Biosynthesis of Nitrogenase Metalloclusters

Ribbe, Markus W.; Hu, Yilin; Hodgson, Keith O.; Hedman, Britt

doi:10.1021/cr400463x

Cited by 123 publications

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“…As part of the catalytic active center in enzymes, molybdate is coordinated to a dithiolene group of a tricyclic pyranopterin monophosphate named molybdopterin (MPT), thereby forming the molybdenum cofactor (Moco) (Johnson and Rajagopalan, 1982). Only in nitrogen fixing bacteria can molybdate be inserted into a FeS cluster based iron-molybdenum cofactor (FeMoco), which forms the active site of nitrogenase (Ribbe et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Shared function and moonlighting proteins in molybdenum cofactor biosynthesis

Leimkühler

2017

Biological Chemistry

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Abstract:The biosynthesis of the molybdenum cofactor (Moco) is a highly conserved pathway in bacteria, archaea and eukaryotes. The molybdenum atom in Mococontaining enzymes is coordinated to the dithiolene group of a tricyclic pyranopterin monophosphate cofactor. The biosynthesis of Moco can be divided into three conserved steps, with a fourth present only in bacteria and archaea:(1) formation of cyclic pyranopterin monophosphate, (2) formation of molybdopterin (MPT), (3) insertion of molybdenum into MPT to form Mo-MPT, and (4) additional modification of Mo-MPT in bacteria with the attachment of a GMP or CMP nucleotide, forming the dinucleotide variants of Moco. While the proteins involved in the catalytic reaction of each step of Moco biosynthesis are highly conserved among the Phyla, a surprising link to other cellular pathways has been identified by recent discoveries. In particular, the pathways for FeS cluster assembly and thio-modifications of tRNA are connected to Moco biosynthesis by sharing the same protein components. Further, proteins involved in Moco biosynthesis are not only shared with other pathways, but additionally have moonlighting roles. This review gives an overview of Moco biosynthesis in bacteria and humans and highlights the shared function and moonlighting roles of the participating proteins.

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Section: Introductionmentioning

confidence: 99%

Shared function and moonlighting proteins in molybdenum cofactor biosynthesis

Leimkühler

2017

Biological Chemistry

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“…: 49-0-3020936369; E-mail: Holger.Dobbek@biologie.hu-berlin.de. 2 The abbreviations used are: ACS, acetyl-CoA synthase; CODH, carbon monoxide dehydrogenase; SEC, size exclusion chromatography; ITC, isothermal titration calorimetry; ICP-OES, inductively coupled plasma optic emission spectrometry; TEV, tobacco etch virus; PIPE, polymerase incomplete primer extension. …”

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“…How metalloenzymes mature has been investigated for some systems, revealing surprisingly complex maturation pathways (2)(3)(4)(5)(6)(7)(8). Enzymes containing nickel, although still relatively small in number, play critical roles in archaea, bacteria, and eukarya, through which they impact the global hydrogen (Ni,Fe-hydrogenase), nitrogen (urease), and carbon (acetylCoA synthase, carbon monoxide dehydrogenase, and methylCoM reductase) cycles (9).…”

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confidence: 99%

“…The nickel-enzymes acetyl-CoA synthase (ACS) 2 and carbon monoxide dehydrogenase (CODH) are found in a variety of anaerobic microbes, including bacterial sulfate reducers, acetogens, and hydrogenogens, as well as archaeal methanogens and sulfate reducers, where they act as the prime CO 2 and CO converter (11)(12)(13)(14). ACS and CODH can be found as independent monofunctional enzymes in Carboxydothermus hydrogenoformans (15) but are typically found in other microorganisms as protein complexes: in acetogens ACS and CODH form a bifunctional (␣␤) 2 complex, whereas in methanogens they are part of a large (␣␤␥␦⑀) 8 multienzyme complex (11,13,15,16).…”

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confidence: 99%

“…ACS and CODH can be found as independent monofunctional enzymes in Carboxydothermus hydrogenoformans (15) but are typically found in other microorganisms as protein complexes: in acetogens ACS and CODH form a bifunctional (␣␤) 2 complex, whereas in methanogens they are part of a large (␣␤␥␦⑀) 8 multienzyme complex (11,13,15,16). CODHs catalyze the reversible reduction of CO 2 to CO at the C-cluster, in which a single nickel ion, embedded within a 3Fe-4S scaffold with an additional iron in exo, binds and activates CO and CO 2 for turnover (17)(18)(19).…”

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AcsF Catalyzes the ATP-dependent Insertion of Nickel into the Ni,Ni-[4Fe4S] Cluster of Acetyl-CoA Synthase

Gregg

Goetzl

Jeoung

et al. 2016

Journal of Biological Chemistry

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Acetyl-CoA synthase (ACS) catalyzes the reversible condensation of CO, CoA, and a methyl-cation to form acetyl-CoA at a unique Ni,Ni-[4Fe4S] cluster (the A-cluster). However, it was unknown which proteins support the assembly of the A-cluster. We analyzed the product of a gene from the cluster containing the ACS gene, cooC2 from Carboxydothermus hydrogenoformans, named AcsF Ch , and showed that it acts as a maturation factor of ACS. AcsF Ch and inactive ACS form a stable 2:1 complex that binds two nickel ions with higher affinity than the individual components. The nickel-bound ACS-AcsF Ch complex remains inactive until MgATP is added, thereby converting inactive to active ACS. AcsF Ch is a MinD-type ATPase and belongs to the CooC protein family, which can be divided into homologous subgroups. We propose that proteins of one subgroup are responsible for assembling the Ni,Ni-[4Fe4S] cluster of ACS, whereas proteins of a second subgroup mature the [Ni4Fe4S] cluster of carbon monoxide dehydrogenases.The cellular maturation of metalloenzymes, previously considered a spontaneous process in vivo, typically depends on a machinery of uptake, storage, processing, and delivery factors (1). How metalloenzymes mature has been investigated for some systems, revealing surprisingly complex maturation pathways (2-8). Enzymes containing nickel, although still relatively small in number, play critical roles in archaea, bacteria, and eukarya, through which they impact the global hydrogen (Ni,Fe-hydrogenase), nitrogen (urease), and carbon (acetylCoA synthase, carbon monoxide dehydrogenase, and methylCoM reductase) cycles (9). For most of these enzymes, we now have a good understanding of how nickel is incorporated into the active site (8, 10).The nickel-enzymes acetyl-CoA synthase (ACS) 2 and carbon monoxide dehydrogenase (CODH) are found in a variety of anaerobic microbes, including bacterial sulfate reducers, acetogens, and hydrogenogens, as well as archaeal methanogens and sulfate reducers, where they act as the prime CO 2 and CO converter (11)(12)(13)(14). ACS and CODH can be found as independent monofunctional enzymes in Carboxydothermus hydrogenoformans (15) but are typically found in other microorganisms as protein complexes: in acetogens ACS and CODH form a bifunctional (␣␤) 2 complex, whereas in methanogens they are part of a large (␣␤␥␦⑀) 8 multienzyme complex (11,13,15,16). CODHs catalyze the reversible reduction of CO 2 to CO at the C-cluster, in which a single nickel ion, embedded within a 3Fe-4S scaffold with an additional iron in exo, binds and activates CO and CO 2 for turnover (17)(18)(19). ACS catalyzes the reversible condensation of CO, CoA, and a methyl-cation donated by the methylated corrinoid iron-sulfur protein to form acetyl-CoA (13). ACS depends on a Ni,Ni-[4Fe4S] cluster (also called A-cluster) for activity, in which the two nickel ions have distinct coordinations: the nickel ion distal to the [4Fe4S] cluster (Ni d ) is coordinated by two amide nitrogen atoms and two cysteine thiolates within a Cys-X-Cys ...

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Nitrogen Fixation

Newton

2015

Kirk-Othmer Encyclopedia of Chemical Technology

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About 80% of the Earth's atmosphere is made up of nitrogen gas (N 2 ), but nitrogen is most often the limiting nutrient for agricultural productivity, because neither plants nor animals can use it directly. It must first be fixed into either ammonium or nitrate. Only the simplest life forms, bacteria and archaea, can produce ammonium from N 2 using the enzyme called nitrogenase. N 2 is also fixed by nonbiological processes, which contribute equally to the total annual fixation rate. In fact, without commercial fertilizers, the human population could not be supported. This article first describes the major industrial processes and their shortcomings, emphasizing the dominant Haber‐Bosch process. Then, an overview of the various biological nitrogen‐fixing systems, both free‐living and symbiotic organisms, focusing on the agriculturally important legume– Rhizobium symbiosis is provided. Nitrogenase is detailed and analyzed next with sections on its evolution, biosynthesis, composition and structure, regulation, and catalytic mechanism, the last of which is now beginning to be understood in some detail. The penultimate section describes attempts to duplicate either the reactivity or the structure of nitrogenase in chemical systems, some of which have achieved limited catalytic capability. Finally, the last section attempts to highlight both the important strides made and the problems that remain. These include limiting losses of applied fertilizer to ground water and atmosphere; careful matching of inoculant with cultivar; reducing fossil fuel energy inputs to fertilizer production; manipulating plant colonization and symbiosis development to produce new pairings; and simplifying the biological process for transfer to other organisms.

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Biosynthesis of Nitrogenase Metalloclusters

Cited by 123 publications

References 128 publications

Shared function and moonlighting proteins in molybdenum cofactor biosynthesis

Shared function and moonlighting proteins in molybdenum cofactor biosynthesis

AcsF Catalyzes the ATP-dependent Insertion of Nickel into the Ni,Ni-[4Fe4S] Cluster of Acetyl-CoA Synthase

Nitrogen Fixation

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