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Young HE, Donohue MP, Smirnova TI, Smirnov AI, Zhou P. The UDP-diacylglucosamine pyrophosphohydrolase LpxH in lipid A biosynthesis utilizes Mn2+ cluster for catalysis. J Biol Chem 2013; 288:26987-27001. [PMID: 23897835 DOI: 10.1074/jbc.m113.497636] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Escherichia coli and the majority of β- and γ-proteobacteria, the fourth step of lipid A biosynthesis, i.e. cleavage of the pyrophosphate group of UDP-2,3-diacyl-GlcN, is carried out by LpxH. LpxH has been previously suggested to contain signature motifs found in the calcineurin-like phosphoesterase (CLP) family of metalloenzymes; however, it cleaves a pyrophosphate bond instead of a phosphoester bond, and its substrate contains nucleoside diphosphate moieties more common to the Nudix family rather than to the CLP family. Furthermore, the extent of biochemical data fails to demonstrate a significant level of metal activation in enzymatic assays, which is inconsistent with the behavior of a metalloenzyme. Here, we report cloning, purification, and detailed enzymatic characterization of Haemophilus influenzae LpxH (HiLpxH). HiLpxH shows over 600-fold stimulation of hydrolase activity in the presence of Mn(2+). EPR studies reveal the presence of a Mn(2+) cluster in LpxH. Finally, point mutants of residues in the conserved metal-binding motifs of the CLP family greatly inhibit HiLpxH activity, highlighting their importance in enzyme function. Contrary to previous analyses of LpxH, we find HiLpxH does not obey surface dilution kinetics. Overall, our work unambiguously establishes LpxH as a calcineurin-like phosphoesterase containing a Mn(2+) cluster coordinated by conserved residues. These results set the scene for further structural investigation of the enzyme and for design of novel antibiotics targeting lipid A biosynthesis.
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Affiliation(s)
- Hayley E Young
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Matthew P Donohue
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - Tatyana I Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - Alex I Smirnov
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710.
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Alberto ME, Marino T, Russo N, Sicilia E, Toscano M. The performance of density functional based methods in the description of selected biological systems and processes. Phys Chem Chem Phys 2012; 14:14943-53. [DOI: 10.1039/c2cp41836c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Alberto ME, Marino T, Ramos MJ, Russo N. Atomistic details of the Catalytic Mechanism of Fe(III)−Zn(II) Purple Acid Phosphatase. J Chem Theory Comput 2010; 6:2424-33. [DOI: 10.1021/ct100187c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Marta E. Alberto
- Dipartimento di Chimica, Università della Calabria,Via P. Bucci, cubo 14c, 87036 Arcavacata di Rende (CS), Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite−Centro d’Eccellenza MIUR, Italy and REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Tiziana Marino
- Dipartimento di Chimica, Università della Calabria,Via P. Bucci, cubo 14c, 87036 Arcavacata di Rende (CS), Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite−Centro d’Eccellenza MIUR, Italy and REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- Dipartimento di Chimica, Università della Calabria,Via P. Bucci, cubo 14c, 87036 Arcavacata di Rende (CS), Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite−Centro d’Eccellenza MIUR, Italy and REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Nino Russo
- Dipartimento di Chimica, Università della Calabria,Via P. Bucci, cubo 14c, 87036 Arcavacata di Rende (CS), Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite−Centro d’Eccellenza MIUR, Italy and REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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Mitić N, Smith SJ, Neves A, Guddat LW, Gahan LR, Schenk G. The catalytic mechanisms of binuclear metallohydrolases. Chem Rev 2007; 106:3338-63. [PMID: 16895331 DOI: 10.1021/cr050318f] [Citation(s) in RCA: 362] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natasa Mitić
- School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
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Marasinghe GPK, Sander IM, Bennett B, Periyannan G, Yang KW, Makaroff CA, Crowder MW. Structural studies on a mitochondrial glyoxalase II. J Biol Chem 2005; 280:40668-75. [PMID: 16227621 PMCID: PMC1343529 DOI: 10.1074/jbc.m509748200] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glyoxalase 2 is a beta-lactamase fold-containing enzyme that appears to be involved with cellular chemical detoxification. Although the cytoplasmic isozyme has been characterized from several organisms, essentially nothing is known about the mitochondrial proteins. As a first step in understanding the structure and function of mitochondrial glyoxalase 2 enzymes, a mitochondrial isozyme (GLX2-5) from Arabidopsis thaliana was cloned, overexpressed, purified, and characterized using metal analyses, EPR and (1)H NMR spectroscopies, and x-ray crystallography. The recombinant enzyme was shown to bind 1.04 +/- 0.15 eq of iron and 1.31 +/- 0.05 eq of Zn(II) and to exhibit k(cat) and K(m) values of 129 +/- 10 s(-1) and 391 +/- 48 microm, respectively, when using S-d-lactoylglutathione as the substrate. EPR spectra revealed that recombinant GLX2-5 contains multiple metal centers, including a predominant Fe(III)Z-n(II) center and an anti-ferromagnetically coupled Fe(III)Fe(II) center. Unlike cytosolic glyoxalase 2 from A. thaliana, GLX2-5 does not appear to specifically bind manganese. (1)H NMR spectra revealed the presence of at least eight paramagnetically shifted resonances that arise from protons in close proximity to a Fe(III)Fe(II) center. Five of these resonances arose from solvent-exchangeable protons, and four of these have been assigned to NH protons on metal-bound histidines. A 1.74-A resolution crystal structure of the enzyme revealed that although GLX2-5 shares a number of structural features with human GLX2, several important differences exist. These data demonstrate that mitochondrial glyoxalase 2 can accommodate a number of different metal centers and that the predominant metal center is Fe(III)Zn(II).
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Affiliation(s)
- Gishanthi P. K. Marasinghe
- From the Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056 and the
| | - Ian M. Sander
- From the Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056 and the
| | - Brian Bennett
- National Biomedical EPR Center, Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226-0509
| | - Gopalraj Periyannan
- From the Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056 and the
| | - Ke-Wu Yang
- From the Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056 and the
| | - Christopher A. Makaroff
- From the Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056 and the
| | - Michael W. Crowder
- From the Department of Chemistry and Biochemistry, Miami University, 160 Hughes Hall, Oxford, OH 45056 and the
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Funhoff EG, Bollen M, Averill BA. The Fe(III)Zn(II) form of recombinant human purple acid phosphatase is not activated by proteolysis. J Inorg Biochem 2005; 99:521-9. [PMID: 15621285 DOI: 10.1016/j.jinorgbio.2004.10.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2004] [Revised: 10/21/2004] [Accepted: 10/25/2004] [Indexed: 10/26/2022]
Abstract
The kinetics and spectroscopic properties of the single polypeptide and proteolytically cleaved form of recombinant Fe(3+)Fe(2+) human purple acid phosphatase (recHPAP) exhibit significant differences, primarily due to a difference in pK(es,1) (the value of an acid dissociation constant of the ES complex). These differences are due to the presence or absence, respectively, of an interaction between an aspartate residue in an exposed loop of the protein and one or more active site residues. To further explore the origin of these differences, the ferrous ion of recHPAP has been replaced by zinc. Analysis of the reconstituted Fe(3+)Zn(2+)recHPAP reveals an unexpected catalytic activity versus pH profile, in that the optimal pH is 6.3, similar to that of the proteolytically cleaved form (6.5). Moreover, replacement of the ferrous ion by zinc increases the turnover number more than 10-fold; the pK(es) values are also shifted as expected for the change in the divalent metal ion. Although the EPR spectra of both single polypeptide and proteolytically cleaved Fe(3+)Zn(2+)-recHPAP are independent of pH over the range 4.5-6.2, the visible spectrum of Fe(3+)Zn(2+)-recHPAP is pH dependent. These results suggest that the properties and environment of the divalent metal are important in determining the catalytic properties of mammalian PAPs, and in particular that a solvent molecule coordinated to the divalent metal ion may play a critical role in the catalytic cycle of these enzymes.
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Affiliation(s)
- Enrico G Funhoff
- SILS, University of Amsterdam, Plantage Muidergracht 12, 1018 TV Amsterdam, The Netherlands
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Dikiy A, Funhoff EG, Averill BA, Ciurli S. New insights into the mechanism of purple acid phosphatase through (1)H NMR spectroscopy of the recombinant human enzyme. J Am Chem Soc 2002; 124:13974-5. [PMID: 12440878 DOI: 10.1021/ja027195q] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton NMR spectra of FeIII-FeII recombinant single polypeptide human PAP (recHPAP) have been measured at, above, and below its pH optimum, as have the spectra of inhibited forms containing fluoride and phosphate, analogues of the substrates hydroxide and phosphate esters, respectively. The results demonstrate that binding of inhibitory anions to the dinuclear mixed-valent site of recHPAP is controlled by protonation of a ligand to the dinuclear center. Thus, the group that is responsible for pKa,1 in the enzymatic activity versus pH profile functions as a "gatekeeper", whose protonation state controls anion binding to the mixed-valent dinuclear site. The correlation between the pKa values observed in kinetics studies and for the spectroscopic changes strongly suggests that this group is the nucleophilic hydroxide that attacks the phosphate ester substrate.
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Affiliation(s)
- Alexander Dikiy
- Department of Agro-Environmental Science and Technology, University of Bologna, Via Filippo Re 8, I-40127 Bologna, Italy
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Uppenberg J, Lindqvist F, Svensson C, Ek-Rylander B, Andersson G. Crystal structure of a mammalian purple acid phosphatase. J Mol Biol 1999; 290:201-11. [PMID: 10388567 DOI: 10.1006/jmbi.1999.2896] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tartrate-resistant acid phosphatase (TRAP) is a mammalian di-iron- containing enzyme that belongs to the family of purple acid phosphatases (PAP). It is highly expressed in a limited number of tissues, predominantly in bone-resorbing osteoclasts and in macrophages of spleen. We have determined the crystal structure of rat TRAP in complex with a phosphate ion to 2.7 A resolution. The fold resembles that of the catalytic domain of kidney bean purple acid phosphatase (KBPAP), although the sequence similarity is limited to the active site residues. A surface loop near the active site is absent due to proteolysis, leaving the active-site easily accessible from the surrounding solvent. This, we believe, gives a structural explanation for the observed proteolytic activation of TRAP. The current structure was determined at a relatively high pH and without any external reducing agents. It is likely that it represents an oxidized and therefore catalytically inactive form of the enzyme.
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Affiliation(s)
- J Uppenberg
- Department of Structural Chemistry, Pharmacia and Upjohn, Lindhagensgatan 133, Stockholm, S-112 87, Sweden.
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