Insights into Nucleotide Signal Transduction in Nitrogenase:  Structure of an Iron Protein with MgADP Bound<sup>,</sup>

Jang, Se Bok; Seefeldt, Lance C.; Peters, John W.

doi:10.1021/bi001705g

Cited by 105 publications

(101 citation statements)

References 29 publications

(34 reference statements)

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“…Thus, these residues are unlikely to interact with MinC directly but may function as a link to surface residues. This would be similar to what is postulated for the switch I region of NifH (18). On the other hand, residue I125 in the switch II region is on the surface in both the monomer and dimer models and therefore might interact directly with MinC.…”

Section: Discussionsupporting

confidence: 79%

The Switch I and II Regions of MinD Are Required for Binding and Activating MinC

Zhou

Lutkenhaus

2004

J Bacteriol

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MinD and MinC cooperate to form an efficient inhibitor of Z-ring formation that is spatially regulated by MinE. MinD activates MinC by recruiting it to the membrane and targeting it to a septal component. To better understand this activation, we have isolated loss-of-function mutations in minD and carried out site-directed mutagenesis. Many of these mutations block MinC-MinD interaction; however, they also prevent MinD self-interaction and membrane binding, suggesting that they affect nucleotide interaction or protein folding. Two mutations in the switch I region (MinD box) and one mutation in the switch II region had little affect on most MinD functions, such as MinD self-interaction, membrane binding, and MinE stimulation; however, they did eliminate MinD-MinC interaction. Two additional mutations in the switch II region did not affect MinC binding. Further study revealed that one of these allowed the MinCD complex to target to the septum but was still deficient in blocking division. These results indicate that the switch I and II regions of MinD are required for interaction with MinC but not MinE and that the switch II region has a role in activating MinC.

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Section: Discussionsupporting

confidence: 79%

The Switch I and II Regions of MinD Are Required for Binding and Activating MinC

Zhou

Lutkenhaus

2004

J Bacteriol

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“…In MinD and NIP, these residues extend the ␤8 and ␣6 equivalents of MobB and form a helixloop combination that creates the nucleotide-binding pocket. In MinD, the helix is ␣9, and the extended helix is ␣10 (42,43). In particular two residues (with MinD numbering) Pro 198 and Asp 200 , which are positioned on these extensions, are conserved in MinD and NIP and provide hydrogen bonding interactions between the main chain and the nucleotide.…”

Section: Resultsmentioning

confidence: 99%

Insight into the Role of Escherichia coli MobB in Molybdenum Cofactor Biosynthesis Based on the High Resolution Crystal Structure

McLuskey

Harrison

Schüttelkopf

et al. 2003

Journal of Biological Chemistry

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Two proteins, which are co-transcribed in Escherichia coli (MobA and MobB), are involved in the attachment of a nucleotide moiety to the molybdenum cofactor to form active molybdopterin guanine dinucleotide. Although not essential for this process, the dimeric MobB increases the activation of molybdoenzymes, incorporating this cofactor by a mechanism that is not understood. The structure of MobB has been elucidated in two crystal forms, one of which has provided a model at 1.9-Å resolution with R work and R free values of 21.5 and 28.7%, respectively. The MobB subunit displays an ␣/␤-fold arranged into a major and minor domain, the latter of which is inserted between the major and minor domains of the partner subunit, creating an elongated dimer constructed around a 16-stranded ␤-sheet. Structural homologues have been identified, and they include a number of nucleotide-binding proteins. Comparisons indicate that although the phosphate-binding regions are highly conserved, MobB lacks the elements of structure required to interact with and efficiently bind a nucleotide base. In the present structure, a sulfate is bound to the Walker A phosphate-binding motif of MobB. The possibility that MobB forms a complex with the nucleotidebinding MobA, the protein with which it is co-transcribed, is explored, and modeling suggests that such a MobA:MobB complex is feasible. This hypothesis is supported by recent biochemical evidence indicating that MobB interacts with several proteins involved in various stages of molybdenum cofactor biosynthesis including MobA. We propose therefore that MobB is an adapter protein that acts in concert with MobA to achieve the efficient biosynthesis and utilization of molybdopterin guanine dinucleotide.Molybdenum is an essential trace element associated with a diverse range of redox-active enzymes (1). Such molybdoenzymes catalyze basic metabolic reactions in the carbon, nitrogen, and sulfur cycles exploiting the redox chemistry of this second row transition metal. With the exception of the nitrogenases that contain an iron-molybdenum-sulfur cluster, molybdenum is integrated into the enzymes as the molybdenum cofactor (Moco), 1 which contains mononuclear molybdenum coordinated to an organic cofactor termed molybdopterin (MPT).

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“…Likewise, the DTAPTGH signature sequence of ArsA (6,16,17) has an exact counterpart in NifH (Fig. 1A) and is believed to correspond to the Switch II region of G-proteins (14). The terms Switch I and Switch II are commonly used in reference to these regions throughout this report.…”

mentioning

confidence: 99%

“…Like ArsA, NifH has two NBSs facing each other and its iron-sulfur center is almost coincident with the As/Sb(III) cluster of ArsA. Because NifH has long been recognized as a relative of G-proteins (12)(13)(14), it has become customary to identify specific regions of ArsA with definitions borrowed from Gprotein terminology. For example, in G-proteins, as well as in ArsA, Mg 2ϩ is coordinated (directly or via a water molecule) by an aspartic acid located in a strand-loop-helix structure that is referred to as the Switch I region (15).…”

mentioning

confidence: 99%

Conformational Changes in Four Regions of the Escherichia coli ArsA ATPase Link ATP Hydrolysis to Ion Translocation

Zhou

Radaev

Rosen

et al. 2001

Journal of Biological Chemistry

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Structures of ArsA with ATP, AMP-PNP, or ADP⅐AlF 3 bound at the A2 nucleotide binding site were determined. Binding of different nucleotides modifies the coordination sphere of Mg 2؉ . In particular, the changes elicited by ADP⅐AlF 3 provide insights into the mechanism of ATP hydrolysis. In-line attack by water onto the ␥-phosphate of ATP would be followed first by formation of a trigonal intermediate and then by breaking of the scissile bond between the ␤-and ␥-phosphates. Motions of amino acid side chains at the A2 nucleotide binding site during ATP binding and hydrolysis propagate at a distance, producing conformational changes in four different regions of the protein corresponding to helices H4 -H5, helices H9 -H10, helices H13-H15, and to the S1-H2-S2 region. These elements are extensions of, respectively, the Switch I and Switch II regions, the A-loop (a small loop near the nucleotide adenine moiety), and the P-loop. Based on the observed conformational changes, it is proposed that ArsA functions as a reciprocating engine that hydrolyzes 2 mol of ATP per each cycle of ion translocation across the membrane.In Escherichia coli resistance to the metalloids arsenic and antimony is conferred by the ars operon of plasmid R773 (1). The arsA and arsB genes of the operon encode, respectively, the catalytic subunit ArsA 1 (ATPase) and the membrane subunit ArsB of a pump that extrudes arsenite (As(III)) and antimonite (Sb(III)) ions from the cytosol (2).Arsenic efflux in bacteria is catalyzed by either ArsB alone, functioning as a secondary transporter, or by the ArsAB complex, functioning as a transport ATPase (3). E. coli can utilize either mode physiologically; however, the ATP-coupled pump is more efficient, capable of producing concentration gradients as high as 10 6 , equivalent to a concentration of 1 nM intracellular arsenite at 1 mM external arsenite.Although bound to ArsB in vivo, ArsA can be expressed and purified as a soluble protein (4) whose ATPase activity is stimulated by As(III) or Sb(III) (5). ArsA is composed of two homologous domains, designated A1 and A2, connected by a linker of 23 amino acids; each domain contains a consensus sequence for a nucleotide binding site (NBS) (see Fig. 1A).We have recently determined the crystal structure of the enzyme in complex with Mg⅐ADP (6). The A1 and A2 halves of the protein are related by a pseudo-2-fold axis of symmetry. The two NBSs are located at the interface between A1 and A2, in close proximity of each other. Both NBSs are formed by residues from both A1 and A2. However, one NBS is contributed mostly by A1 residues and is thereby named A1 NBS; the other NBS is contributed mostly by A2 residues and is named A2 NBS.Also at the interface between A1 and A2, but at the opposite end of the molecule with respect to the NBSs, is a site in which three distinct As(III) or Sb(III) ions bind (6). One of the major unanswered questions in the ArsA mechanism is how the two NBSs work together to provide the energy necessary for ion transfer. It is clear that both NBSs...

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Insights into Nucleotide Signal Transduction in Nitrogenase: Structure of an Iron Protein with MgADP Bound^,

Cited by 105 publications

References 29 publications

The Switch I and II Regions of MinD Are Required for Binding and Activating MinC

The Switch I and II Regions of MinD Are Required for Binding and Activating MinC

Insight into the Role of Escherichia coli MobB in Molybdenum Cofactor Biosynthesis Based on the High Resolution Crystal Structure

Conformational Changes in Four Regions of the Escherichia coli ArsA ATPase Link ATP Hydrolysis to Ion Translocation

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Insights into Nucleotide Signal Transduction in Nitrogenase: Structure of an Iron Protein with MgADP Bound,

Cited by 105 publications

References 29 publications

The Switch I and II Regions of MinD Are Required for Binding and Activating MinC

The Switch I and II Regions of MinD Are Required for Binding and Activating MinC

Insight into the Role of Escherichia coli MobB in Molybdenum Cofactor Biosynthesis Based on the High Resolution Crystal Structure

Conformational Changes in Four Regions of the Escherichia coli ArsA ATPase Link ATP Hydrolysis to Ion Translocation

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Insights into Nucleotide Signal Transduction in Nitrogenase: Structure of an Iron Protein with MgADP Bound^,