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1 College of Theology, Arts and Sciences, Concordia University, Portland, Oregon 97211, USA
2 Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
3 LS-CAT, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
4 Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA
(RECEIVED November 21, 2006; FINAL REVISION March 6, 2007; ACCEPTED March 7, 2007)
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Keywords: structural genomics; Nif3; dimetal; cocatalytic site; PII; CutA; YqfO
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Introduction |
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TOPAbstractIntroductionResults and DiscussionMaterials and MethodsAcknowledgmentsReferences |
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Nif3 was originally identified in yeast as NGG1p-interacting factor 3 through two-hybrid experiments, although the nature and significance of this interaction remains unclear (Martens et al. 1996). Later work has identified and characterized two mammalian members of this family, the human NIF3L1 and its murine homolog Nif3l1, finding that only the N- and C-terminal regions of these proteins are conserved across species (Tascou et al. 2000) and that binding to a putative leucine zipper domain in another protein, NIF3L1 BP1, requires only the C-terminal 100 residues of NIF3L1 (Tascou et al. 2003). Akiyama et al. (2003) have determined that murine Nif31l is involved in neuronal differentiation through interactions with Trip15/CSN2, a component of the COP9 signalosome. These studies indicate that Nif3 proteins in eukaryotes are involved in transcriptional regulation and suggest that they are transported into the nucleus through interactions with other proteins.
In prokaryotes, it is possible that Nif3 proteins are also involved in transcriptional regulation. While the only available structures of Nif3 proteins are those of prokaryotic members, at this time there are no published functional studies of prokaryotic Nif3 proteins. The precise function of this family of proteins remains elusive.
The structures of two prokaryotic members of this family, both conserved hypothetical proteins, have been previously determined by X-ray crystallography in structural genomics efforts. Each molecule of Escherichia coli YbgI (PDB IDs: 1NMP, 1NMO) contains two similar and interlinked 
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domains. Each domain is a three-layer sandwich with helices on the outside and a mixed -sheet in the middle (Ladner et al. 2003). The structure of the other member, an unnamed hypothetical protein from Streptococcus pneumoniae (PDB ID: 2FYW) (B. Nocek, C. Hatzos, J. Abdullah, and A. Joachimiak, unpubl.), is very similar to YbgI; an overlay of 210 C atoms gives an RMSD of <1.5 Å. Their secondary structural topologies are identical except for the addition of a one-turn helix (residues 168–171), which occurs in a loop between -strands 7 and 8 in 2FYW. YbgI was reported to have a dimetal-binding site containing magnesium or iron (depending upon growth and crystallization conditions), while no metals are included in the 2FYW structure. Both reported biological units are toroidal hexamers, described as trimers of dimers. The tori have central openings of 
30 Å, a finding that has led to a comparison with proteins involved in DNA metabolism, where similarly large central openings have been observed as a path for DNA or RNA (Hingorani and O'Donnell 1998; Ladner et al. 2003).
The conserved hypothetical protein encoded by Bacillus cereus ATCC 14579 locus BC_4286 is closely related to Nif3-family proteins named YqfO in other Bacillus species including Bacillus subtilis (locus tag BSU25170, 61% identical, 77% similar), Bacillus licheniformis (locus BLi02696, 62% identical, 77% similar), and even more closely to YqfO of Bacillus thuringiensis (Accession No. AAR97540 [GenBank] , 96% identical, 98% similar), which is another member of the B. cereus group. Searches of Bacillus protein databases reveal conservation of this protein and its distinctive sequence throughout the genus. Therefore, we propose the naming of this previously unnamed B. cereus protein as YqfO. This work reports the structural solution of the conserved hypothetical Nif3-related protein YqfO from B. cereus ATCC 14,579.
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120 x 95 x 95 Å. The shape is composed of a central torus, as described in the structure of YbgI (Ladner et al. 2003), but in which the opening is loosely capped on both sides by an additional domain (Fig. 1). The long, slender connection between domain 2 and domains 1 and 3 leaves large gaps between the cap and the torus. This overall architecture leads to a large, accessible cavity in the center of the hexamer, with maximum internal dimensions of 65 x 35 x 35 Å.
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110-residue insert between the two domains of the others (Fig. 2). BLAST searches (Altschul et al. 1997) find that this insert shares sequence homology with a similar insert in some other hypothetical bacterial Nif3 proteins and limited similarity to the CutA family of bacterial divalent ion tolerance proteins (Supplemental Fig. 1). This insert is found in a minority of bacterial Nif3 family members (>25%). Although there is no significant sequence similarity in this region between bacterial and vertebrate proteins, an insert of similar length (85 residues) is found between conserved regions in vertebrate Nif3-like proteins (Tascou et al. 2000). Interestingly, this insert is not found in other eukaryotic Nif3-like proteins.
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// sandwich topology, with a central, four- or five-stranded, mixed -sheet bounded by two helices on the top and two helices on the bottom. In both domains, one of the helices and one of the strands is "donated" by the other domain, leading to significant intertwining of the domains. Intervening in sequence, but separated in space, the second domain (D2) is connected to the other domains by an extended, antiparallel two-stranded -sheet (Figs. 1–3). In the monomer, D2 is composed of a four-stranded, antiparallel -sheet bounded on one face by two helices, similar to the ferredoxin fold (Fig. 4). The presence of D2 is the greatest difference between YqfO and the previously solved bacterial Nif3 protein structures.
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of 2FYW Lys64 is <0.7 Å from the N
2 of YqfO His68. Tyrosine is the preferred residue in eukaryotic Nif3-like proteins in this position. Interestingly, N2 of absolutely conserved His103 is 3.9 Å and 4.1 Å away from the metal ions in a position that would allow a substrate to approach them. Sequence alignments suggest that the conservation of this dimetal-binding site is central to the function of the bacterial members of the family. The only other residues that are as conserved as these metal-binding residues are a set of glycines found in turns and hydrophobic residues vital to the fold (Fig. 2). In E. coli YbgI, it was suggested that iron or magnesium might be bound in these locations (Ladner et al. 2003). In the preparation of selenomethionyl-YbgI, iron sulfate was added to the minimal growth medium and X-ray fluorescence indicated the presence of iron in the crystals; thus, these metal ions were modeled as iron. However, in the native YbgI protein crystals, there was no anomalous signal, and fluorescence scans did not indicate the presence of iron, zinc, copper, nickel, or cobalt; therefore, the metals were modeled as magnesium. In the reported structure of selenomethionyl 2FYW from S. pneumoniae, despite the conservation of the metal-binding residues (except for the substitution of His68 by lysine as described above) there are no metal ions present. Despite the absence of observed metal ions, the conserved (metal-binding) residues are not significantly shifted from their observed positions in the structures of the proteins with bound metals. In the present case, the metals bound to YqfO were modeled as zinc ions due to the presence of X-ray fluorescence indicative of zinc, the presence of density at their positions in an anomalous difference Fourier map, and the observed geometry of the metals and ligands. Buffers and crystallization solutions used to obtain crystals of YqfO did not contain divalent ions; thus, the protein appears to have carried endogenous metal ions through the purification and crystallization process.
Domains 1 and 3
As described above, the combination of YqfO domains 1 and 3 appears very similar to the previously determined structures of bacterial Nif3 proteins, sharing secondary structure topology, tertiary structure, and quaternary arrangement. All form hexameric rings, complete with central holes, of similar size and shape. As with YbgI (Ladner et al. 2003), searches for proteins with structures similar to domains 1 and 3 with DALI (Holm and Sander 1996) and FATCAT (Ye and Godzik 2003) revealed that the structure of these proteins is unlike anything else currently in the protein data bank. A general description of their structure can be found in Ladner et al. (2003).
Each of the monomers in the hexameric ring of YqfO contains a HEPES molecule bound in a similar position (Fig. 1). The protein–HEPES interactions include contact to a ring nitrogen and the terminal OH from the carboxyl group of Asp320 from a symmetry-related molecule and water-mediated contacts from the sulfate group to the backbone carbonyl oxygen of the same Asp320 and the backbone amide of Tyr85. The HEPES sulfate is near a histidine–lysine pair (His80–Lys83), which likely provides electrostatic attraction. This binding site is not sequestered from solvent nor particularly shape-complementary for HEPES, although it is near an interface between crystallographically related molecules. There are a number of residues nearby that might be involved in ligand binding, including His316, Asp320, Met 323, Asn298, Asn74, Lys77, His80, Lys83, and Tyr85. Of these residues, only His316 and Asp320 display noticeable conservation. Neither YbgI nor 2FYW contain ligand molecules in this position (Ladner et al. 2003). It is tempting to imagine that this HEPES molecule has settled in a substrate-binding site, as it is certainly large enough to accommodate a nucleotide or small peptide. However, at their closest approach, the distance between the nearest bound metal ion and the HEPES molecule hydroxyl group is 11.7 Å. Furthermore, the side chain of well-conserved His316 (from a symmetry-related molecule) intervenes (Fig. 3B). If the metal ions are catalytic, this HEPES-binding site is probably too distant to be a legitimate substrate-binding site unless the chemical mechanism uses the intervening histidine.
A more likely substrate-binding site is found on the opposite side of the dimetal-binding pocket (Fig. 3). This is the same area proposed for an active site in YbgI (Ladner et al. 2003), although of the postulated "conserved" active-site residues in YbgI, only the metal-binding or coordinating residues and His97 (YqfO: His103) are found to be conserved with YqfO. This absolutely conserved histidine is seemingly too far (4 Å) from the metals to be considered coordinated, and is open to a solvent-exposed cleft (Fig. 3), suggesting an essential role for this residue in a possible catalytic mechanism. The general architecture of this area fits the description of a cocatalytic site (Auld 2001) having two proximate metal ions, bridged by an acidic group, with metal-coordinated water molecules. Other proteins with proximate zinc ions include phosphoesterases, aminopeptidases, and –lactamases (Auld 2001); however, the function(s) of this putative catalytic site in YqfO is still unclear.
Domain 2
Three molecules exist in the asymmetric unit, and despite the ring structure of the central torus being composed of a dimer of trimers, in the asymmetric unit, the three chains are connected only by trimerization of D2, with no contact between the D1 and D3 sections (Fig. 1). There is limited interchain contact near the threefold axis between the residues from 233 to 238, at the C terminus of D2. However, the most significant interaction between the D2 domains is the addition of two antiparallel strands from one molecule to extend the already four-stranded mixed -sheet of a neighboring molecule (Fig. 4).
D2 is a member of COG3323 (Tatusov et al. 2000), which has been described only as uncharacterized protein conserved in bacteria (function unknown). This group is dominated by bacterial hypothetical proteins or bacterial proteins of unknown function, and also includes 10 eukaryotic members, eight of them from Pezizomycotina fungi, one each from Dictyostelium discoideum and Giardia lamblia.
D2 shares structure with several well-characterized proteins, including PII (Cheah et al. 1994), GlnK (Xu et al. 1998; Sakai et al. 2005), and CutA (Savchenko et al. 2004), which also form trimers. The trimerization creates clefts in the interfaces of adjacent monomers, nestled in the curves of the trimerization-extended -sheets. Molecules of HEPES are observed in two of these clefts in the YqfO structure (Fig. 4). This ligand-binding cleft appears to be a conserved feature of this fold, although ligand specificity does not appear to be highly conserved. In all cases where a structure is available, this cleft created by trimerization has been conserved and, in most cases, used for binding of a ligand. In crystal structures of Thermatoga maritima PII (PDB ID: 1O51) (Schwarzenbacher et al. 2004), E. coli GlnK (PDBID: 2GNK
[PDB]
) (Xu et al. 1998), and TT1020 (a GlnK homolog from Thermus thermophilus PDBID: 1V3S, 1V9O) (Sakai et al. 2005), ATP, or ADP were found in this cleft. In E. coli, CutA1 is implicated in divalent cation homeostasis (Fong et al. 1995), and its crystal structure (PDBID: 1NAQ) contains in these clefts a mercury ion in one monomer and mercuribenzoic acid (used as a heavy-atom derivative for phasing) in the other two monomers. In PII from cyanobacterium Synechocystis sp. PCC 6803 (PDBID: 1UL3), a glycerol molecule (25% glycerol was used as a cryoprotectant) was found in this cleft (Xu et al. 2003); a similar fold in the C-terminal domain of an ATP phosphoribosyltransferase (ATP-prtase) from Mycobacterium tuberculosis (PDBID: 1NH8) binds free histidine in this cleft (Cho et al. 2003). Despite similar structures, sequence alignments show very little, if any, relevant conservation between D2 and proteins of similar structure, even when sequence alignments are based upon structural overlays (Supplemental Fig. 1). Considering the range of ligands that have already been found to bind in this cleft and the lack of significant conservation in binding residues between YqfO and others, it is difficult to predict the natural ligand of D2, although nucleotides are a tempting guess.
In the structure of YqfO, the binding of HEPES in D2 positions the negatively charged sulfate group in the deepest part of the cleft contacting basic Lys139, with the ring nitrogen atoms being contacted by the acidic side chain of Glu201. It was not immediately apparent how to model nucleotide binding by YqfO, as there is insignificant conservation of binding residues in this cleft. Attempts to model a nucleotide in the cleft phosphates—first, as predicted from the HEPES-binding mode, led to inescapable steric clashes with protein atoms. However, in the structures of PII containing nucleotides in this cleft, the nucleotides are found in the reverse orientation, with the base in the deepest part of the cleft and the phosphates poking out toward the solvent. In the YqfO structure, there are several aromatic rings in the immediate vicinity (Phe143, Tyr167, Phe180), but none are found to be stacking with the ring of the buffer molecule. Considering the binding flexibility of the cleft displayed in proteins with this fold, nucleotides should not be ruled out as possible natural ligands.
Other proteins with structures similar to D2 are regulatory in nature. PII is a well-known regulator of glutamine synthetase and is itself subject to regulation by several mechanisms, including uridylation and phosphorylation (for review, see Ninfa and Jiang 2005). PII binds ATP and -ketoglutarate (-KG) at separate sites, three each per trimer, with negative cooperativity for -KG binding. In the crystal structure, while ATP was found in the cleft, genetic and structural evidence suggests that -KG-binding in PII involves the adjacent T-loop (Jiang et al. 1997; Xu et al. 1998), which appears to be present but not well-conserved in YqfO (Fig. 1; Supplemental material). While this structural domain most commonly exists alone, the M. tuberculosis ATP-prtase has a C-terminal regulatory domain with a structure similar to D2 and N-terminal catalytic domains. Histidine binding in the cleft of this regulatory domain causes trimerization of active dimers into an inactive hexamer, thus inhibiting the first step of histidine biosynthesis (Cho et al. 2003). It appears that none of these domains have catalytic activity, but are instead involved in regulating activity of other domains or protein–protein interactions. Therefore, it is likely that D2 also serves as a signal-sensing regulatory domain, modulating activity of domains 1 and 3 or controlling binding to other proteins.
In the structure of YqfO, a HEPES molecule is bound in the conserved binding cleft in D2 and the domain is trimerized. It is possible that HEPES is serving as a substitute for the natural ligand and has therefore induced trimerization, as is seen in the ATP-prtase (Cho et al. 2003). However, similar proteins such as CutA and PII are trimeric even in the absence of ligand (Arnesano et al. 2003; Ninfa and Jiang 2005). It is more likely that the trimer is the natural state of D2, given the significant interactions between monomers within the D2 trimer. Trimerization of the D2 domains buries over 7000 Å2 of accessible surface area. Binding or release of natural ligand in the D2-conserved cleft might induce a structural change to affect activity in the other domains or effect protein–protein interactions. Histidine binding by the similar domain in the mtATP-prtase, in addition to inducing trimerization, causes a large shift in the position of the regulatory domain with respect to the catalytic domains (Cho et al. 2003). A similar conformational change, caused by binding of natural corepressor, may occur in YqfO bringing the domain 2 into a "closed position" with respect to the alleged catalytic domains, perhaps sealing the openings into the center cavity of the hexamer and sequestering the active sites. Determining the natural ligand(s) of this domain in YqfO will help to illuminate the function(s) of the overall protein.
Structural studies of evolutionarily conserved, uncharacterized proteins can provide clues to their biological function that are otherwise difficult to obtain. In the case of the Nif3 family of proteins, the structure of YqfO presented here suggests that members of this family are enzymes whose activity may be regulated by allosteric ligands. How these functional clues relate to the apparent regulatory roles of the eukaryotic Nif3 proteins remains unknown.
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Crystallization and data collection
Protein crystals were grown by the sitting-drop vapor diffusion method in 96-well Corning crystallization plates using a Hydra II+ robot (Matrix Technologies). Crystals grew from >15 screening conditions (The Pegs, Nextal Biotechnologies); however, most diffracted poorly (resolution >5 Å). The best-diffracting crystals grew at 22°C from a 1:1 mixture of protein solution (described above) and crystallization solution consisting of 0.1 M HEPES (pH 7.5) and 25% w/v PEG 1000. Hexagonal rods of 0.1 x 0.05 x 0.05 mm grew from 2-µL drops. Crystals grew in a trigonal space group that was later determined to be P 32 2 1 with unit cell dimensions of a = b = 95.0 Å, c = 260.7 Å. The solvent content of the crystal was 51.5% with a Matthews coefficient of 2.6, corresponding to three polypeptide chains of 397 residues each in the asymmetric unit.
Data collection and structure solution
Data were collected from derivative crystals and a single native crystal at 100 K at the Advanced Photon Source beamline 5ID-B using a wavelength of 0.94642 Å. Statistics from data collection can be found in Table 1. Data were scaled and processed to 2.2 Å using XDS (Kabsch 1993). Crystals were soaked in solution containing 2.5 mM lead acetate for 30 min to obtain a functional heavy-atom derivative. Heavy-atom sites were located by HySS (Grosse-Kunstleve and Adams 2003), and phases were determined by single isomorphous replacement with anomalous scattering (SIRAS) with the signal from seven lead atoms using SHARP (la Fortelle and Bricogne 1997). A total of 301 of 1191 residues in the asymmetric unit were built by ARP/warp (Perrakis et al. 2001). The initial trace contained pieces of each monomer, which were combined by noncrystallographic threefold symmetry to obtain a more complete monomer model, which was then distributed through the asymmetric unit. Remaining sections of the model were built manually using Turbo-Frodo (Jones 1985).
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The stereochemical quality of the model was analyzed with PROCHECK (Laskowski et al. 1993). A total of 92.4% of the nonglycine residues fall in the most favored regions of the Ramachandran plot, with 7.3% in the additionally allowed and 0.3% in the generously allowed regions. None are found in the disallowed regions. Refinement statistics are shown in Table 1.
Accession code
Atomic coordinates and structure factors have been deposited in the Protein Data Bank and assigned the accession code 2GX8.
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Footnotes |
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Supplemental material: see www.proteinscience.org
Reprint requests to: Wayne F. Anderson, Department of Molecular Pharmacology and Biological Chemistry, Ward 8-264, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave., Chicago, IL 60611, USA; e-mail: wf-anderson{at}northwestern.edu; fax: (312) 503-5349.
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.062674007.
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References |
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