ic060202h] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tetranuclear copper(II) complexes containing alpha-D-glucose-1-phosphate (alpha-D-Glc-1P), [Cu4(mu-OH){mu-(alpha-D-Glc-1P)}2(bpy)4(H2O)2]X3 [X = NO3 (1a), Cl (1b), Br (1c)], and [Cu4(mu-OH){mu-(alpha-D-Glc-1P)}2(phen)4(H2O)2](NO3)3 (2) were prepared by reacting the copper(II) salt with Na2[alpha-D-Glc-1P] in the presence of diimine ancillary ligands, and the structure of 2 was characterized by X-ray crystallography to comprise four {Cu(phen)}2+ fragments connected by the two sugar phosphate dianions in 1,3-O,O' and 1,1-O mu4-bridging fashion as well as a mu-hydroxo anion. The crystal structure of 2 involves two chemically independent complex cations in which the C2 enantiomeric structure for the trapezoidal tetracopper(II) framework is switched according to the orientation of the alpha-D-glucopyranosyl moieties. Temperature-dependent magnetic susceptibility data of 1a indicated that antiferromagnetic spin coupling is operative between the two metal ions joined by the hydroxo bridge (J = -52 cm(-1)) while antiferromagnetic interaction through the Cu-O-Cu sugar phosphate bridges is weak (J = -13 cm(-1)). Complex 1a readily reacted with carboxylic acids to afford the tetranuclear copper(II) complexes, [Cu4{mu-(alpha-D-Glc-1P)}2(mu-CA)2(bpy)4](NO3)2 [CA = CH3COO (3), o-C6H4(COO)(COOH) (4)]. Reactions with m-phenylenediacetic acid [m-C6H4(CH2COOH)2] also gave the discrete tetracopper(II) cationic complex [Cu4{mu-(alpha-D-Glc-1P)}2(mu-m-C6H4(CH2COO)(CH2COOH))2(bpy)4](NO3)2 (5a) as well as the cluster polymer formulated as {[Cu4{mu-(alpha-D-Glc-1P)}2(mu-m-C6H4(CH2COO)2)(bpy)4](NO3)2}n (5b). The tetracopper structure of 1a is converted into a symmetrical rectangular core in complexes 3, 4, and 5b, where the hydroxo bridge is dissociated and, instead, two carboxylate anions bridge another pair of Cu(II) ions in a 1,1-O monodentate fashion. The similar reactions were applied to incorporate sugar acids onto the tetranuclear copper(II) centers. Reactions of 1a with delta-D-gluconolactone, D-glucuronic acid, or D-glucaric acid in dimethylformamide resulted in the formation of discrete tetracopper complexes with sugar acids, [Cu4{mu-(alpha-D-Glc-1P)}2(mu-SA)2(bpy)4](NO3)2 [SA = D-gluconate (6), D-glucuronate (7), D-glucarateH (8a)]. The structures of 6 and 7 were determined by X-ray crystallography to be almost identical with that of 3 with additional chelating coordination of the C-2 hydroxyl group of D-gluconate moieties (6) or the C-5 cyclic O atom of D-glucuronate units (7). Those with D-glucaric acid and D-lactobionic acid afforded chiral one-dimensional polymers, {[Cu4{mu-(alpha-D-Glc-1P)}2(mu-D-glucarate)(bpy)4](NO3)2}n (8b) and {[Cu4{mu-(alpha-D-Glc-1P)}2(mu-D-lactobionate)(bpy)4(H2O)2](NO3)3}n (9), respectively, in which the D-Glc-1P-bridged tetracopper(II) units are connected by sugar acid moieties through the C-1 and C-6 carboxylate O atoms in 8b and the C-1 carboxylate and C-6 alkoxy O atoms of the gluconate chain in 9. When complex 7 containing d-glucuronate moieties was heated in water, the mononuclear copper(II) complex with 2-dihydroxy malonate, [Cu(mu-O2CC(OH)2CO2)(bpy)] (10), and the dicopper(II) complex with oxalate, [Cu2(mu-C2O4)(bpy)2(H2O)2](NO3)2 (11), were obtained as a result of oxidative degradation of the carbohydrates through C-C bond cleavage reactions.
Collapse
Affiliation(s)
- Merii Kato
- Department of Chemistry, Faculty of Science, Nara Women's University, Kitauoya-higashi-machi, Nara 630-8285, Japan
| | | | | | | |
Collapse
|
44
|
Manjasetty BA, Chance MR. Crystal Structure of Escherichia coli L-Arabinose Isomerase (ECAI), The Putative Target of Biological Tagatose Production. J Mol Biol 2006; 360:297-309. [PMID: 16756997 DOI: 10.1016/j.jmb.2006.04.040] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 04/12/2006] [Accepted: 04/19/2006] [Indexed: 10/24/2022]
Abstract
Escherichia coli L-arabinose isomerase (ECAI; EC 5.3.1.4) catalyzes the isomerization of L-arabinose to L-ribulose in vivo. This enzyme is also of commercial interest as it catalyzes the conversion of D-galactose to D-tagatose in vitro. The crystal structure of ECAI was solved and refined at 2.6 A resolution. The subunit structure of ECAI is organised into three domains: an N-terminal, a central and a C-terminal domain. It forms a crystallographic trimeric architecture in the asymmetric unit. Packing within the crystal suggests the idea that ECAI can form a hexameric assembly. Previous electron microscopic and biochemical studies supports that ECAI is hexameric in solution. A comparison with other known structures reveals that ECAI adopts a protein fold most similar to E. coli fucose isomerase (ECFI) despite very low sequence identity 9.7%. The structural similarity between ECAI and ECFI with regard to number of domains, overall fold, biological assembly, and active site architecture strongly suggests that the enzymes have functional similarities. Further, the crystal structure of ECAI forms a basis for identifying molecular determinants responsible for isomerization of arabinose to ribulose in vivo and galactose to tagatose in vitro.
Collapse
Affiliation(s)
- Babu A Manjasetty
- New York Structural Genomix Research Consortium, Center for Synchrotron Biosciences, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | |
Collapse
|
45
|
Meilleur F, Snell EH, van der Woerd MJ, Judge RA, Myles DAA. A quasi-Laue neutron crystallographic study of d-xylose isomerase. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2006; 35:601-9. [PMID: 16673077 DOI: 10.1007/s00249-006-0066-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 03/29/2006] [Accepted: 04/04/2006] [Indexed: 10/24/2022]
Abstract
The location of hydrogen atoms in enzyme structures can bring critical understanding of catalytic mechanism. However, whilst it is often difficult to determine the position of hydrogen atoms using X-ray crystallography even with subatomic (<1.0 A) resolution data available, neutron crystallography provides an experimental tool to directly localize hydrogen/deuterium atoms in biological macromolecules at resolution of 1.5-2.0 A. D-Xylose isomerase (D-xylose ketol-isomerase, EC 5.3.1.5) is a 43 kDa enzyme that catalyses the first reaction in the catabolism of D-xylose. Linearization and isomerization of D-xylose at the active site of D-xylose isomerase rely upon a complex hydrogen transfer. Neutron quasi-Laue data at 2.2 A resolution were collected at room temperature on a partially deuterated Streptomyces rubiginosus D-xylose isomerase crystal using the LADI instrument at ILL with the objective to provide insight into the enzymatic mechanism. The neutron structure shows unambiguously that residue His 53 is doubly protonated at the active site of the enzyme. This suggests that the reaction proceeds through an acid catalyzed opening of the sugar ring, which is in accord with the mechanism suggested by Fenn et al. (Biochemistry 43(21): 6464-6474, 2004). This is the first report of direct observation of double protonation of His 53 and the first validation of the ring opening mechanism at the active site of D-xylose isomerase.
Collapse
Affiliation(s)
- Flora Meilleur
- Institut Laue Langevin, BP 156, 38042, Grenoble, France.
| | | | | | | | | |
Collapse
|
46
|
Kappl R, Ranguelova K, Koch B, Duboc C, Hüttermann J. Multi-frequency high-field EPR studies on metal-substituted xylose isomerase. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2005; 43 Spec no.:S65-73. [PMID: 16235215 DOI: 10.1002/mrc.1691] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The bacterial enzyme D-xylose isomerase (XI) catalyses the conversion of D-xylose to D-xylulose. Each subunit of the homotetrameric protein contains a bimetallic active centre requiring divalent metal ions such as Mg2+, Mn2+ or Co2+ for catalytic activity. We report here on XI in which the metal binding site 1 is specifically loaded with EPR active Mn2+, while binding site 2 is occupied by Co2+ or Cd2+, rendering a catalytically active or inactive species respectively. The Q-band (34 GHz) EPR spectra of these mixed-metal samples (Co2+/Mn2+ and Cd2+/Mn2+ XI) show a clear influence of the metal in site 2 on the Mn2+ EPR parameters. Likewise, a systematic increase of the zero field splitting parameters (zfs) of Mn2+ in site 1 upon incubation with the inhibitor xylitol or substrates for both mixed-metal samples is found. For Co2+/Mn2+ XI complexed with substrate, a drastic line broadening of the central -1/2 <--> +1/2 transition is observed in Q-band EPR, which was not amenable to analysis so far. By means of a multi-frequency approach at frequencies beyond Q-band, the relevant zfs parameters were derived from spectral simulations of EPR spectra measured at 94, 285 and 670 GHz. It is shown that parallel to the increase of the D-value its distribution also grows considerably in going from free Co2+/Mn2+ XI to the species complexed with inhibitor or substrate. For XI with bound substrate, D-values in the range of 70-90 mT and a distribution of about 30 mT were found from simulation trials. The large distribution in zfs values is thought to be correlated to the structural disorder induced by the shift of the metal ion of site 2 into a location necessary for the isomerisation reaction. The results are discussed with respect to high-resolution crystal data.
Collapse
Affiliation(s)
- R Kappl
- Institut fuer Biophysik, FR 2.5, Geb. 76, Klinikum, Universität des Saarlandes, 66421 Homburg, Germany
| | | | | | | | | |
Collapse
|
47
|
Bagchi A, Ghosh TC. Structural insight into the interactions of SoxV, SoxW and SoxS in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle. Biophys Chem 2005; 119:7-13. [PMID: 16183190 DOI: 10.1016/j.bpc.2005.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 08/29/2005] [Accepted: 08/29/2005] [Indexed: 10/25/2022]
Abstract
Microbial redox reactions involving inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically diverse prokaryotes, some of which also take part in the extraction of metal ions from their sulfur containing ores. These sulfur oxidizers oxidize inorganic sulfur compounds like sulfide, thiosulfate etc. to produce reductants that are used for carbon dioxide fixation or in respiratory electron transfer chains. The sulfur oxidizing gene cluster (sox) of alpha-Proteobacteria comprises of at least 15 genes, forming two transcriptional units, viz., soxSR and soxVWXYZABCDEFGH. SoxV is known to be a CcdA homolog involved in the transport of reductants from cytoplasm to periplasm. SoxW and SoxS are periplasmic thioredoxins, which (SoxW) interact with SoxV and thereby help in the redox reactions. We have employed homology modeling to construct the three-dimensional structures of the SoxV, SoxW and SoxS proteins from Rhodovulum sulfidophilum. With the help of docking and molecular dynamics simulations we have identified the amino acid residues of these proteins involved in the interaction. The probable biochemical mechanism of the transport of reductants through the interactions of these proteins has also been investigated. Our study provides a rational basis to interpret the molecular mechanism of the biochemistry of sulfur anion oxidation reactions by these ecologically important organisms.
Collapse
Affiliation(s)
- Angshuman Bagchi
- Bioinformatics Center, Bose Institute, AJC Bose Centenary Building, P1/12 CIT Scheme VIIM, Kolkata 700 054, India.
| | | |
Collapse
|
48
|
Epting KL, Vieille C, Zeikus JG, Kelly RM. Influence of divalent cations on the structural thermostability and thermal inactivation kinetics of class II xylose isomerases. FEBS J 2005; 272:1454-64. [PMID: 15752361 DOI: 10.1111/j.1742-4658.2005.04577.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The effects of divalent metal cations on structural thermostability and the inactivation kinetics of homologous class II d-xylose isomerases (XI; EC 5.3.1.5) from mesophilic (Escherichia coli and Bacillus licheniformis), thermophilic (Thermoanaerobacterium thermosulfurigenes), and hyperthermophilic (Thermotoga neapolitana) bacteria were examined. Unlike the three less thermophilic XIs that were substantially structurally stabilized in the presence of Co2+ or Mn2+ (and Mg2+ to a lesser extent), the melting temperature [(Tm) approximately 100 degrees C] of T. neapolitana XI (TNXI) varied little in the presence or absence of a single type of metal. In the presence of any two of these metals, TNXI exhibited a second melting transition between 110 degrees C and 114 degrees C. TNXI kinetic inactivation, which was non-first order, could be modeled as a two-step sequential process. TNXI inactivation in the presence of 5 mm metal at 99-100 degrees C was slowest in the presence of Mn2+[half-life (t(1/2)) of 84 min], compared to Co2+ (t(1/2) of 14 min) and Mg2+ (t(1/2) of 2 min). While adding Co2+ to Mg2+ increased TNXI's t(1/2) at 99-100 degrees C from 2 to 7.5 min, TNXI showed no significant activity at temperatures above the first melting transition. The results reported here suggest that, unlike the other class II XIs examined, single metals are required for TNXI activity, but are not essential for its structural thermostability. The structural form corresponding to the second melting transition of TNXI in the presence of two metals is not known, but likely results from cooperative interactions between dissimilar metals in the two metal binding sites.
Collapse
Affiliation(s)
- Kevin L Epting
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | | | | | | |
Collapse
|
49
|
Garcia-Viloca M, Poulsen TD, Truhlar DG, Gao J. Sensitivity of molecular dynamics simulations to the choice of the X-ray structure used to model an enzymatic reaction. Protein Sci 2005; 13:2341-54. [PMID: 15322278 PMCID: PMC2280009 DOI: 10.1110/ps.03504104] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A subject of great practical importance that has not received much attention is the question of the sensitivity of molecular dynamics simulations to the initial X-ray structure used to set up the calculation. We have found two cases in which seemingly similar structures lead to quite different results, and in this article we present a detailed analysis of these cases. The first case is acyl-CoA dehydrogenase, and the chief difference of the two structures is attributed to a slight shift in a backbone carbonyl that causes a key residue (the proton-abstracting base) to be in a bad conformation for reaction. The second case is xylose isomerase, and the chief difference of the two structures appears to be the ligand sphere of a Mg2+ metal cofactor that plays an active role in catalysis.
Collapse
Affiliation(s)
- Mireia Garcia-Viloca
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | |
Collapse
|
50
|
Leang K, Takada G, Fukai Y, Morimoto K, Granström TB, Izumori K. Novel reactions of l-rhamnose isomerase from Pseudomonas stutzeri and its relation with d-xylose isomerase via substrate specificity. Biochim Biophys Acta Gen Subj 2004; 1674:68-77. [PMID: 15342115 DOI: 10.1016/j.bbagen.2004.06.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Revised: 05/24/2004] [Accepted: 06/03/2004] [Indexed: 11/26/2022]
Abstract
Escherichia coli strain JM 109 harboring 6 x His-tag L-rhamnose isomerase (L-RhI) from Pseudomonas stutzeri allowed a 20-fold increase in the volumetric yield of soluble enzyme compared to the value for the intrinsic yield. Detailed studies on the substrate specificity of the purified His-tagged protein revealed that it catalyzed previously unknown common and rare aldo/ketotetrose, aldo/ketopentose, and aldo/ketohexose substrates in both D- and L-forms, for instance, erythrose, threose, xylose, lyxose, ribose, glucose, mannose, galactose, altrose, tagatose, sorbose, psicose, and fructose. Using a high enzyme-substrate ratio in extended reactions, the enzyme-catalyzed interconversion reactions from which two different products from one substrate were formed: L-lyxose, L-glucose, L-tagatose and D-allose were isomerized to L-xylulose and L-xylose, L-fructose and L-mannose, L-galactose and L-talose, and D-psicose and D-altrose, in that order. Kinetic studies, however, showed that L-rhamnose with Km and Vmax values of 11 mM and 240 U/mg, respectively, was the most preferred substrate, followed by L-mannose, L-lyxose, D-ribose, and D-allose. Based on the observed catalytic mode of action, these new findings reflected a hitherto undetected interrelation between L-RhI and D-xylose isomerase (D-XI).
Collapse
Affiliation(s)
- Khim Leang
- Department of Biochemistry and Food Science, Faculty of Agriculture and Rare Sugar Research Center, Kagawa University, Ikenobe 2393, Miki-cho, Kagawa 761-0795, Japan
| | | | | | | | | | | |
Collapse
|