Six new candidate members of the α/β twisted open‐sheet family detected by sequence similarity to flavodoxin

Grandori, Rita; Carey, Jannette

doi:10.1002/pro.5560031204

Cited by 47 publications

(76 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Knowing that IL-I binding to IL-1R-bearing cells leads to the activation of a number of kinases, adenyl cyclase, ras itself, sphingomy-elinase, and a variety of other signaling mediators, it seems premature to place the IL-1R into any subcategory of the GTPase superfamily, nor would it be wise to exclude it from any. This paper represents one of only a few reports thus far that use hydropathic profiles to make arguments concerning structural and functional properties of proteins (Grandori & Carey, 1994;Lee et al, 1995). This technique may see wider use in the future as more sequence data become available without known 3D structures or obvious homologies.…”

Section: Discussionmentioning

confidence: 99%

Evidence from sequence information that the interleukin-1 receptor is a transmembrane GTPase

Hopp¹

1995

Protein Sci.

View full text Add to dashboard Cite

Evidence is presented that the cytoplasmic domain of the type I interleukin-1 receptor (IL-1R) may be a GTPase. This domain conserves segments of hydrophobic amino acids that suggest a structural relatedness to the ras protooncogene protein and other members of the GTPase superfamily, despite a lack of significant detectable sequence homology. When the hydrophobic segments of the IL-1R were aligned with similar segments of the GTPases, it became apparent that the IL-1Rs possess a number of conserved amino acids that represent plausible functional residues for base-specific binding of GTP, magnesium chelation, and phosphate ester hydrolysis. Furthermore, a segment of five contiguous residues was found that is identical between ras and the IL-lR, and which is positioned to form part of the guanine base binding pocket. If this model is correct, then the IL-1Rs possess a highly conserved effector protein binding region, but one that is entirely unrelated to the effector regions of other superfamily members. Therefore, if the IL-IR is indeed a GTPase, then its activation function may be directed to as-yet unrecognized effector target proteins, as part of a unique cellular signal transduction pathway.

show abstract

Section: Discussionmentioning

confidence: 99%

Evidence from sequence information that the interleukin-1 receptor is a transmembrane GTPase

Hopp¹

1995

Protein Sci.

View full text Add to dashboard Cite

show abstract

“…The founding member of this family is WrbA. FQR1/WrbA family members share sequence motifs that identify them as candidate flavodoxins, which are flavin-binding proteins that function as electron carriers in redox reactions (Grandori and Carey, 1994). The N-terminal region of FQR1 matches the 17-amino acid-long flavodoxin sig- (Fig.…”

Section: Fqr1 Has Sequence Similarity To a Family Of Qrsmentioning

confidence: 99%

“…Initial studies of the sequence and predicted structure of WrbA family members lead to the proposal that members of this family were novel flavodoxins (Grandori and Carey, 1994): FMN-binding proteins that function in electron transport (for review, see Simondsen and Tollin, 1980). Subsequent studies substantiate the prediction that FQR1/WrbA family members bind FMN (Brock et al, 1995;Grandori et al, 1998).…”

Section: Members Of the Fqr1/wrba Enzyme Family Are Distantly Relatedmentioning

confidence: 99%

FQR1, a Novel Primary Auxin-Response Gene, Encodes a Flavin Mononucleotide-Binding Quinone Reductase

et al. 2002

View full text Add to dashboard Cite

(I.M.S.) FQR1 is a novel primary auxin-response gene that codes for a flavin mononucleotide-binding flavodoxin-like quinone reductase. Accumulation of FQR1 mRNA begins within 10 min of indole-3-acetic acid application and reaches a maximum of approximately 10-fold induction 30 min after treatment. This increase in FQR1 mRNA abundance is not diminished by the protein synthesis inhibitor cycloheximide, demonstrating that FQR1 is a primary auxin-response gene. Sequence analysis reveals that FQR1 belongs to a family of flavin mononucleotide-binding quinone reductases. Partially purified His-tagged FQR1 isolated from Escherichia coli catalyzes the transfer of electrons from NADH and NADPH to several substrates and exhibits in vitro quinone reductase activity. Overexpression of FQR1 in plants leads to increased levels of FQR1 protein and quinone reductase activity, indicating that FQR1 functions as a quinone reductase in vivo. In mammalian systems, glutathione S-transferases and quinone reductases are classified as phase II detoxification enzymes. We hypothesize that the auxin-inducible glutathione S-transferases and quinone reductases found in plants also act as detoxification enzymes, possibly to protect against auxin-induced oxidative stress.Auxin plays a central role in the control of plant growth and development. It can stimulate or inhibit cell expansion, stimulate cell division, promote differentiation of vascular tissues, inhibit shoot branching, and promote lateral root formation. Although recent attempts to unravel these signal transduction pathways have been quite successful, it is clear that we have not identified all of the genes that are upregulated immediately after auxin application.At present, about a half a dozen families of primary auxin-response genes have been identified. These include the Aux/IAA, SAUR, and GH3 families, members of gene families encoding glutathione S-transferases (GST) and 1-aminocyclopropane-1-carboxylic acid synthases, and NAC1 (for review, see Abel and Theologis, 1996;Xie et al., 2000). Of these, the Aux/IAA family is the most thoroughly studied (Abel et al., 1995). Aux/IAA genes are transcriptional regulators, and gain-of-function mutations in some family members have dramatic effects on plant development (Nagpal et al., 2000;Rogg et al., 2001). Transcription of the Aux/IAA genes is under the control of auxin-response elements (AuxREs; for review, see Guilfoyle et al., 1998).The GSTs are a distinct class of auxin-responsive genes (for review, see Marrs, 1996). This family of enzymes was named for its ability to conjugate compounds, including xenobiotic compounds, to the tripeptide glutathione. Once such a complex has formed, the glutathione serves as a tag, marking the complex for transport into the vacuole (for review, see Edwards et al., 2000). As a result of this activity, GSTs protect cells from potentially damaging agents.In mammalian systems, GSTs are classified as phase II detoxifying enzymes. Detoxification of xenobiotic and/or cancer-causing compounds often occu...

show abstract

“…The isoalloxazine ring of the FMN cofactor is in contact with two different regions of the apoprotein that form the FMN binding site: (1) residues situated at the end of strand P3 (here: among others Thr 56) and (2) residues in the loop between strand P4 and helix a 4 (here: among others Tyr 102-Asp 108, loo's loop). In most flavodoxins, the isoalloxazine ring is bracketed by two aromatic side chains (Grandori & Carey, 1994): a tryptophan ring is located at the side of the ribityl side chain of the F M N , and a tyrosine ring is nearly coplanarly stacked at the other side of the isoalloxazine ring.…”

Section: Structure Of Holofivodoxin and Fmn Binding Site Characteristicsmentioning

confidence: 99%

Apparent local stability of the secondary structure of Azotobacter vinelandii holoflavodoxin II as probed by hydrogen exchange: Implications for redox potential regulation and flavodoxin folding

et al. 1998

View full text Add to dashboard Cite

As a first step to determine the folding pathway of a protein with an cy/P doubly wound topology, the 'H, "C, and "N backbone chemical shifts of Azotobacter vinelandii holoflavodoxin I1 (179 residues) have been determined using multidimensional NMR spectroscopy. Its secondary structure is shown to contain a five-stranded parallel P-sheet (p2-pl-p3-p4-/?5) and five a-helices. Exchange rates for the individual amide protons of holoflavodoxin were determined using the hydrogen exchange method. The amide protons of 65 residues distributed throughout the structure of holoflavodoxin exchange slowly at pH* 6.2 ( k , < s-I) and can be used as probes in future folding studies. Measured exchange rates relate to apparent local free energies for transient opening. We propose that the amide protons in the core of holoflavodoxin only exchange by global unfolding of the apo state of the protein. The results obtained are discussed with respect to their implications for flavodoxin folding and for modulation of the flavin redox potential by the apoprotein. We do not find any evidence that A. vinelandii holoflavodoxin I1 is divided into two subdomains based on its amide proton exchange rates, as opposed to what is found for the structurally but not sequentially homologous cylp doubly wound protein Che Y.Keywords: flavodoxin; hydrogenJdeuterium exchange; NMR spectroscopy; protein folding; protein stability; redox potential regulation We have chosen Azotobacter vinelandii (strain ATCC 478) flavodoxin I1 as a model protein to study protein folding. A flavodoxin was chosen because it adopts one of the nine protein domain superfolds (Orengo et al., 1994), the alp doubly wound topology, Abbreviations Amp, ampicillin; ct, constant-time; CSI, chemical shift index; DSS, 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt: fid, free induction decay; PC,, free energy for transient opening; AG;;;, apparent free energy for transient opening in holoflavodoxin; PC,+ equlllbrium free energy of global unfolding; HSQC, heteronuclear single-quantum coherence; IPTG, isopropyl P-D-thiogalactopyranoside; kex, measured amide proton exchange rate; kin,, sequence-specific intrinsic amide proton exchange rate; &, dissociation constant; NOE, nuclear overhauser effect; NOESY, NOE spectroscopy: NMR, nuclear magnetic resonance; pH*, glass-electrode reading of the pH meter at room temperature, uncorrected for isotope

show abstract

Six new candidate members of the α/β twisted open‐sheet family detected by sequence similarity to flavodoxin

Cited by 47 publications

References 54 publications

Evidence from sequence information that the interleukin-1 receptor is a transmembrane GTPase

Evidence from sequence information that the interleukin-1 receptor is a transmembrane GTPase

FQR1, a Novel Primary Auxin-Response Gene, Encodes a Flavin Mononucleotide-Binding Quinone Reductase

Apparent local stability of the secondary structure of Azotobacter vinelandii holoflavodoxin II as probed by hydrogen exchange: Implications for redox potential regulation and flavodoxin folding

Contact Info

Product

Resources

About