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Michalak AL, Trieger GW, Trieger KA, Godula K. Stem Cell Microarrays for Assessing Growth Factor Signaling in Engineered Glycan Microenvironments. Adv Healthc Mater 2022; 11:e2101232. [PMID: 34541824 PMCID: PMC8854331 DOI: 10.1002/adhm.202101232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/19/2021] [Indexed: 02/03/2023]
Abstract
Extracellular glycans, such as glycosaminoglycans (GAGs), provide an essential regulatory component during the development and maintenance of tissues. GAGs, which harbor binding sites for a range of growth factors (GFs) and other morphogens, help establish gradients of these molecules in the extracellular matrix (ECM) and promote the formation of active signaling complexes when presented at the cell surface. As such, GAGs have been pursued as biologically active components for the development of biomaterials for cell-based regenerative therapies. However, their structural complexity and compositional heterogeneity make establishing structure-function relationships for this class of glycans difficult. Here, a stem cell array platform is described, in which chemically modified heparan sulfate (HS) GAG polysaccharides are conjugated to a gelatin matrix and introduced into a polyacrylamide hydrogel network. This array allowed for direct analysis of HS contributions to the signaling via the FGF2-dependent mitogen activated protein kinase (MAPK) pathway in mouse embryonic stem cells. With the recent emergence of powerful synthetic and recombinant technologies to produce well-defined GAG structures, a platform for analyzing both growth factor binding and signaling in response to the presence of these biomolecules will provide a powerful tool for integrating glycans into biomaterials to advance their biological properties and applications.
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Affiliation(s)
- Austen L. Michalak
- Deparment of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Greg W. Trieger
- Deparment of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Kelsey A. Trieger
- Deparment of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Kamil Godula
- Deparment of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA,Glycobiology Research and Training Center, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
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2
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Huddleston JP, Raushel FM. Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in Escherichia coli K12. Biochemistry 2019; 58:3354-3364. [PMID: 31314509 DOI: 10.1021/acs.biochem.9b00327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ydj gene cluster is annotated to catalyze the catabolism of an unknown carbohydrate. Previously, YdjI, a class II aldolase, was shown to catalyze the retro-aldol cleavage of l-glycero-l-galacto-octuluronate-1-phosphate into DHAP and l-arabinuronate. In this report, the functional characterization of YdjH is presented. YdjH catalyzes the phosphorylation of 2-keto-monosaccharides at the C1 hydroxyl group with a substrate profile significantly more stringent than that of YdjI. Similar to YdjI, YdjH shows a strong preference for higher-order monosaccharides (seven to nine carbons) with a carboxylate terminus. The best substrate was determined to be l-glycero-l-galacto-octuluronate, yielding l-glycero-l-galacto-octuluronate-1-phosphate with a kcat of 16 s-1 and a kcat/Km of 2.1 × 104 M-1 s-1. This is apparently the first reported example of kinase activity with eight-carbon monosaccharides. Two crystal structures of YdjH were previously determined to 2.15 and 1.8 Å resolution (Protein Data Bank entries 3H49 and 3IN1 ). We present an analysis of the active site layout and use computational docking to identify potential key residues in the binding of l-glycero-l-galacto-octuluronate.
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Affiliation(s)
- Jamison P Huddleston
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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Iradi-Serrano M, Tola-García L, Cortese MS, Ugalde U. The Early Asexual Development Regulator fluG Codes for a Putative Bifunctional Enzyme. Front Microbiol 2019; 10:778. [PMID: 31057506 PMCID: PMC6478659 DOI: 10.3389/fmicb.2019.00778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/27/2019] [Indexed: 11/13/2022] Open
Abstract
FluG is a long recognized early regulator of asexual development in Aspergillus nidulans. fluG null mutants show profuse aerial growth and no conidial production. Initial studies reported sequence homology of FluG with a prokaryotic type I glutamine synthetase, but catalytic activity has not been demonstrated. In this study, we conducted an in-depth analysis of the FluG sequence, which revealed a single polypeptide containing a putative N-terminal amidohydrolase region linked to a putative C-terminal γ-glutamyl ligase region. Each region corresponded, separately and completely, to respective single function bacterial enzymes. Separate expression of these regions confirmed that the C-terminal region was essential for asexual development. The N-terminal region alone did not support conidial development, but contributed to increased conidial production under high nutrient availability. Point mutations directed at respective key catalytic residues in each region demonstrated that they were essential for biological function. Moreover, the substitution of the N- and C-terminal regions with homologs from Lactobacillus paracasei and Pseudomonas aeruginosa, respectively, maintained functionality, albeit with altered characteristics. Taken together, the results lead us to conclude that FluG is a bifunctional enzyme that participates in an as yet unidentified metabolic or signaling pathway involving a γ-glutamylated intermediate that contributes to developmental fate.
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Affiliation(s)
| | | | | | - Unai Ugalde
- Microbial Biochemistry Laboratory, Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country, San Sebastian, Spain
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van der Klis F, van Haveren J, van Es DS, Bitter JH. Synthesis of Furandicarboxylic Acid Esters From Nonfood Feedstocks Without Concomitant Levulinic Acid Formation. CHEMSUSCHEM 2017; 10:1460-1468. [PMID: 28124823 PMCID: PMC5413837 DOI: 10.1002/cssc.201700051] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Indexed: 05/14/2023]
Abstract
5-Hydroxymethylfurfural (HMF) is a versatile intermediate in biomass conversion pathways. However, the notoriously unstable nature of HMF imposes challenges to design selective routes to chemicals such as furan-2,5-dicarboxylic acid (FDCA). Here, a new strategy for obtaining furans is presented, bypassing the formation of the unstable HMF. Instead of starting with glucose/fructose and thus forming HMF as an intermediate, the new route starts from uronic acids, which are abundantly present in many agro residues such as sugar beet pulp, potato pulp, and citrus peels. Conversion of uronic acids, via ketoaldonic acids, to the intermediate formylfuroic acid (FFA) esters, and subsequently to FDCA esters, proceeds without formation of levulinic acid or insoluble humins. This new route provides an attractive strategy to valorize agricultural waste streams and a route to furanic building blocks without the co-production of levulinic acid or humins.
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Affiliation(s)
- Frits van der Klis
- Wageningen University Biobased Chemistry and TechnologyBornse Weilanden 96708WGWageningenThe Netherlands
- Wageningen Food & Biobased ResearchBornse Weilanden 96708WGWageningenThe Netherlands
| | - Jacco van Haveren
- Wageningen Food & Biobased ResearchBornse Weilanden 96708WGWageningenThe Netherlands
| | - Daan S. van Es
- Wageningen Food & Biobased ResearchBornse Weilanden 96708WGWageningenThe Netherlands
| | - Johannes H. Bitter
- Wageningen University Biobased Chemistry and TechnologyBornse Weilanden 96708WGWageningenThe Netherlands
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Mehtiö T, Toivari M, Wiebe MG, Harlin A, Penttilä M, Koivula A. Production and applications of carbohydrate-derived sugar acids as generic biobased chemicals. Crit Rev Biotechnol 2015; 36:904-16. [DOI: 10.3109/07388551.2015.1060189] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Tuomas Mehtiö
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Mervi Toivari
- VTT Technical Research Centre of Finland, Espoo, Finland
| | | | - Ali Harlin
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland, Espoo, Finland
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Huo L, Liu F, Iwaki H, Li T, Hasegawa Y, Liu A. Human α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD): a structural and mechanistic unveiling. Proteins 2014; 83:178-87. [PMID: 25392945 DOI: 10.1002/prot.24722] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/28/2014] [Accepted: 11/04/2014] [Indexed: 11/07/2022]
Abstract
Human α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase determines the fate of tryptophan metabolites in the kynurenine pathway by controlling the quinolinate levels for de novo nicotinamide adenine dinucleotide biosynthesis. The unstable nature of its substrate has made gaining insight into its reaction mechanism difficult. Our electron paramagnetic resonance (EPR) spectroscopic study on the Cu-substituted human enzyme suggests that the native substrate does not directly ligate to the metal ion. Substrate binding did not result in a change of either the hyperfine structure or the super-hyperfine structure of the EPR spectrum. We also determined the crystal structure of the human enzyme in its native catalytically active state (at 1.99 Å resolution), a substrate analogue-bound form (2.50 Å resolution), and a selected active site mutant form with one of the putative substrate binding residues altered (2.32 Å resolution). These structures illustrate that each asymmetric unit contains three pairs of dimers. Consistent with the EPR findings, the ligand-bound complex structure shows that the substrate analogue does not directly coordinate to the metal ion but is bound to the active site by two arginine residues through noncovalent interactions.
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Affiliation(s)
- Lu Huo
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303
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Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM. The evolution of enzyme function in the isomerases. Curr Opin Struct Biol 2014; 26:121-30. [PMID: 25000289 PMCID: PMC4139412 DOI: 10.1016/j.sbi.2014.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 06/02/2014] [Accepted: 06/10/2014] [Indexed: 01/14/2023]
Abstract
The advent of computational approaches to measure functional similarity between enzymes adds a new dimension to existing evolutionary studies based on sequence and structure. This paper reviews research efforts aiming to understand the evolution of enzyme function in superfamilies, presenting a novel strategy to provide an overview of the evolution of enzymes belonging to an individual EC class, using the isomerases as an exemplar.
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Affiliation(s)
- Sergio Martinez Cuesta
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Syed Asad Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
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Kamat SS, Holmes-Hampton GP, Bagaria A, Kumaran D, Tichy SE, Gheyi T, Zheng X, Bain K, Groshong C, Emtage S, Sauder JM, Burley SK, Swaminathan S, Lindahl PA, Raushel FM. The catalase activity of diiron adenine deaminase. Protein Sci 2011; 20:2080-94. [PMID: 21998098 DOI: 10.1002/pro.748] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 09/28/2011] [Accepted: 09/29/2011] [Indexed: 11/05/2022]
Abstract
Adenine deaminase (ADE) from the amidohydrolase superfamily (AHS) of enzymes catalyzes the conversion of adenine to hypoxanthine and ammonia. Enzyme isolated from Escherichia coli was largely inactive toward the deamination of adenine. Molecular weight determinations by mass spectrometry provided evidence that multiple histidine and methionine residues were oxygenated. When iron was sequestered with a metal chelator and the growth medium supplemented with Mn(2+) before induction, the post-translational modifications disappeared. Enzyme expressed and purified under these conditions was substantially more active for adenine deamination. Apo-enzyme was prepared and reconstituted with two equivalents of FeSO(4). Inductively coupled plasma mass spectrometry and Mössbauer spectroscopy demonstrated that this protein contained two high-spin ferrous ions per monomer of ADE. In addition to the adenine deaminase activity, [Fe(II) /Fe(II) ]-ADE catalyzed the conversion of H(2)O(2) to O(2) and H(2)O. The values of k(cat) and k(cat)/K(m) for the catalase activity are 200 s(-1) and 2.4 × 10(4) M(-1) s(-1), respectively. [Fe(II)/Fe(II)]-ADE underwent more than 100 turnovers with H(2)O(2) before the enzyme was inactivated due to oxygenation of histidine residues critical for metal binding. The iron in the inactive enzyme was high-spin ferric with g(ave) = 4.3 EPR signal and no evidence of anti-ferromagnetic spin-coupling. A model is proposed for the disproportionation of H(2)O(2) by [Fe(II)/Fe(II)]-ADE that involves the cycling of the binuclear metal center between the di-ferric and di-ferrous oxidation states. Oxygenation of active site residues occurs via release of hydroxyl radicals. These findings represent the first report of redox reaction catalysis by any member of the AHS.
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Affiliation(s)
- Siddhesh S Kamat
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3012, USA
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Xiang DF, Patskovsky Y, Xu C, Fedorov AA, Fedorov EV, Sisco AA, Sauder JM, Burley SK, Almo SC, Raushel FM. Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily . Biochemistry 2010; 49:6791-803. [PMID: 20604542 PMCID: PMC2914802 DOI: 10.1021/bi100897u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two uncharacterized enzymes from the amidohydrolase superfamily belonging to cog1228 were cloned, expressed, and purified to homogeneity. The two proteins, Sgx9260c ( gi|44242006 ) and Sgx9260b ( gi|44479596 ), were derived from environmental DNA samples originating from the Sargasso Sea. The catalytic function and substrate profiles for Sgx9260c and Sgx9260b were determined using a comprehensive library of dipeptides and N-acyl derivative of l-amino acids. Sgx9260c catalyzes the hydrolysis of Gly-l-Pro, l-Ala-l-Pro, and N-acyl derivatives of l-Pro. The best substrate identified to date is N-acetyl-l-Pro with a value of k(cat)/K(m) of 3 x 10(5) M(-1) s(-1). Sgx9260b catalyzes the hydrolysis of l-hydrophobic l-Pro dipeptides and N-acyl derivatives of l-Pro. The best substrate identified to date is N-propionyl-l-Pro with a value of k(cat)/K(m) of 1 x 10(5) M(-1) s(-1). Three-dimensional structures of both proteins were determined by X-ray diffraction methods (PDB codes 3MKV and 3FEQ ). These proteins fold as distorted (beta/alpha)(8)-barrels with two divalent cations in the active site. The structure of Sgx9260c was also determined as a complex with the N-methylphosphonate derivative of l-Pro (PDB code 3N2C ). In this structure the phosphonate moiety bridges the binuclear metal center, and one oxygen atom interacts with His-140. The alpha-carboxylate of the inhibitor interacts with Tyr-231. The proline side chain occupies a small substrate binding cavity formed by residues contributed from the loop that follows beta-strand 7 within the (beta/alpha)(8)-barrel. A total of 38 other proteins from cog1228 are predicted to have the same substrate profile based on conservation of the substrate binding residues. The structure of an evolutionarily related protein, Cc2672 from Caulobacter crecentus, was determined as a complex with the N-methylphosphonate derivative of l-arginine (PDB code 3MTW ).
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Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Yury Patskovsky
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Chengfu Xu
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Alexander A. Fedorov
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Elena V. Fedorov
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Abby A. Sisco
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - J. Michael Sauder
- Lilly Biotechnology Center, Eli Lilly and Company, 10300 Campus Point Dr., San Diego, California 92121
| | - Stephen K. Burley
- Lilly Biotechnology Center, Eli Lilly and Company, 10300 Campus Point Dr., San Diego, California 92121
| | - Steven C. Almo
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461,(SCA) telephone: (718) 430-2746; fax: (718)-430-8565;
| | - Frank M. Raushel
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012,To whom correspondence may be addressed: (FMR) telephone: (979) 845-3373; fax: (979)-845-9452;
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Hall RS, Agarwal R, Hitchcock D, Sauder JM, Burley SK, Swaminathan S, Raushel FM. Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase . Biochemistry 2010; 49:4374-82. [PMID: 20415463 DOI: 10.1021/bi100252s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two previously uncharacterized proteins have been identified that efficiently catalyze the deamination of isoxanthopterin and pterin 6-carboxylate. The genes encoding these two enzymes, NYSGXRC-9339a ( gi|44585104 ) and NYSGXRC-9236b ( gi|44611670 ), were first identified from DNA isolated from the Sargasso Sea as part of the Global Ocean Sampling Project. The genes were synthesized, and the proteins were subsequently expressed and purified. The X-ray structure of Sgx9339a was determined at 2.7 A resolution (Protein Data Bank entry 2PAJ ). This protein folds as a distorted (beta/alpha)(8) barrel and contains a single zinc ion in the active site. These enzymes are members of the amidohydrolase superfamily and belong to cog0402 within the clusters of orthologous groups (COG). Enzymes in cog0402 have previously been shown to catalyze the deamination of guanine, cytosine, S-adenosylhomocysteine, and 8-oxoguanine. A small compound library of pteridines, purines, and pyrimidines was used to probe catalytic activity. The only substrates identified in this search were isoxanthopterin and pterin 6-carboxylate. The kinetic constants for the deamination of isoxanthopterin with Sgx9339a were determined to be 1.0 s(-1), 8.0 muM, and 1.3 x 10(5) M(-1) s(-1) (k(cat), K(m), and k(cat)/K(m), respectively). The active site of Sgx9339a most closely resembles the active site for 8-oxoguanine deaminase (Protein Data Bank entry 2UZ9 ). A model for substrate recognition of isoxanthopterin by Sgx9339a was proposed on the basis of the binding of guanine and xanthine in the active site of guanine deaminase. Residues critical for substrate binding appear to be conserved glutamine and tyrosine residues that form hydrogen bonds with the carbonyl oxygen at C4, a conserved threonine residue that forms hydrogen bonds with N5, and another conserved threonine residue that forms hydrogen bonds with the carbonyl group at C7. These conserved active site residues were used to identify 24 other genes which are predicted to deaminate isoxanthopterin.
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Affiliation(s)
- Richard S Hall
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012, USA
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