Tryptophan synthase: the workings of a channeling nanomachine

Dunn, Michael F.; Niks, Dimitri; Ngo, Huu; Barends, T.R.M.; Schlichting, Ilme

doi:10.1016/j.tibs.2008.04.008

Cited by 142 publications

(240 citation statements)

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“…Such a conformational change upon substrate binding was also observed for stTrpB1. 25,26 As predicted by homology modeling (Figure 1), the cofactor within the active site in the crystal structure is coordinated with hydrogen bonding interactions to Thr133, Ser264, and Ser411 ( Figure 2C). Binding of O-phospho-L-serine leads to a reorientation of Thr133 and Arg337, which facilitates the coordination of the carbonyl and the phosphate groups of PLP.…”

Section: ■ Results and Discussionmentioning

confidence: 72%

TrpB2 Enzymes are O-Phospho-l-serine Dependent Tryptophan Synthases

et al. 2014

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ABSTRACT:The rapid increase of the number of sequenced genomes asks for the functional annotation of the encoded enzymes. We used a combined computational−structural approach to determine the function of the TrpB2 subgroup of the tryptophan synthase β chain/β chain-like TrpB1−TrpB2 family (IPR023026). The results showed that TrpB2 enzymes are O-phospho-L-serine dependent tryptophan synthases, whereas TrpB1 enzymes catalyze the L-serine dependent synthesis of tryptophan. We found a single residue being responsible for the different substrate specificities of TrpB1 and TrpB2 and confirmed this finding by mutagenesis studies and crystallographic analysis of a TrpB2 enzyme with bound O-phospho-Lserine.

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Section: ■ Results and Discussionmentioning

confidence: 72%

TrpB2 Enzymes are O-Phospho-l-serine Dependent Tryptophan Synthases

et al. 2014

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“…These two chains on May 10, 2018 by guest http://iai.asm.org/ make up the tetrameric ␣ 2 ␤ 2 tryptophan synthase enzyme complex that catalyzes the final steps in tryptophan biosynthesis. The ␣ subunits convert indole-3-glycerolphosphate to indole and glyceraldehyde 3-phosphate, while the ␤ subunits catalyze the condensation of indole and serine to tryptophan (8,25,30). The trpA and trpB genes are positioned next to each other in the Francisella genome (Fig.…”

Section: Resultsmentioning

confidence: 99%

Indoleamine 2,3-Dioxygenase 1 Is a Lung-Specific Innate Immune Defense Mechanism That Inhibits Growth ofFrancisella tularensisTryptophan Auxotrophs

Peng

Monack

2010

Infect Immun

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Upon microbial challenge, organs at various anatomic sites of the body employ different innate immune mechanisms to defend against potential infections. Accordingly, microbial pathogens evolved to subvert these organ-specific host immune mechanisms to survive and grow in infected organs. Francisella tularensis is a bacterium capable of infecting multiple organs and thus encounters a myriad of organ-specific defense mechanisms. This suggests that F. tularensis may possess specific factors that aid in evasion of these innate immune defenses. We carried out a microarray-based, negative-selection screen in an intranasal model of Francisella novicida infection to identify Francisella genes that contribute to bacterial growth specifically in the lungs of mice. Genes in the bacterial tryptophan biosynthetic pathway were identified as being important for F. novicida growth specifically in the lungs. In addition, a host tryptophan-catabolizing enzyme, indoleamine 2,3-dioxygenase 1 (IDO1), is induced specifically in the lungs of mice infected with F. novicida or Streptococcus pneumoniae. Furthermore, the attenuation of F. novicida tryptophan mutant bacteria was rescued in the lungs of IDO1 ؊/؊ mice. IDO1 is a lung-specific innate immune mechanism that controls pulmonary Francisella infections.

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“…Conformational changes, such as gating, occur in other bifunctional enzymes, including tryptophan synthase (20) and glutamine amidotransferases (21), two well-studied bifunctional enzymes. Parallels between PutA and tryptophan synthase are especially apparent.…”

Section: Discussionmentioning

confidence: 99%

“…Parallels between PutA and tryptophan synthase are especially apparent. Tryptophan synthase exhibits an elegant mechanism of allosteric control in which chemical events in the α-and β-catalytic sites induce conformational changes that synchronize catalysis at the two sites and prevent escape of the intermediate indole (20). The closure of the PRODH site upon proline binding is analogous to the closure of the α-subunit of tryptophan synthase by 3-indole-D-glycerol 3′-phosphate in that the inducing ligand is the first substrate of the pathway.…”

Section: Discussionmentioning

confidence: 99%

Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site

Singh¹,

Arentson

Becker

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

120

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Proline utilization A (PutA) proteins are bifunctional peripheral membrane flavoenzymes that catalyze the oxidation of L-proline to L-glutamate by the sequential activities of proline dehydrogenase and aldehyde dehydrogenase domains. Located at the inner membrane of Gram-negative bacteria, PutAs play a major role in energy metabolism by coupling the oxidation of proline imported from the environment to the reduction of membrane-associated quinones. Here, we report seven crystal structures of the 1,004-residue PutA from Geobacter sulfurreducens, along with determination of the protein oligomeric state by small-angle X-ray scattering and kinetic characterization of substrate channeling and quinone reduction. The structures reveal an elaborate and dynamic tunnel system featuring a 75-Å-long tunnel that links the two active sites and six smaller tunnels that connect the main tunnel to the bulk medium. The locations of these tunnels and their responses to ligand binding and flavin reduction suggest hypotheses about how proline, water, and quinones enter the tunnel system and where L-glutamate exits. Kinetic measurements show that glutamate production from proline occurs without a lag phase, consistent with substrate channeling and implying that the observed tunnel is functionally relevant. Furthermore, the structure of reduced PutA complexed with menadione bisulfite reveals the elusive quinone-binding site. The benzoquinone binds within 4.0 Å of the flavin si face, consistent with direct electron transfer. The location of the quinone site implies that the concave surface of the PutA dimer approaches the membrane. Altogether, these results provide insight into how PutAs couple proline oxidation to quinone reduction.proline catabolism | X-ray crystallography | membrane association P roline catabolism is an important pathway in bioenergetics and has been implicated in tumor suppression (1), lifespan extension (2), production of fungal virulence factors (3), and bacterial virulence (4, 5). The pathway (Fig. 1A) comprises the flavoenzyme proline dehydrogenase (PRODH) and the aldehyde dehydrogenase (ALDH) superfamily member Δ 1 -pyrroline-5-carboxylate (P5C) dehydrogenase (P5CDH, also known as ALDH4A1). PRODH catalyzes the FAD-dependent oxidation of proline to P5C. P5CDH is a misnomer, as the enzyme catalyzes the oxidization of L-glutamate-γ-semialdehyde (GSA), which is the hydrolysis product of P5C. The electrons abstracted from proline by PRODH flow into the electron transport chain whereas the carbon skeleton of L-proline ultimately enters the citric acid cycle via α-ketoglutarate.Curiously, in Gram-negative bacteria, PRODH and P5CDH are combined into a single polypeptide, which is known as proline utilization A (PutA). Two functional classes of PutA exist: bifunctional and trifunctional (6). Bifunctional PutAs, which are the focus of this work, are peripheral membrane-associated enzymes that exhibit both PRODH and P5CDH catalytic activities. Localization of PutA at the inner bacterial membrane facilitates the efficient...

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Tryptophan synthase: the workings of a channeling nanomachine

Cited by 142 publications

References 50 publications

TrpB2 Enzymes are O-Phospho-l-serine Dependent Tryptophan Synthases

TrpB2 Enzymes are O-Phospho-l-serine Dependent Tryptophan Synthases

Indoleamine 2,3-Dioxygenase 1 Is a Lung-Specific Innate Immune Defense Mechanism That Inhibits Growth ofFrancisella tularensisTryptophan Auxotrophs

Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site

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