Nitrogenase assembly

Hu, Yilin; Ribbe, Markus W.

doi:10.1016/j.bbabio.2012.12.001

Cited by 66 publications

(51 citation statements)

References 59 publications

(82 reference statements)

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“…[9] for a review), different overall nitrogen-catalyzed reactions are found in textbooks. The following is a discussion on the pitfalls that may cause such discrepancies.…”

Section: The Nitrogenase-catalyzed Reactionmentioning

confidence: 99%

What is the true nitrogenase reaction? A guided approach

Ipata

Pesi

2015

Biochem Molecular Bio Educ

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Only diazotrophic bacteria, called Rizhobia, living as symbionts in the root nodules of leguminous plants and certain free-living prokaryotic cells can fix atmospheric N 2 . In these microorganisms, nitrogen fixation is carried out by the nitrogenase protein complex. However, the reduction of nitrogen to ammonia has an extremely high activation energy due to the stable (unreactive) NBN triple bond. The structural and functional features of the nitrogenase protein complex, based on the stepwise transfer of eight electrons from reduced ferredoxin to the nitrogenase, coupled to the hydrolysis of 16 ATP molecules, to fix one N 2 molecule into two NH 3 molecules, is well understood. Yet, a number of different nitrogenase-catalyzed reactions are present in biochemistry textbooks, which might cause misinterpretation. In this article, we show that when trying to balance the reaction catalyzed by the nitrogenase protein complex, it is important to show explicitly the 16 H 1 released by the hydrolysis of the 16 ATP molecules needed to fix the atmospheric N 2 V C 2015 by the International Union of Biochemistry and Molecular Biology, 43(3):142-144, 2015.

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“…[9] for a review), different overall nitrogen-catalyzed reactions are found in textbooks. The following is a discussion on the pitfalls that may cause such discrepancies.…”

Section: The Nitrogenase-catalyzed Reactionmentioning

confidence: 99%

What is the true nitrogenase reaction? A guided approach

Ipata

Pesi

2015

Biochem Molecular Bio Educ

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“…In this minireview, we describe a model for mammalian cobalamin trafficking, which includes strategies for conversion of inactive precursors to the active cofactor forms methylcobalamin (MeCbl) 3 and 5Ј-deoxyadenosylcobalamin (AdoCbl; coenzyme B 12 ) and discuss the human diseases that result from impairments along the trafficking highway. We posit that the navigation strategy for B 12 , in which a rare, reactive, and high value cofactor is sequestered and targeted to client proteins, might represent a general archetype for the trafficking of other essential but scarce organic and organometallic cofactors.…”

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confidence: 99%

“…Similarly, elaboration of metals into clusters often occurs on chaperones that subsequently transfer the cofactor to target proteins. The interprotein transfer of metals can occur via ligand exchange reactions that are driven by differences in metal coordination geometry and affinity between the donor and acceptor proteins (2,3). Seclusion of cofactors in chaperones during assembly/processing into their active forms minimizes unwanted side reactions, whereas guided delivery averts dilution and promotes specificity of cofactor docking.…”

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confidence: 99%

Navigating the B12 Road: Assimilation, Delivery, and Disorders of Cobalamin

Gherasim

Lofgren

Banerjee

2013

Journal of Biological Chemistry

175

123

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The reactivity of the cobalt-carbon bond in cobalamins is the key to their chemical versatility, supporting both methyl transfer and isomerization reactions. During evolution of higher eukaryotes that utilize vitamin B 12 , the high reactivity of the cofactor coupled with its low abundance pressured development of an efficient system for uptake, assimilation, and delivery of the cofactor to client B 12 -dependent enzymes. Although most proteins suspected to be involved in B 12 trafficking were discovered by 2009, the recent identification of a new protein reveals that the quest for elucidating the intracellular B 12 highway is still far from complete. Herein, we review the biochemistry of cobalamin trafficking.Cofactors are variously deployed in nature to stabilize macromolecular structures, expand catalytic functionality, transport gases, transduce signals, and function as sensors. Due to their relative rarity and/or reactivity, cells have evolved strategies for sequestering and regulating the movement of cofactors from their point of entry into the cell to their point of docking in target proteins (1). A subset of cofactors, i.e. the vitamins, is obtained in a precursor form from the diet. Reactions catalyzing the assimilation of inactive cofactors into their active forms are integral to their trafficking pathways. Similarly, elaboration of metals into clusters often occurs on chaperones that subsequently transfer the cofactor to target proteins. The interprotein transfer of metals can occur via ligand exchange reactions that are driven by differences in metal coordination geometry and affinity between the donor and acceptor proteins (2, 3). Seclusion of cofactors in chaperones during assembly/processing into their active forms minimizes unwanted side reactions, whereas guided delivery averts dilution and promotes specificity of cofactor docking.In contrast to our understanding of cellular strategies used for trafficking metals (4 -6) and metal clusters (7), significantly less is known about strategies for shepherding organic and organometallic cofactors to target proteins. This picture has been changing, however, with the convergence of clinical genetics and biochemical approaches that are beginning to illuminate an elaborate pathway for assimilation and delivery of dietary vitamin B 12 or cobalt-containing cobalamin, a complex organometallic cofactor (8 -10). Much less is known about how the tetrapyrrolic cousins of B 12 , e.g. iron protoporphyrin (heme), nickel corphin (F430), and magnesium chlorin (chlorophyll), are guided to specific destinations.In this minireview, we describe a model for mammalian cobalamin trafficking, which includes strategies for conversion of inactive precursors to the active cofactor forms methylcobalamin (MeCbl) 3 and 5Ј-deoxyadenosylcobalamin (AdoCbl; coenzyme B 12 ) and discuss the human diseases that result from impairments along the trafficking highway. We posit that the navigation strategy for B 12 , in which a rare, reactive, and high value cofactor is sequestered and targ...

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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%

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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Nitrogenase assembly

Cited by 66 publications

References 59 publications

What is the true nitrogenase reaction? A guided approach

What is the true nitrogenase reaction? A guided approach

Navigating the B12 Road: Assimilation, Delivery, and Disorders of Cobalamin

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

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