5DJ1
| Structure of the PLP-Dependent L-Arginine Hydroxylase MppP Holoenzyme | Descriptor: | CHLORIDE ION, MAGNESIUM ION, PLP-Dependent L-Arginine Hydroxylase MppP | Authors: | Silvaggi, N.R, Han, L. | Deposit date: | 2015-09-01 | Release date: | 2015-11-25 | Last modified: | 2017-05-03 | Method: | X-RAY DIFFRACTION (2.102 Å) | Cite: | Streptomyces wadayamensis MppP Is a Pyridoxal 5'-Phosphate-Dependent l-Arginine alpha-Deaminase, gamma-Hydroxylase in the Enduracididine Biosynthetic Pathway. Biochemistry, 54, 2015
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5KRQ
| Renalase in complex with NADPH | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, Renalase | Authors: | Silvaggi, N.R, Moran, G.R, Roman, J.V. | Deposit date: | 2016-07-07 | Release date: | 2016-11-02 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.086 Å) | Cite: | Ligand binding phenomena that pertain to the metabolic function of renalase. Arch.Biochem.Biophys., 612, 2016
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4ZCD
| Renalase in complex with NAD+ | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, FORMIC ACID, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | Authors: | Silvaggi, N.R, Moran, G.R, Roman, J.V. | Deposit date: | 2015-04-15 | Release date: | 2015-07-15 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.6605 Å) | Cite: | Bacterial Renalase: Structure and Kinetics of an Enzyme with 2- and 6-Dihydro-beta-NAD(P) Oxidase Activity from Pseudomonas phaseolicola. Biochemistry, 54, 2015
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4ZCC
| Renalase in complex with NADH | Descriptor: | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, FLAVIN-ADENINE DINUCLEOTIDE, FORMIC ACID, ... | Authors: | Silvaggi, N.R, Moran, G.R, Roman, J.V. | Deposit date: | 2015-04-15 | Release date: | 2015-07-15 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.997 Å) | Cite: | Bacterial Renalase: Structure and Kinetics of an Enzyme with 2- and 6-Dihydro-beta-NAD(P) Oxidase Activity from Pseudomonas phaseolicola. Biochemistry, 54, 2015
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4JM3
| Enduracididine Biosynthesis Enzyme MppR with HEPES Buffer Bound | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Putative uncharacterized protein mppR | Authors: | Silvaggi, N.R. | Deposit date: | 2013-03-13 | Release date: | 2013-07-03 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Structural and Functional Characterization of MppR, an Enduracididine Biosynthetic Enzyme from Streptomyces hygroscopicus: Functional Diversity in the Acetoacetate Decarboxylase-like Superfamily. Biochemistry, 52, 2013
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4JME
| Enduracididine biosynthesis enzyme MppR complexed with 2-keto-enduracididine | Descriptor: | (4R)-4-(2-carboxyethyl)imidazolidin-2-iminium, Putative uncharacterized protein mppR | Authors: | Silvaggi, N.R. | Deposit date: | 2013-03-13 | Release date: | 2013-07-03 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structural and Functional Characterization of MppR, an Enduracididine Biosynthetic Enzyme from Streptomyces hygroscopicus: Functional Diversity in the Acetoacetate Decarboxylase-like Superfamily. Biochemistry, 52, 2013
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4LZL
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4JMC
| Enduracididine biosynthesis enzyme MppR complexed with pyruvate | Descriptor: | PYRUVIC ACID, Putative uncharacterized protein mppR | Authors: | Silvaggi, N.R. | Deposit date: | 2013-03-13 | Release date: | 2013-07-03 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (1.72 Å) | Cite: | Structural and Functional Characterization of MppR, an Enduracididine Biosynthetic Enzyme from Streptomyces hygroscopicus: Functional Diversity in the Acetoacetate Decarboxylase-like Superfamily. Biochemistry, 52, 2013
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5U8K
| RitR mutant - C128S | Descriptor: | Response regulator | Authors: | Silvaggi, N.R, Han, L. | Deposit date: | 2016-12-14 | Release date: | 2017-12-20 | Last modified: | 2018-11-28 | Method: | X-RAY DIFFRACTION (1.69 Å) | Cite: | RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization. PLoS Pathog., 14, 2018
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6PAY
| Structure of HsICDH1:Mg(II):ICT:NADPH(50%) complex reveals structural basis for observation of half-sites reactivity | Descriptor: | FORMIC ACID, ISOCITRIC ACID, Isocitrate dehydrogenase [NADP] cytoplasmic, ... | Authors: | Silvaggi, N.R, Melkonian, T.R, Roman, J.V, Moran, G.R. | Deposit date: | 2019-06-12 | Release date: | 2019-09-18 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.199 Å) | Cite: | Transient-State Analysis of Human Isocitrate Dehydrogenase I: Accounting for the Interconversion of Active and Non-Active Conformational States. Biochemistry, 58, 2019
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6WEY
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5V8U
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5VFA
| RitR Mutant - C128D | Descriptor: | Response regulator | Authors: | Han, L, Silvaggi, N.R. | Deposit date: | 2017-04-07 | Release date: | 2018-04-11 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.452 Å) | Cite: | RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization. PLoS Pathog., 14, 2018
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1IKI
| COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH THE PRODUCTS OF A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT | Descriptor: | D-ALANINE, D-ALANYL-D-ALANINE CARBOXYPEPTIDASE, GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE | Authors: | Mcdonough, M.A, Anderson, J.W, Silvaggi, N.R, Pratt, R.F, Knox, J.R, Kelly, J.A. | Deposit date: | 2001-05-03 | Release date: | 2002-09-11 | Last modified: | 2023-08-16 | Method: | X-RAY DIFFRACTION (1.25 Å) | Cite: | Structures of two kinetic intermediates reveal species specificity of penicillin-binding proteins. J.Mol.Biol., 322, 2002
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1IKG
| MICHAELIS COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT | Descriptor: | D-ALANYL-D-ALANINE CARBOXYPEPTIDASE, GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANYL-D-ALANINE | Authors: | Mcdonough, M.A, Anderson, J.W, Silvaggi, N.R, Pratt, R.F, Knox, J.R, Kelly, J.A. | Deposit date: | 2001-05-03 | Release date: | 2002-09-11 | Last modified: | 2023-08-16 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Structures of two kinetic intermediates reveal species specificity of penicillin-binding proteins. J.Mol.Biol., 322, 2002
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1YQS
| Inhibition of the R61 DD-Peptidase by N-benzoyl-beta-sultam | Descriptor: | 2-(BENZOYLAMINO)ETHANESULFONIC ACID, D-alanyl-D-alanine carboxypeptidase, GLYCEROL | Authors: | Ahmed, N, Cordaro, M, Laws, A.P, Delmarcelle, M, Silvaggi, N.R, Kelly, J.A, Page, M.I. | Deposit date: | 2005-02-02 | Release date: | 2005-06-28 | Last modified: | 2023-08-23 | Method: | X-RAY DIFFRACTION (1.05 Å) | Cite: | Inactivation of Bacterial dd-Peptidase by beta-Sultams. Biochemistry, 44, 2005
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6EEJ
| Streptomyces bingchenggensis Aldolase-Dehydratase in covalent complex with dienone product. | Descriptor: | (3E,5E)-6-(4-nitrophenyl)-2-oxohexa-3,5-dienoic acid, Acetoacetate decarboxylase, FORMIC ACID, ... | Authors: | Mydy, L.S, Silvaggi, N.R. | Deposit date: | 2018-08-14 | Release date: | 2019-08-14 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (1.892 Å) | Cite: | Mechanistic Studies of theStreptomyces bingchenggensisAldolase-Dehydratase: Implications for Substrate and Reaction Specificity in the Acetoacetate Decarboxylase-like Superfamily. Biochemistry, 58, 2019
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3U3H
| X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde | Descriptor: | (2R)-propane-1,1,2,3-tetrol, (4R)-2-METHYLPENTANE-2,4-DIOL, FORMIC ACID, ... | Authors: | Allen, K.N, Silvaggi, N.R, Toteva, M.M, Richard, J.P. | Deposit date: | 2011-10-05 | Release date: | 2011-10-26 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (0.97 Å) | Cite: | Binding Energy and Catalysis by d-Xylose Isomerase: Kinetic, Product, and X-ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde. Biochemistry, 50, 2011
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6VW4
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6C8T
| The structure of MppP soaked with the substrate L-Arg | Descriptor: | (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine, CHLORIDE ION, PLP-Dependent L-Arginine Hydroxylase MppP | Authors: | Han, L, Silvaggi, N.R. | Deposit date: | 2018-01-25 | Release date: | 2018-09-05 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase. Biochemistry, 57, 2018
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6C92
| The structure of MppP soaked with the product 2-ketoarginine | Descriptor: | (4S)-5-carbamimidamido-4-hydroxy-2-oxopentanoic acid, (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine, PLP-Dependent L-Arginine Hydroxylase MppP | Authors: | Han, L, Silvaggi, N.R. | Deposit date: | 2018-01-25 | Release date: | 2018-09-05 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.834 Å) | Cite: | Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase. Biochemistry, 57, 2018
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6C9B
| The structure of MppP soaked with the products 4HKA and 2KA | Descriptor: | (4S)-5-carbamimidamido-4-hydroxy-2-oxopentanoic acid, CHLORIDE ION, PLP-Dependent L-Arginine Hydroxylase MppP | Authors: | Han, L, Silvaggi, N.R. | Deposit date: | 2018-01-26 | Release date: | 2018-04-04 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.689 Å) | Cite: | Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase. Biochemistry, 57, 2018
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1HVB
| CRYSTAL STRUCTURE OF STREPTOMYCES R61 DD-PEPTIDASE COMPLEXED WITH A NOVEL CEPHALOSPORIN ANALOG OF CELL WALL PEPTIDOGLYCAN | Descriptor: | 5-{3-(S)-(4-(R)-ACETYLAMINO-4-CARBOXY-BUTYRYLAMINO)-3-[1-(R)-(1-(R)-CARBOXY-ETHYLCARBAMOYL)-ETHYLCARBAMOYL]-PROPYL}-2-( CARBOXY-PHENYLACETYLAMINO-METHYL)-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID, D-ALANYL-D-ALANINE CARBOXYPEPTIDASE | Authors: | McDonough, M.A, Lee, W, Silvaggi, N.R, Mobashery, S, Kelly, J.A. | Deposit date: | 2001-01-08 | Release date: | 2001-02-07 | Last modified: | 2023-08-09 | Method: | X-RAY DIFFRACTION (1.17 Å) | Cite: | A 1.2-A snapshot of the final step of bacterial cell wall biosynthesis. Proc.Natl.Acad.Sci.USA, 98, 2001
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4ZBT
| Streptomyces bingchenggensis aldolase-dehydratase in Schiff base complex with pyruvate | Descriptor: | 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL, Acetoacetate decarboxylase, DI(HYDROXYETHYL)ETHER, ... | Authors: | Mydy, L.S, Silvaggi, N.R. | Deposit date: | 2015-04-15 | Release date: | 2015-06-17 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Sbi00515, a Protein of Unknown Function from Streptomyces bingchenggensis, Highlights the Functional Versatility of the Acetoacetate Decarboxylase Scaffold. Biochemistry, 54, 2015
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4ZBO
| Streptomyces bingchenggensis acetoacetate decarboxylase in non-covalent complex with potassium formate | Descriptor: | 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL, 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL, Acetoacetate decarboxylase, ... | Authors: | Mydy, L.S, Silvaggi, N.R. | Deposit date: | 2015-04-15 | Release date: | 2015-06-17 | Last modified: | 2023-05-17 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Sbi00515, a Protein of Unknown Function from Streptomyces bingchenggensis, Highlights the Functional Versatility of the Acetoacetate Decarboxylase Scaffold. Biochemistry, 54, 2015
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