Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase

Carbone, Vincenzo; Schofield, Linley R.; Sang, Carrie; Dey, Debjit; Hannus, Ingegerd M.; Martin, William; Sutherland-Smith, Andrew J.; Ronimus, Ron S.

doi:10.1074/jbc.m115.647461

Cited by 18 publications

(27 citation statements)

References 70 publications

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“…The reaction rate with NADPH (

V_{max}^{NADPH}

= 0.007 ± 0.01 μmol/sec/mg) was only 2.4% of that with NADH (

V_{max}^{NADH}

= 0.30 ± 0.027 μmol/sec/mg), indicating that NADH is favored as the natural cofactor. This finding is a striking feature of P. calidifontis G1PDH, because the four previously characterized G1PDHs show a significant preference for NADPH when V max / K m values are compared, indicating that the P. calidifontis enzyme is a novel type of G1PDH. The K m value for NADH and NADPH was determined to be 0.077 ± 0.01 m M and 0.031 ± 0.011 m M respectively, when 4 m M DHAP was used.…”

Section: Resultsmentioning

confidence: 76%

“…Previous studies on M. thermoautotrophicus G1PDH have suggested that this enzyme is a homooctamer in solution, whereas A. pernix G1PDH forms a dimeric structure . On the other hand, M. jannaschii G1PDH was proposed to have a monomeric structure, although the enzyme forms a dimeric structure in a crystal form. In this regard, P. calidifontis G1PDH differs substantially from the three other G1PDHs previously described.…”

Section: Resultsmentioning

confidence: 98%

“…Within the genomic sequence of the hyperthermophilic archaeon Pyrobaculum calidifontis , we found a gene (open reading frame identification number Pcal_0566) whose predicted amino acid sequence exhibits 41, 45, and 46% identities to those of the previously characterized G1PDHs from M. jannaschii , Aeropyrum pernix, and Sulfolobus tokodaii, respectively. In this study, we expressed the gene Pcal_0566, characterized the enzyme produced, and revealed the enzyme to be G1PDH having strong preference for NADH as the coenzyme.…”

Section: Introductionmentioning

confidence: 89%

“…Based on the glycerol dehydrogenase structure, homology modeling of G1PDH from Methanothermobacter thermoautotrophicus was performed, and the enzyme's putative active site and hydride transfer mechanism from the substrate to NAD during catalysis (pro‐ R specific) have been predicted . Most recently, the first structures of archaeal G1PDH from the hyperthermophilic methanogen Methanocaldococcus jannaschii with the bound substrate DHAP, product G1P, and cofactors NADPH and Zn 2+ have been determined . The structures provided key evidence for the reaction mechanism in the stereo‐specific addition for the NAD(P)H‐based pro‐ R hydride transfer and the coordination of Zn 2+ during catalysis.…”

Section: Introductionmentioning

confidence: 99%

“…However, information on the structure of G1PDH remains limited. Indeed, crystal structures of only the M. jannaschii enzyme have been reported so far …”

Section: Introductionmentioning

confidence: 99%

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Unique coenzyme binding mode of hyperthermophilic archaealsn-glycerol-1-phosphate dehydrogenase fromPyrobaculum calidifontis

et al. 2016

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A gene encoding an sn-glycerol-1-phosphate dehydrogenase (G1PDH) was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The gene was overexpressed in Escherichia coli, and its product was purified and characterized. In contrast to conventional G1PDHs, the expressed enzyme showed strong preference for NADH: the reaction rate (V ) with NADPH was only 2.4% of that with NADH. The crystal structure of the enzyme was determined at a resolution of 2.45 Å. The asymmetric unit consisted of one homohexamer. Refinement of the structure and HPLC analysis showed the presence of the bound cofactor NADPH in subunits D, E, and F, even though it was not added in the crystallization procedure. The phosphate group at C2' of the adenine ribose of NADPH is tightly held through the five biased hydrogen bonds with Ser40 and Thr42. In comparison with the known G1PDH structure, the NADPH molecule was observed to be pushed away from the normal coenzyme binding site. Interestingly, the S40A/T42A double mutant enzyme acquired much higher reactivity than the wild-type enzyme with NADPH, which suggests that the biased interactions around the C2'-phosphate group make NADPH binding insufficient for catalysis. Our results provide a unique structural basis for coenzyme preference in NAD(P)-dependent dehydrogenases. Proteins 2016; 84:1786-1796. © 2016 Wiley Periodicals, Inc.

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“…The reaction rate with NADPH (

V_{max}^{NADPH}

= 0.007 ± 0.01 μmol/sec/mg) was only 2.4% of that with NADH (

V_{max}^{NADH}

Section: Resultsmentioning

confidence: 76%

Section: Resultsmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 89%

Section: Introductionmentioning

confidence: 99%

“…However, information on the structure of G1PDH remains limited. Indeed, crystal structures of only the M. jannaschii enzyme have been reported so far …”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Unique coenzyme binding mode of hyperthermophilic archaealsn-glycerol-1-phosphate dehydrogenase fromPyrobaculum calidifontis

et al. 2016

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The crystal structure of methanogen McrD, a methyl‐coenzyme M reductase‐associated protein

Sutherland‐Smith,

Carbone,

Schofield

et al. 2024

FEBS Open Bio

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Methyl‐coenzyme M reductase (MCR) is a multi‐subunit (α2β2γ2) enzyme responsible for methane formation via its unique F430 cofactor. The genes responsible for producing MCR (mcrA, mcrB and mcrG) are typically colocated with two other highly conserved genes mcrC and mcrD. We present here the high‐resolution crystal structure for McrD from a human gut methanogen Methanomassiliicoccus luminyensis strain B10. The structure reveals that McrD comprises a ferredoxin‐like domain assembled into an α + β barrel‐like dimer with conformational flexibility exhibited by a functional loop. The description of the M. luminyensis McrD crystal structure contributes to our understanding of this key conserved methanogen protein typically responsible for promoting MCR activity and the production of methane, a greenhouse gas.

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Proton gradients at the origin of life

Lane

2017

BioEssays

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Chemiosmotic coupling - the harnessing of electrochemical ion gradients across membranes to drive metabolism - is as universally conserved as the genetic code. As argued previously in these pages, such deep conservation suggests that ion gradients arose early in evolution, and might have played a role in the origin of life. Alkaline hydrothermal vents harbour pH gradients of similar polarity and magnitude to those employed by modern cells, one of many properties that make them attractive models for life's origin. Their congruence with the physiology of anaerobic autotrophs that use the acetyl CoA pathway to fix CO gives the alkaline vent model broad appeal to biologists. Recently, however, a paper by Baz Jackson criticized the hypothesis, concluding that natural pH gradients were unlikely to have played any role in the origin of life. Unfortunately, Jackson mainly criticized his own interpretations of the theory, not what the literature says. This counterpoint is intended to set the record straight.

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Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase

Cited by 18 publications

References 70 publications

Unique coenzyme binding mode of hyperthermophilic archaealsn-glycerol-1-phosphate dehydrogenase fromPyrobaculum calidifontis

Unique coenzyme binding mode of hyperthermophilic archaealsn-glycerol-1-phosphate dehydrogenase fromPyrobaculum calidifontis

The crystal structure of methanogen McrD, a methyl‐coenzyme M reductase‐associated protein

Proton gradients at the origin of life

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