Investigation of the Catalytic Mechanism of the Hotdog-Fold Enzyme Superfamily Pseudomonas sp. Strain CBS3 4-Hydroxybenzoyl-CoA Thioesterase

Zhihao Zhuang; John Latham; Feng Song; Wenhai Zhang; Michael Trujillo; Debra Dunaway-Mariano

doi:10.1021/bi2013917

The Catalytic Mechanism of the Hotdog-fold Enzyme Superfamily 4-Hydroxybenzoyl-CoA Thioesterase from Arthrobacter sp. Strain SU

Biochemistry ◽

10.1021/bi301059m ◽

2012 ◽

Vol 51 (35) ◽

pp. 7000-7016 ◽

Cited By ~ 18

Author(s):

Feng Song ◽

James B. Thoden ◽

Zhihao Zhuang ◽

John Latham ◽

Michael Trujillo ◽

...

Keyword(s):

Catalytic Mechanism ◽

Enzyme Superfamily ◽

Hotdog Fold

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High resolution X-ray crystal structures of l-phenylalanine oxidase (deaminating and decarboxylating) from Pseudomonas sp. P-501. Structures of the enzyme-ligand complex and catalytic mechanism

The Journal of Biochemistry ◽

10.1093/jb/mvr103 ◽

2011 ◽

Vol 150 (6) ◽

pp. 659-669 ◽

Cited By ~ 10

Author(s):

Koh Ida ◽

Masaya Suguro ◽

Haruo Suzuki

Keyword(s):

High Resolution ◽

Crystal Structures ◽

Catalytic Mechanism ◽

Pseudomonas Sp ◽

Ligand Complex ◽

X Ray

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Mechanistic studies of the agmatine deiminase from Listeria monocytogenes

Biochemical Journal ◽

10.1042/bcj20160221 ◽

2016 ◽

Vol 473 (11) ◽

pp. 1553-1561 ◽

Cited By ~ 5

Author(s):

Charles A. Soares ◽

Bryan Knuckley

Keyword(s):

Listeria Monocytogenes ◽

Catalytic Mechanism ◽

Mechanistic Studies ◽

New Class ◽

Enzyme Superfamily ◽

Agmatine Deiminase ◽

Inhibition Studies

Mechanistic and inhibition studies of the agmatine deiminase found in Listeria monocytogenes reveal a novel catalytic mechanism for the guanidinium-modifying enzyme superfamily. The results of the present study suggest that a new class of mechanism-based inactivators is needed.

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Catalytic Mechanism of the Hotdog-Fold Thioesterase PA1618 Revealed by X-ray Structure Determination of a Substrate-Bound Oxygen Ester Analogue Complex

ChemBioChem ◽

10.1002/cbic.201700322 ◽

2017 ◽

Vol 18 (19) ◽

pp. 1935-1943

Author(s):

John A. Latham ◽

Tianyang Ji ◽

Kaila Matthews ◽

Patrick S. Mariano ◽

Karen N. Allen ◽

...

Keyword(s):

Structure Determination ◽

Catalytic Mechanism ◽

X Ray ◽

Hotdog Fold

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Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a “bond rotation” catalytic mechanism

Journal of Biological Chemistry ◽

10.1074/jbc.ra119.011752 ◽

2019 ◽

Vol 295 (7) ◽

pp. 2113-2124 ◽

Cited By ~ 2

Author(s):

Ningning Zhuang ◽

Hao Zhang ◽

Lingting Li ◽

Xiaoxian Wu ◽

Chen Yang ◽

...

Keyword(s):

Crystal Structures ◽

Catalytic Mechanism ◽

Enzymatic Assays ◽

Bond Rotation ◽

Arginine Dihydrolase ◽

Arginine Catabolism ◽

Enzyme Superfamily ◽

Covalently Linked ◽

Biochemical Analyses ◽

Guanidino Group

A recently discovered ornithine–ammonia cycle (OAC) serves as a conduit in the nitrogen storage and remobilization machinery in cyanobacteria. The OAC involves an arginine catabolic reaction catalyzed by the arginine dihydrolase ArgZ whose catalytic mechanism is unknown. Here we determined the crystal structures at 1.2–3.0 Å of unliganded ArgZ from the cyanobacterium Synechocystis sp. PCC6803 and of ArgZ complexed with its substrate arginine, a covalently linked reaction intermediate, or the reaction product ornithine. The structures reveal that a key residue, Asn71, in the ArgZ active center functions as the determinant distinguishing ArgZ from other members of the guanidino group–modifying enzyme superfamily. The structures, along with biochemical evidence from enzymatic assays coupled with electrospray ionization MS techniques, further suggest that ArgZ-catalyzed conversion of arginine to ornithine, ammonia, and carbon dioxide consists of two successive cycles of amine hydrolysis. Finally, we show that arginine dihydrolases are broadly distributed among bacteria and metazoans, suggesting that the OAC may be frequently used for redistribution of nitrogen from arginine catabolism or nitrogen fixation.

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The BH1999 Protein of Bacillus halodurans C-125 Is Gentisyl-Coenzyme A Thioesterase

Journal of Bacteriology ◽

10.1128/jb.186.2.393-399.2004 ◽

2004 ◽

Vol 186 (2) ◽

pp. 393-399 ◽

Cited By ~ 15

Author(s):

Zhihao Zhuang ◽

Feng Song ◽

Hideto Takami ◽

Debra Dunaway-Mariano

Keyword(s):

Active Site ◽

Coenzyme A ◽

Ph Dependence ◽

Oxidative Degradation ◽

Bacillus Halodurans ◽

Enzyme Superfamily ◽

Coa Thioesters ◽

Hotdog Fold ◽

Hydrolysis Of ◽

Aspartate Residue

ABSTRACT In this study, we have shown that recombinant BH1999 from Bacillus halodurans catalyzes the hydrolysis of gentisyl coenzyme A (CoA) (2,5-dihydroxybenzoyl-coenzyme A) at physiological pH with a k cat/Km of 1.6 × 106 M−1 s−1 and the hydrolysis of 3-hydroxybenzoyl-CoA with a k cat/Km of 3.0 × 105 M−1 s−1. All other acyl-CoA thioesters tested had low or no substrate activity. The BH1999 gene is juxtaposed with a gene cluster that contains genes believed to function in gentisate oxidative degradation. It is hypothesized that BH1999 functions as a gentisyl-CoA thioesterase. Gentisyl-CoA thioesterase shares the backbone fold and the use of an active site aspartate residue to mediate catalysis with the 4-hydroxybenzoyl-CoA thioesterase of the hotdog fold enzyme superfamily. A comparative study of these two enzymes showed that they differ greatly in the rate contribution made by the catalytic aspartate, in the pH dependence of catalysis, and in substrate specificity.

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Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

Biochemical Journal ◽

10.1042/bcj20190399 ◽

2019 ◽

Vol 476 (21) ◽

pp. 3333-3353 ◽

Cited By ~ 3

Author(s):

Malti Yadav ◽

Kamalendu Pal ◽

Udayaditya Sen

Keyword(s):

Active Site ◽

Metal Binding ◽

Metal Ion ◽

Triosephosphate Isomerase ◽

Catalytic Mechanism ◽

Degradation Mechanism ◽

Structural Basis ◽

Conserved Residues ◽

Phosphodiester Bond ◽

Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

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