Pyruvate Formate-lyase, Evidence for an Open Conformation Favored in the Presence of Its Activating Enzyme

Peng, Yi; Veneziano, Susan E.; Gillispie, Gregory D.; Broderick, Joan B.

doi:10.1074/jbc.m109.096875

Cited by 39 publications

(57 citation statements)

References 39 publications

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“…This means that a local movement of the glycine loop out of the protein core, a global structural change, or a combination of both must happen to achieve radical formation. PFL has been shown to exist in solution in both open and closed forms, and the equilibrium between these forms is thought to be modulated by the activating enzyme (40). Direct structural evidence for conformational changes, similar to the changes observed for K. pneumoniae CutC, has also been observed for BSS (17).…”

Section: Discussionmentioning

confidence: 80%

Structure and Function of CutC Choline Lyase from Human Microbiota Bacterium Klebsiella pneumoniae

Kalnins

Kuka

Grı̄nberga

et al. 2015

Journal of Biological Chemistry

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Background:The bacterial glycyl radical enzyme CutC converts choline to trimethylamine, a metabolite involved in pathogenesis of several diseases. Results: The structures of substrate-bound and substrate-free CutC revealed significant differences. Conclusion: Choline binding to the active site triggers a conformational change from the open to closed form. Significance: A novel substrate-driven conformational mechanism and a potential target for drug design have been identified.

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Section: Discussionmentioning

confidence: 80%

Structure and Function of CutC Choline Lyase from Human Microbiota Bacterium Klebsiella pneumoniae

Kalnins

Kuka

Grı̄nberga

et al. 2015

Journal of Biological Chemistry

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“…This interaction is not present in the structural models of PFL. However, PFL remains somewhat unique in that it has also been shown to exhibit "half-sites" reactivity (19,20,41) and appears to have a "repair peptide," YfiD, which can be post-translationally activated by PFL-AE. The activated YfiD can replace any glycyl radical domains in PFL that have been oxygen damaged (42).…”

Section: Discussionmentioning

confidence: 99%

“…In vitro, the catalytic [4Fe-4S] can be reduced from the 2ϩ to the 1ϩ oxidation state using a biological reducing system, such as a NADPH flavodoxin/oxidoreductase and flavodoxin system (18). In addition, chemical reductants such as sodium dithionite or a light-driven reducing system are also effective electron donors (19,20). The activation process, or generation of the catalytic glycyl radical, is further complicated by recent observations that demonstrate the substrate for the GRE accelerates the activation rate (21).…”

mentioning

confidence: 99%

1,2-Propanediol Dehydration in Roseburia inulinivorans

LaMattina

Keul

Reitzer

et al. 2016

Journal of Biological Chemistry

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Glycyl radical enzymes (GREs) represent a diverse superfamily of enzymes that utilize a radical mechanism to catalyze difficult, but often essential, chemical reactions. In this work we present the first biochemical and structural data for a GRE-type diol dehydratase from the organism Roseburia inulinivorans (RiDD). Despite high sequence (48% identity) and structural similarity to the GRE-type glycerol dehydratase from Clostridium butyricum, we demonstrate that the RiDD is in fact a diol dehydratase. In addition, the RiDD will utilize both (S)-1,2-propanediol and (R)-1,2-propanediol as a substrate, with an observed preference for the S enantiomer. Based on the new structural information we developed and successfully tested a hypothesis that explains the functional differences we observe.

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“…In the class II RNR from Lactobacillus leichmannii, coenzyme B 12 binding causes a shift in a small number of residues exterior to the barrel, which closes the barrel and shields the cofactor from solvent (48). In PFL, the G• domain must exit the active site to become accessible to its partner activating enzyme for radical generation, and circular dichroism spectroscopy shows that binding of PFL to its activase is accompanied by enhanced enzyme conformational flexibility (49,50). The recent structure of the G• enzyme benzylsuccinate synthase (51) reveals a clamshell-like opening of the barrel, allowing release of the G• domain from the interior of the protein, which would again allow for G• formation.…”

Section: Reaction Conditionsmentioning

confidence: 99%

The class III ribonucleotide reductase from Neisseria bacilliformis can utilize thioredoxin as a reductant

Wei¹,

Funk²,

Rosado³

et al. 2014

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

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The class III anaerobic ribonucleotide reductases (RNRs) studied to date couple the reduction of ribonucleotides to deoxynucleotides with the oxidation of formate to CO 2 . Here we report the cloning and heterologous expression of the Neisseria bacilliformis class III RNR and show that it can catalyze nucleotide reduction using the ubiquitous thioredoxin/thioredoxin reductase/NADPH system. We present a structural model based on a crystal structure of the homologous Thermotoga maritima class III RNR, showing its architecture and the position of conserved residues in the active site. Phylogenetic studies suggest that this form of class III RNR is present in bacteria and archaea that carry out diverse types of anaerobic metabolism.T he class III ribonucleotide reductases (RNRs) are glycyl radical enzymes present in many strict and facultative anaerobes that catalyze the conversion of nucleotides to deoxynucleotides (1, 2) via a mechanism involving complex free radical chemistry and are largely responsible for providing the balanced pool of deoxynucleotides required for DNA synthesis and repair (3). The class III RNRs that have been characterized thus far obtain the reducing equivalents required to make deoxynucleoside triphosphates (dNTPs) from the oxidation of formate to CO 2 (4). Here we report a second subtype of class III RNR from Neisseria bacilliformis, which can obtain its reducing equivalents from the thioredoxin (TrxA)/thioredoxin reductase (TrxB)/ NADPH system. RNRs provide the only pathway for de novo biosynthesis of dNTPs (5). They share a structurally homologous active site architecture in the α subunit and a partially conserved, radicalbased reduction mechanism. RNRs have been isolated and characterized from all kingdoms of life and, based on the characterization of these proteins thus far, are divided into three classes (I, II, and III) according to the metallo-cofactor used to generate a thiyl radical that initiates the radical-dependent reduction chemistry (6). The class I RNRs use cofactors generated by the reaction of reduced metals (Fe, Mn, and Fe/Mn) and O 2 and are present only in aerobic organisms. The class II RNRs use adenosylcobalamin in an O 2 -independent reaction and are present in both aerobes and anaerobes. The class III RNR uses an O 2 -sensitive glycyl radical (G•) (2) situated in the α protein (NrdD), which is generated by a separate activating enzyme (NrdG) via radical S-adenosylmethionine (SAM)-[4Fe4S] 1+ chemistry (7,8). The class III RNRs are only found in facultative and obligate anaerobes. A second distinction between the three classes has been the source of the reducing equivalents for nucleotide reduction. In the class I and II RNRs, they are provided by a redoxin (thioredoxin, glutaredoxin, or NrdH), which is rereduced by thioredoxin reductase and NADPH (9-11). In contrast, for the bacteriophage T4 (12), its Gram-negative host Escherichia coli (1), and the Gram-positive Lactococcus lactis (13), the only class III RNRs characterized in detail to date, nucleotide reduction i...

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Pyruvate Formate-lyase, Evidence for an Open Conformation Favored in the Presence of Its Activating Enzyme

Cited by 39 publications

References 39 publications

Structure and Function of CutC Choline Lyase from Human Microbiota Bacterium Klebsiella pneumoniae

Structure and Function of CutC Choline Lyase from Human Microbiota Bacterium Klebsiella pneumoniae

1,2-Propanediol Dehydration in Roseburia inulinivorans

The class III ribonucleotide reductase from Neisseria bacilliformis can utilize thioredoxin as a reductant

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