1
|
Ferré J. Biosynthesis of Pteridines in Insects: A Review. INSECTS 2024; 15:370. [PMID: 38786926 PMCID: PMC11121863 DOI: 10.3390/insects15050370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Pteridines are important cofactors for many biological functions of all living organisms, and they were first discovered as pigments of insects, mainly in butterfly wings and the eye and body colors of insects. Most of the information on their structures and biosynthesis has been obtained from studies with the model insects Drosophila melanogaster and the silkworm Bombyx mori. This review discusses, and integrates into one metabolic pathway, the different branches which lead to the synthesis of the red pigments "drosopterins", the yellow pigments sepiapterin and sepialumazine, the orange pigment erythropterin and its related yellow metabolites (xanthopterin and 7-methyl-xanthopterin), the colorless compounds with violet fluorescence (isoxanthopterin and isoxantholumazine), and the branch leading to tetrahydrobiopterin, the essential cofactor for the synthesis of aromatic amino acids and biogenic amines.
Collapse
Affiliation(s)
- Juan Ferré
- Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, 46100 Burjassot, Spain
| |
Collapse
|
2
|
Shek R, Hilaire T, Sim J, French JB. Structural Determinants for Substrate Selectivity in Guanine Deaminase Enzymes of the Amidohydrolase Superfamily. Biochemistry 2019; 58:3280-3292. [PMID: 31283204 DOI: 10.1021/acs.biochem.9b00341] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanine deaminase is a metabolic enzyme, found in all forms of life, which catalyzes the conversion of guanine to xanthine. Despite the availability of several crystal structures, the molecular determinants of substrate orientation and mechanism remain to be elucidated for the amidohydrolase family of guanine deaminase enzymes. Here, we report the crystal structures of Escherichia coli and Saccharomyces cerevisiae guanine deaminase enzymes (EcGuaD and Gud1, respectively), both members of the amidohydrolase superfamily. EcGuaD and Gud1 retain the overall TIM barrel tertiary structure conserved among amidohydrolase enzymes. Both proteins also possess a single zinc cation with trigonal bipyrimidal coordination geometry within their active sites. We also determined a liganded structure of Gud1 bound to the product, xanthine. Analysis of this structure, along with kinetic data of native and site-directed mutants of EcGuaD, identifies several key residues that are responsible for substrate recognition and catalysis. In addition, after a small library of compounds had been screened, two guanine derivatives, 8-azaguanine and 1-methylguanine, were identified as EcGuaD substrates. Interestingly, both EcGuaD and Gud1 also exhibit secondary ammeline deaminase activity. Overall, this work details key structural features of substrate recognition and catalysis of the amidohydrolase family of guanine deaminase enzymes in support of our long-term goal to engineer these enzymes with altered activity and substrate specificity.
Collapse
Affiliation(s)
- Roger Shek
- Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Tylene Hilaire
- Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Jasper Sim
- Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Jarrod B French
- Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States.,Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| |
Collapse
|
3
|
Nemmara VV, Xiang DF, Fedorov AA, Fedorov EV, Bonanno JB, Almo SC, Raushel FM. Substrate Profile of the Phosphotriesterase Homology Protein from Escherichia coli. Biochemistry 2018; 57:6219-6227. [PMID: 30277746 PMCID: PMC6643279 DOI: 10.1021/acs.biochem.8b00935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The phosphotriesterase homology protein (PHP) from Escherichia coli is a member of a family of proteins that is related to phosphotriestrase (PTE), a bacterial enzyme from cog1735 with unusual substrate specificity toward the hydrolysis of synthetic organic phosphates and phosphonates. PHP was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of PHP was determined at a resolution of 1.84 Å with zinc and phosphate in the active site. The protein folds as a distorted (β/α)8-barrel and possesses a binuclear metal center in the active site. The catalytic function and substrate profile of PHP were investigated using a structure-guided approach that combined bioinformatics, computational docking, organic synthesis, and steady-state enzyme kinetics. PHP was found to catalyze the hydrolysis of phosphorylated glyceryl acetates. The best substrate was 1,2-diacetyl glycerol-3-phosphate with a kcat/ Km of 4.9 × 103 M-1 s-1. The presence of a phosphate group in the substrate was essential for enzymatic hydrolysis by the enzyme. It was surprising, however, to find that PHP was unable to hydrolyze any of the lactones tested as potential substrates, unlike most of the other enzymes from cog1735.
Collapse
Affiliation(s)
- Venkatesh V Nemmara
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Dao Feng Xiang
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - A A Fedorov
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - E V Fedorov
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Jeffrey B Bonanno
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Steven C Almo
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| |
Collapse
|
4
|
Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR. Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. Nucleic Acids Res 2017; 45:10811-10823. [PMID: 28977401 PMCID: PMC5737381 DOI: 10.1093/nar/gkx699] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/02/2017] [Indexed: 11/29/2022] Open
Abstract
The discovery of structured non-coding RNAs (ncRNAs) in bacteria can reveal new facets of biology and biochemistry. Comparative genomics analyses executed by powerful computer algorithms have successfully been used to uncover many novel bacterial ncRNA classes in recent years. However, this general search strategy favors the discovery of more common ncRNA classes, whereas progressively rarer classes are correspondingly more difficult to identify. In the current study, we confront this problem by devising several methods to select subsets of intergenic regions that can concentrate these rare RNA classes, thereby increasing the probability that comparative sequence analysis approaches will reveal their existence. By implementing these methods, we discovered 224 novel ncRNA classes, which include ROOL RNA, an RNA class averaging 581 nt and present in multiple phyla, several highly conserved and widespread ncRNA classes with properties that suggest sophisticated biochemical functions and a multitude of putative cis-regulatory RNA classes involved in a variety of biological processes. We expect that further research on these newly found RNA classes will reveal additional aspects of novel biology, and allow for greater insights into the biochemistry performed by ncRNAs.
Collapse
Affiliation(s)
- Zasha Weinberg
- HHMI, Yale University, Box 208103, New Haven, CT 06520-8103, USA
| | - Christina E Lünse
- Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA
| | - Keith A Corbino
- HHMI, Yale University, Box 208103, New Haven, CT 06520-8103, USA
| | - Tyler D Ames
- Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA
| | - James W Nelson
- Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA
| | - Adam Roth
- HHMI, Yale University, Box 208103, New Haven, CT 06520-8103, USA
| | - Kevin R Perkins
- Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA
| | - Madeline E Sherlock
- Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA
| | - Ronald R Breaker
- HHMI, Yale University, Box 208103, New Haven, CT 06520-8103, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA
| |
Collapse
|
5
|
Abstract
Abstract
Pteridines and their derivatives function as intermediates in the metabolism of several vitamins and cofactors, and their relevance to disease has inspired new efforts to study their roles as disease biomarkers. Recent analytical advances, such as the emergence of sensitive mass spectrometry techniques, new workflows for measuring pteridine derivatives in their native oxidation states and increased multiplexing capacities for the simultaneous determination of many pteridine derivatives, have enabled researchers to explore the roles of urinary pteridines as disease biomarkers at much lower levels with greater accuracy than with previous technologies or methods. As a result, urinary pteridines are being increasingly studied as putative cancer biomarkers with promising results being reported from exploratory studies. In addition, the role of urinary neopterin as a universal biomarker for immune system activation is being investigated in new diseases where it is anticipated to become a useful supplementary marker in clinical diagnostic settings. In summary, this review provides an overview of recent developments in the clinical study of urinary pteridines as disease biomarkers, covers the most promising aspects of advanced analytical techniques being developed for the determination of urinary pteridines and discusses the major challenges associated with implementing pteridine biomarkers in clinical laboratory settings.
Collapse
Affiliation(s)
- Casey Burton
- Department of Chemistry and Center for Single Nanoparticle, Single Cell, and Single Molecule Monitoring, Missouri University of Science and Technology, Rolla, MO, USA
| | - Yinfa Ma
- Department of Chemistry and Center for Single Nanoparticle, Single Cell, and Single Molecule Monitoring, Missouri University of Science and Technology, 400 West 11th Street, Rolla, MO 65409, USA
| |
Collapse
|
6
|
Abstract
Genomic studies focus on key metabolites and pathways that, despite their obvious anthropocentric design, keep being 'predicted', while this is only finding again what is already known. As increasingly more genomes are sequenced, this lightpost effect may account at least in part for our failure to understand the function of a continuously growing number of genes. Core metabolism often goes astray, accidentally producing a variety of unexpected compounds. Catabolism of these forgotten metabolites makes an essential part of the functions coded in metagenomes. Here, I explore the fate of a limited number of those: compounds resulting from radical reactions and molecules derived from some reactive intermediates produced during normal metabolism. I try both to update investigators with the most recent literature and to uncover old articles that may open up new research avenues in the genome exploration of metabolism. This should allow us to foresee further developments in experimental genomics and genome annotation.
Collapse
Affiliation(s)
- Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐Salpêtrière47 Boulevard de l'HôpitalParis75013France
| |
Collapse
|
7
|
Jayaraman A, Thandeeswaran M, Priyadarsini U, Sabarathinam S, Nawaz KAA, Palaniswamy M. Characterization of unexplored amidohydrolase enzyme-pterin deaminase. Appl Microbiol Biotechnol 2016; 100:4779-89. [PMID: 27094187 DOI: 10.1007/s00253-016-7513-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 11/30/2022]
Abstract
Pterin deaminase is an amidohydrolase enzyme hydrolyzing pteridines to form lumazine derivatives and ammonia. The enzyme captured the attention of scientists as early as 1959 and had been patented for its application as an anticancer agent. It is ubiquitously present in prokaryotes and has been reported in some eukaryotes such as honey bee, silkworm and rats. The enzyme has been observed to have a spectrum of substrates with the formation of respective lumazines. The role of the substrates of the enzyme in various metabolic pathways warrants a significant role in the biological activity of both prokaryotes and eukaryotes. Even though the functions of the enzyme have been explored in prokaryotes, their niche in the eukaryotic system is not clear. There is very few information on the structural and functional properties of the enzyme. This review has been congregated to emphasize the significance of pterin deaminase and analyzes the lacunae in understanding the biological characters of the enzyme.
Collapse
Affiliation(s)
- Angayarkanni Jayaraman
- Cancer Therapeutics Lab, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, 641046, Tamilnadu, India.
| | - Murugesan Thandeeswaran
- Cancer Therapeutics Lab, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, 641046, Tamilnadu, India
| | | | - Shanmugam Sabarathinam
- Cancer Therapeutics Lab, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, 641046, Tamilnadu, India
| | - K A Ayub Nawaz
- Cancer Therapeutics Lab, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, 641046, Tamilnadu, India
| | - Muthusamy Palaniswamy
- Department of Microbiology, Karpagam University, Coimbatore, 641021, Tamilnadu, India
| |
Collapse
|
8
|
Fedorov A, Martí-Arbona R, Nemmara VV, Hitchcock D, Fedorov EV, Almo SC, Raushel FM. Structure of N-formimino-L-glutamate iminohydrolase from Pseudomonas aeruginosa. Biochemistry 2015; 54:890-7. [PMID: 25559274 PMCID: PMC4357388 DOI: 10.1021/bi501299y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/24/2014] [Indexed: 11/30/2022]
Abstract
N-Formimino-l-glutamate iminohydrolase (HutF), from Pseudomonas aeruginosa with a locus tag of Pa5106 ( gi|15600299 ), is a member of the amidohydrolase superfamily. This enzyme catalyzes the deamination of N-formimino-l-glutamate to N-formyl-l-glutamate and ammonia in the histidine degradation pathway. The crystal structure of Pa5106 was determined in the presence of the inhibitors N-formimino-l-aspartate and N-guanidino-l-glutaric acid at resolutions of 1.9 and 1.4 Å, respectively. The structure of an individual subunit is composed of two domains with the larger domain folding as a distorted (β/α)8-barrel. The (β/α)8-barrel domain is composed of eight β-strands flanked by 11 α-helices, whereas the smaller domain is made up of eight β-strands. The active site of Pa5106 contains a single zinc atom that is coordinated by His-56, His-58, His-232, and Asp-320. The nucleophilic solvent water molecule coordinates with the zinc atom at a distance of 2.0 Å and is hydrogen bonded to Asp-320 and His-269. The α-carboxylate groups of both inhibitors are hydrogen bonded to the imidazole moiety of His-206, the hydroxyl group of Tyr-121, and the side chain amide group of Gln-61. The side chain carboxylate groups of the two inhibitors are ion-paired with the guanidino groups of Arg-209 and Arg-82. Computational docking of high-energy tetrahedral intermediate forms of the substrate, N-formimino-l-glutamate, to the three-dimensional structure of Pa5106 suggests that this compound likely undergoes a re-faced nucleophilic attack at the formimino group by the metal-bound hydroxide. A catalytic mechanism of the reaction catalyzed by Pa5106 is proposed.
Collapse
Affiliation(s)
- Alexander
A. Fedorov
- Albert
Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United
States
| | - Ricardo Martí-Arbona
- Department of Chemistry and Department of Biochemistry &
Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Venkatesh V. Nemmara
- Department of Chemistry and Department of Biochemistry &
Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Daniel Hitchcock
- Department of Chemistry and Department of Biochemistry &
Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Elena V. Fedorov
- Albert
Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United
States
| | - Steven C. Almo
- Albert
Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United
States
| | - Frank M. Raushel
- Department of Chemistry and Department of Biochemistry &
Biophysics, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
9
|
Hobbs ME, Williams HJ, Hillerich B, Almo SC, Raushel FM. l-Galactose metabolism in Bacteroides vulgatus from the human gut microbiota. Biochemistry 2014; 53:4661-70. [PMID: 24963813 PMCID: PMC4108180 DOI: 10.1021/bi500656m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A previously
unknown metabolic pathway for the utilization of l-galactose
was discovered in a prevalent gut bacterium, Bacteroides vulgatus. The new pathway consists of three
previously uncharacterized enzymes that were found to be responsible
for the conversion of l-galactose to d-tagaturonate.
Bvu0219 (l-galactose dehydrogenase) was determined to oxidize l-galactose to l-galactono-1,5-lactone with kcat and kcat/Km values of 21 s–1 and 2.0
× 105 M–1 s–1,
respectively. The kinetic product of Bvu0219 is rapidly converted
nonenzymatically to the thermodynamically more stable l-galactono-1,4-lactone.
Bvu0220 (l-galactono-1,5-lactonase) hydrolyzes both the kinetic
and thermodynamic products of Bvu0219 to l-galactonate. However, l-galactono-1,5-lactone is estimated to be hydrolyzed 300-fold
faster than its thermodynamically more stable counterpart, l-galactono-1,4-lactone. In the final step of this pathway, Bvu0222
(l-galactonate dehydrogenase) oxidizes l-galactonate
to d-tagaturonate with kcat and kcat/Km values of
0.6 s–1 and 1.7 × 104 M–1 s–1, respectively. In the reverse direction, d-tagaturonate is reduced to l-galactonate with values
of kcat and kcat/Km of 90 s–1 and 1.6
× 105 M–1 s–1,
respectively. d-Tagaturonate is subsequently converted to d-glyceraldehyde and pyruvate through enzymes encoded within
the degradation pathway for d-glucuronate and d-galacturonate.
Collapse
Affiliation(s)
- Merlin Eric Hobbs
- Department of Biochemistry and Biophysics, §Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | | | | | | | | |
Collapse
|
10
|
ZHANG XIN, LEI MING. WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613410022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.
Collapse
Affiliation(s)
- XIN ZHANG
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing 100029, P. R. China
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - MING LEI
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| |
Collapse
|
11
|
Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry 2013; 52:6525-36. [PMID: 23972005 DOI: 10.1021/bi400750a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Proteins of unknown function belonging to cog1816 and cog0402 were characterized. Sav2595 from Steptomyces avermitilis MA-4680, Acel0264 from Acidothermus cellulolyticus 11B, Nis0429 from Nitratiruptor sp. SB155-2 and Dr0824 from Deinococcus radiodurans R1 were cloned, purified, and their substrate profiles determined. These enzymes were previously incorrectly annotated as adenosine deaminases or chlorohydrolases. It was shown here that these enzymes actually deaminate 6-aminodeoxyfutalosine. The deamination of 6-aminodeoxyfutalosine is part of an alternative menaquinone biosynthetic pathway that involves the formation of futalosine. 6-Aminodeoxyfutalosine is deaminated by these enzymes with catalytic efficiencies greater than 10(5) M(-1) s(-1), Km values of 0.9-6.0 μM, and kcat values of 1.2-8.6 s(-1). Adenosine, 2'-deoxyadenosine, thiomethyladenosine, and S-adenosylhomocysteine are deaminated at least an order of magnitude slower than 6-aminodeoxyfutalosine. The crystal structure of Nis0429 was determined and the substrate, 6-aminodeoxyfutalosine, was positioned in the active site on the basis of the presence of adventitiously bound benzoic acid. In this model, Ser-145 interacts with the carboxylate moiety of the substrate. The structure of Dr0824 was also determined, but a collapsed active site pocket prevented docking of substrates. A computational model of Sav2595 was built on the basis of the crystal structure of adenosine deaminase and substrates were docked. The model predicted a conserved arginine after β-strand 1 to be partially responsible for the substrate specificity of Sav2595.
Collapse
Affiliation(s)
- Alissa M Goble
- Department of Chemistry, Texas A&M University , P.O. Box 30012, College Station, Texas 77843-3012, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Kim J, Copley SD. The orphan protein bis-γ-glutamylcystine reductase joins the pyridine nucleotide disulfide reductase family. Biochemistry 2013; 52:2905-13. [PMID: 23560638 DOI: 10.1021/bi4003343] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Facile DNA sequencing became possible decades after many enzymes had been purified and characterized. Consequently, there are still "orphan" enyzmes for which activities are known but for which encoding genes have not been identified. Identification of the genes encoding orphan enzymes is important because it allows correct annotation of genes of unknown function or with misassigned function. Bis-γ-glutamylcystine reductase (GCR) is an orphan protein that was purified in 1988. This enzyme catalyzes the reduction of bis-γ-glutamylcystine. γ-Glutamylcysteine is the major low-molecular weight thiol in halobacteria. We purified GCR from Halobacterium sp. NRC-1 and identified the sequence of 23 tryptic peptides by nano-liquid chromatography electrospray ionization tandem mass spectrometry. These peptides cover 62% of the protein predicted to be encoded by a gene in Halobacterium sp. NRC-1 that is annotated as mercuric reductase. GCR and mercuric reductase activities were assayed using enzyme that was expressed in Escherichia coli and refolded from inclusion bodies. The enzyme had robust GCR activity but no mercuric reductase activity. The genomes of most, but not all, halobacteria for which whole genome sequences are available have close homologues of GCR, suggesting that there is more to be learned about the low-molecular weight thiols used in halobacteria.
Collapse
Affiliation(s)
- Juhan Kim
- Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO 80309, USA
| | | |
Collapse
|
13
|
Fan H, Hitchcock DS, Seidel RD, Hillerich B, Lin H, Almo SC, Sali A, Shoichet BK, Raushel FM. Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking. J Am Chem Soc 2013; 135:795-803. [PMID: 23256477 PMCID: PMC3557803 DOI: 10.1021/ja309680b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Of the over 22 million protein sequences in the nonredundant TrEMBL database, fewer than 1% have experimentally confirmed functions. Structure-based methods have been used to predict enzyme activities from experimentally determined structures; however, for the vast majority of proteins, no such structures are available. Here, homology models of a functionally uncharacterized amidohydrolase from Agrobacterium radiobacter K84 (Arad3529) were computed on the basis of a remote template structure. The protein backbone of two loops near the active site was remodeled, resulting in four distinct active site conformations. Substrates of Arad3529 were predicted by docking of 57,672 high-energy intermediate (HEI) forms of 6440 metabolites against these four homology models. On the basis of docking ranks and geometries, a set of modified pterins were suggested as candidate substrates for Arad3529. The predictions were tested by enzymology experiments, and Arad3529 deaminated many pterin metabolites (substrate, k(cat)/K(m) [M(-1) s(-1)]): formylpterin, 5.2 × 10(6); pterin-6-carboxylate, 4.0 × 10(6); pterin-7-carboxylate, 3.7 × 10(6); pterin, 3.3 × 10(6); hydroxymethylpterin, 1.2 × 10(6); biopterin, 1.0 × 10(6); d-(+)-neopterin, 3.1 × 10(5); isoxanthopterin, 2.8 × 10(5); sepiapterin, 1.3 × 10(5); folate, 1.3 × 10(5), xanthopterin, 1.17 × 10(5); and 7,8-dihydrohydroxymethylpterin, 3.3 × 10(4). While pterin is a ubiquitous oxidative product of folate degradation, genomic analysis suggests that the first step of an undescribed pterin degradation pathway is catalyzed by Arad3529. Homology model-based virtual screening, especially with modeling of protein backbone flexibility, may be broadly useful for enzyme function annotation and discovering new pathways and drug targets.
Collapse
Affiliation(s)
- Hao Fan
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
- Department of Pharmaceutical Chemistry, University of California, San Francisco
- California Institute for Quantitative Biosciences, University of California, San Francisco
| | - Daniel S. Hitchcock
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843
| | - Ronald D. Seidel
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Brandan Hillerich
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Henry Lin
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Steven C. Almo
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
- Department of Pharmaceutical Chemistry, University of California, San Francisco
- California Institute for Quantitative Biosciences, University of California, San Francisco
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Frank M. Raushel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| |
Collapse
|
14
|
Xiang DF, Kolb P, Fedorov AA, Xu C, Fedorov EV, Narindoshivili T, Williams HJ, Shoichet BK, Almo SC, Raushel FM. Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones. Biochemistry 2012; 51:1762-73. [PMID: 22313111 PMCID: PMC3298459 DOI: 10.1021/bi201838b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two enzymes of unknown function from the cog1735 subset of the amidohydrolase superfamily (AHS), LMOf2365_2620 (Lmo2620) from Listeria monocytogenes str. 4b F2365 and Bh0225 from Bacillus halodurans C-125, were cloned, expressed, and purified to homogeneity. The catalytic functions of these two enzymes were interrogated by an integrated strategy encompassing bioinformatics, computational docking to three-dimensional crystal structures, and library screening. The three-dimensional structure of Lmo2620 was determined at a resolution of 1.6 Å with two phosphates and a binuclear zinc center in the active site. The proximal phosphate bridges the binuclear metal center and is 7.1 Å from the distal phosphate. The distal phosphate hydrogen bonds with Lys-242, Lys-244, Arg-275, and Tyr-278. Enzymes within cog1735 of the AHS have previously been shown to catalyze the hydrolysis of substituted lactones. Computational docking of the high-energy intermediate form of the KEGG database to the three-dimensional structure of Lmo2620 highly enriched anionic lactones versus other candidate substrates. The active site structure and the computational docking results suggested that probable substrates would likely include phosphorylated sugar lactones. A small library of diacid sugar lactones and phosphorylated sugar lactones was synthesized and tested for substrate activity with Lmo2620 and Bh0225. Two substrates were identified for these enzymes, D-lyxono-1,4-lactone-5-phosphate and l-ribono-1,4-lactone-5-phosphate. The k(cat)/K(m) values for the cobalt-substituted enzymes with these substrates are ~10(5) M(-1) s(-1).
Collapse
Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158-2330
| | - Alexander A. Fedorov
- 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
| | - Elena V. Fedorov
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Tamari Narindoshivili
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Howard J. Williams
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158-2330,To whom correspondence may be addressed: (FMR) telephone: (979) 845-3373; fax: (979)-845-9452; , (SCA) telephone: (718) 430-2746; fax: (718)-430-8565; , (BKS) telephone: (415)-514-4126; fax: (415)-514-4260;
| | - Steven C. Almo
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461,To whom correspondence may be addressed: (FMR) telephone: (979) 845-3373; fax: (979)-845-9452; , (SCA) telephone: (718) 430-2746; fax: (718)-430-8565; , (BKS) telephone: (415)-514-4126; fax: (415)-514-4260;
| | - 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; , (SCA) telephone: (718) 430-2746; fax: (718)-430-8565; , (BKS) telephone: (415)-514-4126; fax: (415)-514-4260;
| |
Collapse
|
15
|
Abstract
An enzyme of unknown function within the amidohydrolase superfamily was discovered to catalyze the hydrolysis of N-6-substituted adenine derivatives, several of which are cytokinins. Cytokinins are a common type of plant hormone and N-6-substituted adenines are also found as modifications to tRNA. Patl2390, from Pseudoalteromonas atlantica T6c, was shown to hydrolytically deaminate N-6-isopentenyladenine to hypoxanthine and isopentenylamine with a k(cat)/K(m) of 1.2 × 10(7) M(-1) s(-1). Additional substrates include N-6-benzyl adenine, cis- and trans-zeatin, kinetin, O-6-methylguanine, N-6-butyladenine, N-6-methyladenine, N,N-dimethyladenine, 6-methoxypurine, 6-chloropurine, and 6-thiomethylpurine. This enzyme does not catalyze the deamination of adenine or adenosine. A comparative model of Patl2390 was computed using the three-dimensional crystal structure of Pa0148 (PDB code 3PAO ) as a structural template, and docking was used to refine the model to accommodate experimentally identified substrates. This is the first identification of an enzyme that will hydrolyze an N-6-substituted side chain larger than methylamine from adenine.
Collapse
Affiliation(s)
- Alissa M. Goble
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77843-3012, United States
| | - Hao Fan
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158, United States
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77843-3012, United States
| |
Collapse
|
16
|
Goble AM, Zhang Z, Sauder JM, Burley SK, Swaminathan S, Raushel FM. Pa0148 from Pseudomonas aeruginosa catalyzes the deamination of adenine. Biochemistry 2011; 50:6589-97. [PMID: 21710971 DOI: 10.1021/bi200868u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Four proteins from NCBI cog1816, previously annotated as adenosine deaminases, have been subjected to structural and functional characterization. Pa0148 (Pseudomonas aeruginosa PAO1), AAur1117 (Arthrobacter aurescens TC1), Sgx9403e, and Sgx9403g have been purified and their substrate profiles determined. Adenosine is not a substrate for any of these enzymes. All of these proteins will deaminate adenine to produce hypoxanthine with k(cat)/K(m) values that exceed 10(5) M(-1) s(-1). These enzymes will also accept 6-chloropurine, 6-methoxypurine, N-6-methyladenine, and 2,6-diaminopurine as alternate substrates. X-ray structures of Pa0148 and AAur1117 have been determined and reveal nearly identical distorted (β/α)(8) barrels with a single zinc ion that is characteristic of members of the amidohydrolase superfamily. Structures of Pa0148 with adenine, 6-chloropurine, and hypoxanthine were also determined, thereby permitting identification of the residues responsible for coordinating the substrate and product.
Collapse
Affiliation(s)
- Alissa M Goble
- Department of Chemistry, P.O. Box 30012, Texas A&M University , College Station, Texas 77843-3012, United States
| | | | | | | | | | | |
Collapse
|
17
|
Hitchcock DS, Fedorov AA, Fedorov EV, Dangott LJ, Almo SC, Raushel FM. Rescue of the orphan enzyme isoguanine deaminase. Biochemistry 2011; 50:5555-7. [PMID: 21604715 DOI: 10.1021/bi200680y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytosine deaminase (CDA) from Escherichia coli was shown to catalyze the deamination of isoguanine (2-oxoadenine) to xanthine. Isoguanine is an oxidation product of adenine in DNA that is mutagenic to the cell. The isoguanine deaminase activity in E. coli was partially purified by ammonium sulfate fractionation, gel filtration, and anion exchange chromatography. The active protein was identified by peptide mass fingerprint analysis as cytosine deaminase. The kinetic constants for the deamination of isoguanine at pH 7.7 are as follows: k(cat) = 49 s(-1), K(m) = 72 μM, and k(cat)/K(m) = 6.7 × 10(5) M(-1) s(-1). The kinetic constants for the deamination of cytosine are as follows: k(cat) = 45 s(-1), K(m) = 302 μM, and k(cat)/K(m) = 1.5 × 10(5) M(-1) s(-1). Under these reaction conditions, isoguanine is the better substrate for cytosine deaminase. The three-dimensional structure of CDA was determined with isoguanine in the active site.
Collapse
Affiliation(s)
- Daniel S Hitchcock
- Department of Biochemistry and Biophysics and Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| | | | | | | | | | | |
Collapse
|
18
|
Hall RS, Fedorov AA, Xu C, Fedorov EV, Almo SC, Raushel FM. Three-dimensional structure and catalytic mechanism of cytosine deaminase. Biochemistry 2011; 50:5077-85. [PMID: 21545144 DOI: 10.1021/bi200483k] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytosine deaminase (CDA) from E. coli is a member of the amidohydrolase superfamily. The structure of the zinc-activated enzyme was determined in the presence of phosphonocytosine, a mimic of the tetrahedral reaction intermediate. This compound inhibits the deamination of cytosine with a K(i) of 52 nM. The zinc- and iron-containing enzymes were characterized to determine the effect of the divalent cations on activation of the hydrolytic water. Fe-CDA loses activity at low pH with a kinetic pK(a) of 6.0, and Zn-CDA has a kinetic pK(a) of 7.3. Mutation of Gln-156 decreased the catalytic activity by more than 5 orders of magnitude, supporting its role in substrate binding. Mutation of Glu-217, Asp-313, and His-246 significantly decreased catalytic activity supporting the role of these three residues in activation of the hydrolytic water molecule and facilitation of proton transfer reactions. A library of potential substrates was used to probe the structural determinants responsible for catalytic activity. CDA was able to catalyze the deamination of isocytosine and the hydrolysis of 3-oxauracil. Large inverse solvent isotope effects were obtained on k(cat) and k(cat)/K(m), consistent with the formation of a low-barrier hydrogen bond during the conversion of cytosine to uracil. A chemical mechanism for substrate deamination by CDA was proposed.
Collapse
Affiliation(s)
- Richard S Hall
- Department of Chemistry, Texas A&M University, College Station, Texas 77842-3012, United States
| | | | | | | | | | | |
Collapse
|