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1.
Commun Chem ; 5(1): 169, 2022 Dec 07.
Article in English | MEDLINE | ID: mdl-36697690

ABSTRACT

Biosensor techniques have become increasingly important for fragment-based drug discovery during the last years. The AAA+ ATPase p97 is an essential protein with key roles in protein homeostasis and a possible target for cancer chemotherapy. Currently available p97 inhibitors address its ATPase activity and globally impair p97-mediated processes. In contrast, inhibition of cofactor binding to the N-domain by a protein-protein-interaction inhibitor would enable the selective targeting of specific p97 functions. Here, we describe a biolayer interferometry-based fragment screen targeting the N-domain of p97 and demonstrate that a region known as SHP-motif binding site can be targeted with small molecules. Guided by molecular dynamics simulations, the binding sites of selected screening hits were postulated and experimentally validated using protein- and ligand-based NMR techniques, as well as X-ray crystallography, ultimately resulting in the first structure of a small molecule in complex with the N-domain of p97. The identified fragments provide insights into how this region could be targeted and present first chemical starting points for the development of a protein-protein interaction inhibitor preventing the binding of selected cofactors to p97.

2.
Subcell Biochem ; 93: 221-272, 2019.
Article in English | MEDLINE | ID: mdl-31939153

ABSTRACT

p97 belongs to the functional diverse superfamily of AAA+ (ATPases Associated with diverse cellular Activities) ATPases and is characterized by an N-terminal regulatory domain and two stacked hexameric ATPase domains forming a central protein conducting channel. p97 is highly versatile and has key functions in maintaining protein homeostasis including protein quality control mechanisms like the ubiquitin proteasome system (UPS) and autophagy to disassemble polyubiquitylated proteins from chromatin, membranes, macromolecular protein complexes and aggregates which are either degraded by the proteasome or recycled. p97 can use energy derived from ATP hydrolysis to catalyze substrate unfolding and threading through its central channel. The function of p97 in a large variety of different cellular contexts is reflected by its simultaneous association with different cofactors, which are involved in substrate recognition and processing, thus leading to the formation of transient multi-protein complexes. Dysregulation in protein homeostasis and proteotoxic stress are often involved in the development of cancer and neurological diseases and targeting the UPS including p97 in cancer is a well-established pharmacological strategy. In this chapter we will describe structural and functional aspects of the p97 interactome in regulating diverse cellular processes and will discuss the role of p97 in targeted cancer therapy.


Subject(s)
Adenosine Triphosphatases/chemistry , Adenosine Triphosphatases/metabolism , Nuclear Proteins/chemistry , Nuclear Proteins/metabolism , Proteostasis , Humans , Neoplasms/drug therapy , Neoplasms/enzymology , Neoplasms/metabolism , Proteasome Endopeptidase Complex/metabolism , Ubiquitin/metabolism
3.
Front Mol Biosci ; 4: 21, 2017.
Article in English | MEDLINE | ID: mdl-28451587

ABSTRACT

The hexameric type II AAA ATPase (ATPase associated with various activities) p97 (also referred to as VCP, Cdc48, and Ter94) is critically involved in a variety of cellular activities including pathways such as DNA replication and repair which both involve chromatin remodeling, and is a key player in various protein quality control pathways mediated by the ubiquitin proteasome system as well as autophagy. Correspondingly, p97 has been linked to various pathophysiological states including cancer, neurodegeneration, and premature aging. p97 encompasses an N-terminal domain, two highly conserved ATPase domains and an unstructured C-terminal tail. This enzyme hydrolyzes ATP and utilizes the resulting energy to extract or disassemble protein targets modified with ubiquitin from stable protein assemblies, chromatin and membranes. p97 participates in highly diverse cellular processes and hence its activity is tightly controlled. This is achieved by multiple regulatory cofactors, which either associate with the N-terminal domain or interact with the extreme C-terminus via distinct binding elements and target p97 to specific cellular pathways, sometimes requiring the simultaneous association with more than one cofactor. Most cofactors are recruited to p97 through conserved binding motifs/domains and assist in substrate recognition or processing by providing additional molecular properties. A tight control of p97 cofactor specificity and diversity as well as the assembly of higher-order p97-cofactor complexes is accomplished by various regulatory mechanisms, which include bipartite binding, binding site competition, changes in oligomeric assemblies, and nucleotide-induced conformational changes. Furthermore, post-translational modifications (PTMs) like acetylation, palmitoylation, phosphorylation, SUMOylation, and ubiquitylation of p97 have been reported which further modulate its diverse molecular activities. In this review, we will describe the molecular basis of p97-cofactor specificity/diversity and will discuss how PTMs can modulate p97-cofactor interactions and affect the physiological and patho-physiological functions of p97.

4.
Structure ; 24(1): 127-139, 2016 Jan 05.
Article in English | MEDLINE | ID: mdl-26712278

ABSTRACT

p97 belongs to the superfamily of AAA+ ATPases and is characterized by a tandem AAA module, an N-terminal domain involved in substrate and cofactor interactions, and a functionally important unstructured C-terminal tail. The ATPase activity is controlled by an intradomain communication within the same protomer and an interdomain communication between neighboring protomers. Here, we present for the first time crystal structures in which the physiologically relevant p97 hexamer constitutes the content of the asymmetric unit, namely in the apo state without nucleotide in either the D1 or D2 module and in the pre-activated state with ATPγS bound to both modules. The structures provide new mechanistic insights into the interdomain communication mediated by conformational changes of the C terminus as well as an intersubunit signaling network, which couples the nucleotide state to the conformation of the central putative substrate binding pore.


Subject(s)
Adenosine Triphosphatases/chemistry , Adenosine Triphosphate/metabolism , Nuclear Proteins/chemistry , Signal Transduction , Adenosine Triphosphatases/metabolism , Amino Acid Sequence , Binding Sites , Humans , Hydrolysis , Molecular Sequence Data , Nuclear Proteins/metabolism , Protein Binding , Protein Subunits/chemistry , Protein Subunits/metabolism
5.
Structure ; 24(1): 140-147, 2016 Jan 05.
Article in English | MEDLINE | ID: mdl-26712280

ABSTRACT

The type II AAA ATPase p97 interacts with a large number of cofactors that regulate its function by recruiting it to different cellular pathways. Most of the cofactors interact with the N-terminal (N) domain of p97, either via ubiquitin-like domains or short linear binding motifs. While some linear binding motifs form α helices, another group features short stretches of unstructured hydrophobic sequences as found in the so-called SHP (BS1, binding segment 1) motif. Here we present the crystal structure of a SHP-binding motif in complex with p97, which reveals a so far uncharacterized binding site on the p97 N domain that is different from the conserved binding surface of all other known p97 cofactors. This finding explains how cofactors like UFD1/NPL4 and p47 can utilize a bipartite binding mechanism to interact simultaneously with the same p97 monomer via their ubiquitin-like domain and SHP motif.


Subject(s)
Adenosine Triphosphatases/chemistry , Nuclear Proteins/chemistry , Proteins/chemistry , Adaptor Proteins, Vesicular Transport , Adenosine Triphosphatases/metabolism , Amino Acid Motifs , Amino Acid Sequence , Binding Sites , Coenzymes/chemistry , Coenzymes/metabolism , Humans , Intracellular Signaling Peptides and Proteins , Molecular Sequence Data , Nuclear Proteins/metabolism , Protein Binding , Proteins/metabolism
6.
FEBS Lett ; 589(19 Pt A): 2578-89, 2015 Sep 14.
Article in English | MEDLINE | ID: mdl-26320413

ABSTRACT

p97 (also known as Cdc48, Ter94, and VCP) is an essential, abundant and highly conserved ATPase driving the turnover of ubiquitylated proteins in eukaryotes. Even though p97 is involved in highly diverse cellular pathways and processes, it exhibits hardly any substrate specificity on its own. Instead, it relies on a large number of regulatory cofactors controlling substrate specificity and turnover. The complexity as well as temporal and spatial regulation of the interactions between p97 and its cofactors is only beginning to be understood at the molecular level. Here, we give an overview on the structural framework of p97 interactions with its cofactors, the emerging principles underlying the assembly of complexes with different cofactors, and the pathogenic effects of disease-associated p97 mutations on cofactor binding.


Subject(s)
Adenosine Triphosphatases/chemistry , Cell Cycle Proteins/chemistry , Protein Structure, Tertiary , Adenosine Triphosphatases/genetics , Adenosine Triphosphatases/metabolism , Amino Acid Sequence , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Humans , Models, Molecular , Molecular Sequence Data , Mutation , Protein Binding , Sequence Homology, Amino Acid , Substrate Specificity , Valosin Containing Protein
7.
Biochemistry ; 52(7): 1134-6, 2013 Feb 19.
Article in English | MEDLINE | ID: mdl-23286307

ABSTRACT

MoaA, a radical S-adenosylmethionine enzyme, catalyzes the first step in molybdopterin biosynthesis. This reaction involves a complex rearrangement in which C8 of guanosine triphosphate is inserted between C2' and C3' of the ribose. This study identifies the site of initial hydrogen atom abstraction by the adenosyl radical and advances a mechanistic proposal for this unprecedented reaction.


Subject(s)
Coenzymes/metabolism , Hydrolases/chemistry , Hydrolases/metabolism , Metalloproteins/metabolism , Pteridines/metabolism , Carbon , Catalysis , Coenzymes/chemistry , Guanosine Triphosphate/chemistry , Guanosine Triphosphate/metabolism , Magnetic Resonance Spectroscopy , Metalloproteins/chemistry , Models, Chemical , Molybdenum Cofactors , Pteridines/chemistry , Ribose/chemistry , Spectrometry, Mass, Electrospray Ionization
8.
Methods Mol Biol ; 832: 547-76, 2012.
Article in English | MEDLINE | ID: mdl-22350912

ABSTRACT

The conjugation of ubiquitin and related modifiers to selected proteins represents a general mechanism to alter the function of these protein targets, thereby increasing the complexity of the cellular proteome. Ubiquitylation is catalyzed by a hierarchical enzyme cascade consisting of ubiquitin activating, ubiquitin conjugating, and ubiquitin ligating enzymes, and their combined action results in a diverse topology of ubiquitin-linkages on the modified proteins. Counteracting this machinery are various deubiquitylating enzymes while ubiquitin recognition in all its facets is accomplished by numerous ubiquitin-binding elements. In the following chapter, we attempt to provide an overview on enzymes involved in ubiquitylation as well as the removal of ubiquitin and proteins involved in the recognition and binding of ubiquitin from a structural biologist's perspective.


Subject(s)
Sumoylation/physiology , Ubiquitin-Activating Enzymes/metabolism , Ubiquitin-Conjugating Enzymes/metabolism , Ubiquitin-Protein Ligases/metabolism , Ubiquitination/physiology , Binding Sites , Protein Binding , Protein Processing, Post-Translational , Protein Structure, Secondary , Saccharomyces cerevisiae/metabolism , Small Ubiquitin-Related Modifier Proteins/metabolism , Structure-Activity Relationship , Ubiquitin/metabolism , Ubiquitin/ultrastructure , Ubiquitin-Activating Enzymes/genetics , Ubiquitin-Conjugating Enzymes/genetics , Ubiquitin-Protein Ligases/genetics , Ubiquitins
9.
FEBS J ; 279(5): 816-31, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22221834

ABSTRACT

Fe(II)/α-ketoglutarate-dependent oxygenases are versatile catalysts associated with a number of different biological functions in which they use the oxidizing power of activated dioxygen to convert a variety of substrates. A mononuclear nonheme iron center is used to couple the decarboxylation of the cosubstrate α-ketoglutarate with a two-electron oxidation of the substrate, which is a hydroxylation in most cases. Although Fe(II)/α-ketoglutarate-dependent oxygenases have diverse amino acid sequences and substrate specifity, it is assumed that they share a common mechanism. One representative of this enzyme family is the Fe(II)/α-ketoglutarate-dependent taurine dioxygenase that catalyzes the hydroxylation of taurine yielding sulfite and aminoacetaldehyde. Its mechanism has been studied in detail becoming a model system for the whole enzyme family. However, its oligomeric state and architecture have been disputed. Here, we report the biochemical and kinetic characterization of the Fe(II)/α-ketoglutarate-dependent taurine dioxygenase from Pseudomonas putida KT2440 (TauD(Pp) ). We also present three crystal structures of the apo form of this enzyme. Comparisons with taurine dioxygenase from Escherichia coli (TauD(Ec) ) demonstrate that both enzymes are quite similar regarding their spectra, structure and kinetics, and only minor differences for the accumulation of intermediates during the reaction have been observed. Structural data and analytical gel filtration, as well as sedimentation velocity analytical ultracentrifugation, show that both TauD(Pp) and TauD(Ec) are tetramers in solution and in the crystals, which is in contrast to the earlier description of taurine dioxygenase from E. coli as a dimer. Database The atomic coordinates and structure factors have been deposited with the Brookhaven Protein Data Bank (entry 3PVJ, 3V15, 3V17) Structured digital abstract • tauDpp and tauDpp bind by molecular sieving (View interaction) • tauDpp and tauDpp bind by x-ray crystallography (View interaction) • tauDEc and tauDEc bind by molecular sieving (View interaction).


Subject(s)
Escherichia coli/enzymology , Ferrous Compounds/metabolism , Ketoglutaric Acids/metabolism , Mixed Function Oxygenases/chemistry , Mixed Function Oxygenases/metabolism , Pseudomonas putida/enzymology , Binding Sites , Catalysis , Catalytic Domain , Crystallization , Crystallography, X-Ray , Kinetics , Magnetic Resonance Spectroscopy , Models, Molecular , Oxidation-Reduction , Protein Conformation , Protein Multimerization , Substrate Specificity , Taurine/metabolism , Ultracentrifugation
10.
J Biol Chem ; 286(44): 38679-38690, 2011 Nov 04.
Article in English | MEDLINE | ID: mdl-21914798

ABSTRACT

The AAA (ATPase associated with various cellular activities) ATPase p97, also referred to as valosin-containing protein (VCP), mediates essential cellular processes, including ubiquitin-dependent protein degradation, and has been linked to several human proteinopathies. p97 interacts with multiple cofactors via its N-terminal (p97N) domain, a subset of which contain the VCP-interacting motif (VIM). We have determined the crystal structure of the p97N domain in complex with the VIM of the ubiquitin E3 ligase gp78 at 1.8 Å resolution. The α-helical VIM peptide binds into a groove located in between the two subdomains of the p97N domain. Interaction studies of several VIM proteins reveal that these cofactors display dramatically different affinities, ranging from high affinity interactions characterized by dissociation constants of ∼20 nm for gp78 and ANKZF1 to only weak binding in our assays. The contribution of individual p97 residues to VIM binding was analyzed, revealing that identical substitutions do not affect all cofactors in the same way. Taken together, the biochemical and structural studies define the framework for recognition of VIM-containing cofactors by p97. Of particular interest to the regulation of p97 by its cofactors, our structure reveals that the bound α-helical peptides of VIM-containing cofactors overlap with the binding site for cofactors containing the ubiquitin regulatory X (UBX) domain present in the UBX protein family or the ubiquitin-like domain of NPL4 as further corroborated by biochemical data. These results extend the concept that competitive binding is a crucial determinant in p97-cofactor interactions.


Subject(s)
Adenosine Triphosphatases/chemistry , Cell Cycle Proteins/chemistry , Amino Acid Motifs , Binding, Competitive , Cloning, Molecular , Crystallography, X-Ray/methods , Endoplasmic Reticulum/metabolism , Humans , Kinetics , Models, Molecular , Mutagenesis, Site-Directed , Protein Binding , Protein Structure, Secondary , Protein Structure, Tertiary , Ubiquitin/chemistry , Ubiquitin-Protein Ligases/chemistry , Valosin Containing Protein
11.
Structure ; 19(6): 833-43, 2011 Jun 08.
Article in English | MEDLINE | ID: mdl-21645854

ABSTRACT

The hexameric AAA ATPase p97 is involved in several human proteinopathies and mediates ubiquitin-dependent protein degradation among other essential cellular processes. Via its N-terminal domain (N domain), p97 interacts with multiple regulatory cofactors including the UFD1/NPL4 heterodimer and members of the "ubiquitin regulatory X" (UBX) domain protein family; however, the principles governing cofactor selectivity remain to be deciphered. Our crystal structure of the FAS-associated factor 1 (FAF1)UBX domain in complex with the p97N domain reveals that the signature Phe-Pro-Arg motif known to be crucial for interactions of UBX domains with p97 adopts a cis-proline configuration, in contrast to a cis-trans mixture we derive for the isolated FAF1UBX domain. Biochemical studies confirm that binding critically depends on a proline at this position. Furthermore, we observe that the UBX proteins FAF1 and UBXD7 only bind to p97-UFD1/NPL4, but not free p97, thus demonstrating for the first time a hierarchy in p97-cofactor interactions.


Subject(s)
Adaptor Proteins, Signal Transducing/chemistry , Adenosine Triphosphatases/chemistry , Coenzymes/chemistry , Nuclear Proteins/chemistry , Adaptor Proteins, Vesicular Transport , Amino Acid Motifs , Amino Acid Sequence , Apoptosis Regulatory Proteins , Calorimetry , Carrier Proteins/chemistry , Chromatography, Gel , Conserved Sequence , Crystallography, X-Ray , Humans , Intracellular Signaling Peptides and Proteins , Molecular Sequence Data , Protein Binding , Protein Interaction Domains and Motifs , Protein Structure, Quaternary , Protein Structure, Tertiary , Proteins/chemistry , Surface Properties , Titrimetry , Ubiquitin/chemistry , Ubiquitinated Proteins/chemistry
12.
J Biol Chem ; 285(26): 20390-8, 2010 Jun 25.
Article in English | MEDLINE | ID: mdl-20427284

ABSTRACT

Proteins containing ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains interact with various binding partners and function as hubs during ubiquitin-mediated protein degradation. A common interaction of the budding yeast UBL-UBA proteins Rad23 and Dsk2 with the E4 ubiquitin ligase Ufd2 has been described in endoplasmic reticulum-associated degradation among other pathways. The UBL domains of Rad23 and Dsk2 play a prominent role in this process by interacting with Ufd2 and different subunits of the 26 S proteasome. Here, we report crystal structures of Ufd2 in complex with the UBL domains of Rad23 and Dsk2. The N-terminal UBL-interacting region of Ufd2 exhibits a unique sequence pattern, which is distinct from any known ubiquitin- or UBL-binding domain identified so far. Residue-specific differences exist in the interactions of these UBL domains with Ufd2, which are coupled to subtle differences in their binding affinities. The molecular details of their differential interactions point to a role for adaptive evolution in shaping these interfaces.


Subject(s)
Cell Cycle Proteins/chemistry , DNA-Binding Proteins/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Ubiquitin-Conjugating Enzymes/chemistry , Ubiquitins/chemistry , Amino Acid Sequence , Binding Sites/genetics , Binding, Competitive , Calorimetry/methods , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Crystallography, X-Ray , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Fungal Proteins/chemistry , Fungal Proteins/genetics , Fungal Proteins/metabolism , Immunoblotting , Models, Molecular , Molecular Sequence Data , Mutation , Protein Binding , Protein Structure, Secondary , Protein Structure, Tertiary , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Sequence Homology, Amino Acid , Surface Plasmon Resonance , Thermodynamics , Titrimetry/methods , Ubiquitin/metabolism , Ubiquitin-Conjugating Enzymes/genetics , Ubiquitin-Conjugating Enzymes/metabolism , Ubiquitins/genetics , Ubiquitins/metabolism
13.
Protein Sci ; 18(12): 2480-91, 2009 Dec.
Article in English | MEDLINE | ID: mdl-19798741

ABSTRACT

Rhodaneses/sulfurtransferases are ubiquitous enzymes that catalyze the transfer of sulfane sulfur from a donor molecule to a thiophilic acceptor via an active site cysteine that is modified to a persulfide during the reaction. Here, we present the first crystal structure of a triple-domain rhodanese-like protein, namely YnjE from Escherichia coli, in two states where its active site cysteine is either unmodified or present as a persulfide. Compared to well-characterized tandem domain rhodaneses, which are composed of one inactive and one active domain, YnjE contains an extra N-terminal inactive rhodanese-like domain. Phylogenetic analysis reveals that YnjE triple-domain homologs can be found in a variety of other gamma-proteobacteria, in addition, some single-, tandem-, four and even six-domain variants exist. All YnjE rhodaneses are characterized by a highly conserved active site loop (CGTGWR) and evolved independently from other rhodaneses, thus forming their own subfamily. On the basis of structural comparisons with other rhodaneses and kinetic studies, YnjE, which is more similar to thiosulfate:cyanide sulfurtransferases than to 3-mercaptopyruvate:cyanide sulfurtransferases, has a different substrate specificity that depends not only on the composition of the active site loop with the catalytic cysteine at the first position but also on the surrounding residues. In vitro YnjE can be efficiently persulfurated by the cysteine desulfurase IscS. The catalytic site is located within an elongated cleft, formed by the central and C-terminal domain and is lined by bulky hydrophobic residues with the catalytic active cysteine largely shielded from the solvent.


Subject(s)
Escherichia coli Proteins/chemistry , Escherichia coli/enzymology , Sulfurtransferases/chemistry , Thiosulfate Sulfurtransferase/chemistry , Amino Acid Sequence , Catalytic Domain , Crystallography, X-Ray , Escherichia coli Proteins/genetics , Models, Molecular , Molecular Sequence Data , Mutagenesis, Site-Directed , Phylogeny , Protein Structure, Tertiary , Sequence Alignment , Sulfurtransferases/genetics
14.
J Am Chem Soc ; 131(26): 9184-5, 2009 Jul 08.
Article in English | MEDLINE | ID: mdl-19566093

ABSTRACT

The S-adenosylmethionine-dependent enzyme MoaA, in concert with MoaC, catalyzes the first step of molybdenum cofactor biosynthesis, the conversion of guanosine 5'-triphosphate (5'-GTP) into precursor Z. A published X-ray crystal structure of MoaA with the substrate 5'-GTP revealed that the substrate might be bound to the unique iron of one of two 4Fe-4S clusters through either or both the amino and N1 nitrogen nuclei. Use of 35 GHz continuous-wave ENDOR spectroscopy of MoaA with unlabeled and (15)N-labeled substrate and a reduced [4Fe-4S](+) cluster now demonstrates that only one nitrogen nucleus is bound to the cluster. Experiments with the substrate analogue inosine 5'-triphosphate further demonstrate that it is the N1 nitrogen that binds. Two of the more distant nitrogen nuclei have also been detected by 35 GHz pulsed ENDOR spectroscopy, allowing a rough approximation of their distances from the cluster to be calculated. Combining this information with the crystal structure, we propose that the guanine base adopts the enol tautomer as N1 binds to Fe4 and the O6-H hydroxyl group forms a hydrogen bond with S4 of the 4Fe-4S cluster, and that this binding-induced tautomerization may have important mechanistic ramifications.


Subject(s)
Electron Spin Resonance Spectroscopy , Guanine/chemistry , Guanosine Triphosphate/metabolism , Hydrolases/chemistry , Hydrolases/metabolism , Staphylococcus aureus/enzymology , Binding Sites , Crystallography, X-Ray , Guanine/metabolism , Guanosine Triphosphate/chemistry , Hydrolases/genetics , Iron-Sulfur Proteins/chemistry , Iron-Sulfur Proteins/genetics , Iron-Sulfur Proteins/metabolism , Models, Molecular , Mutation , Protein Binding , Protein Conformation
15.
PLoS Biol ; 6(6): e149, 2008 Jun 24.
Article in English | MEDLINE | ID: mdl-18578568

ABSTRACT

DNA damage recognition by the nucleotide excision repair pathway requires an initial step identifying helical distortions in the DNA and a proofreading step verifying the presence of a lesion. This proofreading step is accomplished in eukaryotes by the TFIIH complex. The critical damage recognition component of TFIIH is the XPD protein, a DNA helicase that unwinds DNA and identifies the damage. Here, we describe the crystal structure of an archaeal XPD protein with high sequence identity to the human XPD protein that reveals how the structural helicase framework is combined with additional elements for strand separation and DNA scanning. Two RecA-like helicase domains are complemented by a 4Fe4S cluster domain, which has been implicated in damage recognition, and an alpha-helical domain. The first helicase domain together with the helical and 4Fe4S-cluster-containing domains form a central hole with a diameter sufficient in size to allow passage of a single stranded DNA. Based on our results, we suggest a model of how DNA is bound to the XPD protein, and can rationalize several of the mutations in the human XPD gene that lead to one of three severe diseases, xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy.


Subject(s)
Archaeal Proteins/chemistry , Iron-Sulfur Proteins/chemistry , Xeroderma Pigmentosum Group D Protein/chemistry , Amino Acid Sequence , Animals , Archaeal Proteins/genetics , Base Sequence , Crystallography, X-Ray , DNA Primers , DNA Repair , Humans , Iron-Sulfur Proteins/genetics , Models, Molecular , Molecular Sequence Data , Protein Conformation , Sequence Homology, Amino Acid , Static Electricity , Xeroderma Pigmentosum Group D Protein/genetics
16.
Biochemistry ; 47(24): 6479-89, 2008 Jun 17.
Article in English | MEDLINE | ID: mdl-18491921

ABSTRACT

Because of mechanistic parallels in the activation of ubiquitin and the biosynthesis of several sulfur-containing cofactors, we have characterized the human Urm1 and Saccharomyces cerevisiae Uba4 proteins, which are very similar in sequence to MOCS2A and MOCS3, respectively, two proteins essential for the biosynthesis of the molybdenum cofactor (Moco) in humans. Phylogenetic analyses of MOCS3 homologues showed that Uba4 is the MOCS3 homologue in yeast and thus the only remaining protein of the Moco biosynthetic pathway in this organism. Because of the high levels of sequence identity of human MOCS3 and yeast Uba4, we purified Uba4 and characterized the catalytic activity of the protein in detail. We demonstrate that the C-terminal domain of Uba4, like MOCS3, has rhodanese activity and is able to transfer the sulfur from thiosulfate to cyanide in vitro. In addition, we were able to copurify stable heterotetrameric complexes of Uba4 with both human Urm1 and MOCS2A. The N-terminal domain of Uba4 catalyzes the activation of either MOCS2A or Urm1 by formation of an acyl-adenylate bond. After adenylation, persulfurated Uba4 was able to form a thiocarboxylate group at the C-terminal glycine of either Urm1 or MOCS2A. The formation of a thioester intermediate between Uba4 and Urm1 or MOCS2A was not observed. The functional similarities between Uba4 and MOCS3 further demonstrate the evolutionary link between ATP-dependent protein conjugation and ATP-dependent cofactor sulfuration.


Subject(s)
Carrier Proteins/metabolism , Nucleotidyltransferases/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Structural Homology, Protein , Sulfur/metabolism , Sulfurtransferases/metabolism , Thiosulfate Sulfurtransferase/metabolism , Ubiquitin/chemistry , Ubiquitin/metabolism , Ubiquitins/chemistry , Ubiquitins/metabolism , Binding Sites/genetics , Carrier Proteins/chemistry , Carrier Proteins/genetics , Cell Line, Tumor , Coenzymes/biosynthesis , Coenzymes/chemistry , Coenzymes/genetics , Dimerization , Evolution, Molecular , Humans , Metalloproteins/biosynthesis , Metalloproteins/chemistry , Metalloproteins/genetics , Molybdenum Cofactors , Nucleotidyltransferases/chemistry , Pteridines/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/isolation & purification , Sulfur/chemistry , Sulfurtransferases/chemistry , Sulfurtransferases/genetics , Thiosulfate Sulfurtransferase/chemistry , Ubiquitins/genetics
17.
Proc Natl Acad Sci U S A ; 103(18): 6829-34, 2006 May 02.
Article in English | MEDLINE | ID: mdl-16632608

ABSTRACT

The first step in molybdenum cofactor biosynthesis, the conversion of 5'-GTP to precursor Z, an oxygen-sensitive tetrahydropyranopterin is catalyzed by the S-adenosylmethionine (SAM)-dependent enzyme MoaA and the accessory protein MoaC. This reaction involves the radical-initiated intramolecular rearrangement of the guanine C8 atom. MoaA harbors an N-terminal [4Fe-4S] cluster, which is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical (5'-dA*), and a C-terminal [4Fe-4S] cluster presumably involved in substrate binding and/or activation. Biochemical studies identified residues involved in 5'-GTP binding and the determinants of nucleotide specificity. The crystal structure of MoaA in complex with 5'-GTP confirms the biochemical data and provides valuable insights into the subsequent radical reaction. MoaA binds 5'-GTP with high affinity and interacts through its C-terminal [4Fe-4S] cluster with the guanine N1 and N2 atoms, in a yet uncharacterized binding mode. The tightly anchored triphosphate moiety prevents the escape of radical intermediates. This structure also visualizes the L-Met and 5'-dA cleavage products of SAM. Rotation of the 5'-dA ribose and/or conformational changes of the guanosine are proposed to bring the 5'-deoxyadenosyl radical into close proximity of either the ribose C2' and C3' or the guanine C8 carbon atoms leading to hydrogen abstraction.


Subject(s)
Guanosine Triphosphate/metabolism , Hydrolases/metabolism , S-Adenosylmethionine/metabolism , Staphylococcus aureus/enzymology , Binding Sites , Coenzymes/biosynthesis , Crystallography, X-Ray , Guanosine Triphosphate/analogs & derivatives , Hydrolases/chemistry , Hydrolases/genetics , Iron-Sulfur Proteins/chemistry , Iron-Sulfur Proteins/genetics , Iron-Sulfur Proteins/metabolism , Metalloproteins/biosynthesis , Models, Molecular , Molecular Structure , Molybdenum Cofactors , Protein Conformation , Pteridines , S-Adenosylmethionine/chemistry , S-Adenosylmethionine/genetics
18.
Proc Natl Acad Sci U S A ; 101(35): 12870-5, 2004 Aug 31.
Article in English | MEDLINE | ID: mdl-15317939

ABSTRACT

The MoaA and MoaC proteins catalyze the first step during molybdenum cofactor biosynthesis, the conversion of a guanosine derivative to precursor Z. MoaA belongs to the S-adenosylmethionine (SAM)-dependent radical enzyme superfamily, members of which catalyze the formation of protein and/or substrate radicals by reductive cleavage of SAM by a [4Fe-4S] cluster. A defined in vitro system is described, which generates precursor Z and led to the identification of 5'-GTP as the substrate. The structures of MoaA in the apo-state (2.8 angstroms) and in complex with SAM (2.2 angstroms) provide valuable insights into its mechanism and help to define the defects caused by mutations in the human ortholog of MoaA that lead to molybdenum cofactor deficiency, a usually fatal disease accompanied by severe neurological symptoms. The central core of each subunit of the MoaA dimer is an incomplete triosephosphate isomerase barrel formed by the N-terminal part of the protein, which contains the [4Fe-4S] cluster typical for SAM-dependent radical enzymes. SAM is the fourth ligand to the cluster and binds to its unique Fe as an N/O chelate. The lateral opening of the incomplete triosephosphate isomerase barrel is covered by the C-terminal part of the protein containing an additional [4Fe-4S] cluster, which is unique to MoaA proteins. Both FeS clusters are separated by approximately 17 angstroms, with a large active site pocket between. The noncysteinyl-ligated unique Fe site of the C-terminal [4Fe-4S] cluster is proposed to be involved in the binding and activation of 5'-GTP.


Subject(s)
Bacterial Proteins/chemistry , Coenzymes/deficiency , Metalloproteins/deficiency , Nuclear Proteins/genetics , S-Adenosylmethionine/metabolism , Binding Sites , Carbon-Carbon Lyases , Catalytic Domain , Coenzymes/biosynthesis , Dimerization , Humans , Metalloproteins/biosynthesis , Molybdenum Cofactors , Mutation , Nuclear Proteins/metabolism , Pteridines , Staphylococcus aureus/chemistry , Staphylococcus aureus/enzymology
19.
J Biol Chem ; 279(33): 34721-32, 2004 Aug 13.
Article in English | MEDLINE | ID: mdl-15180982

ABSTRACT

The human proteins MOCS1A and MOCS1B catalyze the conversion of a guanosine derivative to precursor Z during molybdenum cofactor biosynthesis. MOCS1A shares homology with S-adenosylmethionine (AdoMet)-dependent radical enzymes, which catalyze the formation of protein and/or substrate radicals by reductive cleavage of AdoMet through a [4Fe-4S] cluster. Sequence analysis of MOCS1A showed two highly conserved cysteine motifs, one near the N terminus and one near the C terminus. MOCS1A was heterologously expressed in Escherichia coli and purified under aerobic and anaerobic conditions. Individual mutations of the conserved cysteines to serine revealed that all are essential for synthesis of precursor Z in vivo. The type and properties of the iron-sulfur (FeS) clusters were investigated using a combination of UV-visible absorption, variable temperature magnetic circular dichroism, resonance Raman, Mössbauer, and EPR spectroscopies coupled with iron and acid-labile sulfide analyses. The results indicated that anaerobically purified MOCS1A is a monomeric protein containing two oxygen-sensitive FeS clusters, each coordinated by only three cysteine residues. A redox-active [4Fe-4S](2+,+) cluster is ligated by an N-terminal CX(3)CX(2)C motif as is the case with all other AdoMet-dependent radical enzymes investigated thus far. A C-terminal CX(2)CX(13)C motif that is unique to MOCS1A and its orthologs primarily ligates a [3Fe-4S](0) cluster. However, MOCS1A could be reconstituted in vitro under anaerobic conditions to yield a form containing two [4Fe-4S](2+) clusters. The N-terminal [4Fe-4S](2+) cluster was rapidly degraded by oxygen via a semistable [2Fe-2S](2+) cluster intermediate, and the C-terminal [4Fe-4S](2+) cluster was rapidly degraded by oxygen to yield a semistable [3Fe-4S](0) cluster intermediate.


Subject(s)
Coenzymes/metabolism , Iron-Sulfur Proteins/chemistry , Metalloproteins/metabolism , Nuclear Proteins/chemistry , Nuclear Proteins/physiology , Oxygen/metabolism , Pteridines/metabolism , Amino Acid Motifs , Amino Acid Sequence , Carbon-Carbon Lyases , Catalysis , Circular Dichroism , Conserved Sequence , Cysteine/chemistry , Electron Spin Resonance Spectroscopy , Escherichia coli/metabolism , Humans , Iron/chemistry , Iron-Sulfur Proteins/metabolism , Magnetics , Molecular Sequence Data , Molybdenum Cofactors , Mutation , Oxygen/chemistry , Protein Structure, Tertiary , Sequence Homology, Amino Acid , Serine/chemistry , Spectrophotometry , Spectroscopy, Mossbauer , Spectrum Analysis, Raman , Ultraviolet Rays
20.
Hum Mol Genet ; 13(12): 1249-55, 2004 Jun 15.
Article in English | MEDLINE | ID: mdl-15115759

ABSTRACT

Substitution therapies for orphan genetic diseases, including enzyme replacement methods, are frequently hampered by the limited availability of the required therapeutic substance. We describe the isolation of a pterin intermediate from bacteria that was successfully used for the therapy of a hitherto incurable and lethal disease. Molybdenum cofactor (Moco) deficiency is a pleiotropic genetic disorder characterized by the loss of the molybdenum-dependent enzymes sulphite oxidase, xanthine oxidoreductase and aldehyde oxidase due to mutations in Moco biosynthesis genes. An intermediate of this pathway-'precursor Z'-is more stable than the cofactor itself and has an identical structure in all phyla. Thus, it was overproduced in the bacterium Escherichia coli, purified and used to inject precursor Z-deficient knockout mice that display a phenotype which resembles that of the human deficiency state. Precursor Z-substituted mice reach adulthood and fertility. Biochemical analyses further suggest that the described treatment can lead to the alleviation of most symptoms associated with human Moco deficiency.


Subject(s)
Coenzymes/biosynthesis , Coenzymes/deficiency , Deficiency Diseases/drug therapy , Deficiency Diseases/metabolism , Escherichia coli Proteins/therapeutic use , Metalloproteins/biosynthesis , Metalloproteins/deficiency , Protein Precursors/therapeutic use , Animals , Coenzymes/genetics , Coenzymes/metabolism , Deficiency Diseases/pathology , Enzyme Activation , Escherichia coli Proteins/administration & dosage , Escherichia coli Proteins/genetics , Escherichia coli Proteins/isolation & purification , Metalloproteins/genetics , Metalloproteins/metabolism , Mice , Mice, Knockout , Models, Animal , Molybdenum Cofactors , Protein Precursors/administration & dosage , Protein Precursors/genetics , Protein Precursors/isolation & purification , Pteridines/metabolism
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