biology

RUFY2

RUFY2 is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand RUFY2 rather than just read about it. In short: RUN and FYVE domain containing 2 (RUFY2) is a protein that in humans is encoded by the RUFY2 gene. The RUFY2 gene is named for two of its domains, the RUN domain and FYVE domains.

Key takeaways

RUFY2 belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect RUFY2 to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of RUFY2 from memory before moving on to harder problems.

Reference excerpt

RUN and FYVE domain containing 2 (RUFY2) is a protein that in humans is encoded by the RUFY2 gene. The RUFY2 gene is named for two of its domains, the RUN domain and FYVE domains. RUFY2 is a member of the RUFY family of proteins that include RUFY1, RUFY2, RUFY3, and RUFY4. RUFY2 protein has a dynamic role in endosomal membrane trafficking.

Gene

The human RUFY2 gene is located on the long (q) arm of chromosome 10 at region 21 band 3, from base pair 70,100,864 to base pair 70,167,051 on the reverse strand (Build GRCh37/hg19) (map). The gene produces a 2,080 base pair mRNA. There are 18 predicted exons in the human gene with 13 alternative transcripts.

Gene neighborhood 8,180 base pairs upstream of RUFY2 is the protein-coding gene for phenazine biosynthesis-like protein domain containing (PBLD). While 6,770 base pairs downstream from RUFY2 is a DNA2 conserved helicase/nuclease involved in the maintenance of mitochondrial and nuclear DNA stability.

Protein

The protein of RUFY2 consists of 655 amino acid residues. RUFY2 protein contains a N-terminal RUN domain and a C-terminal FYVE domain with 2 coiled coil domains in between. The molecular weight of the mature protein is 70.0 kdal with an isoelectric point of 5.494. PHYRE2 protein tertiary structure tool suggests that RUFY2 has 15 alpha helices and the longest helix spanning amino acids 199...512 as seen in the figure to the right. RUFY2 is a soluble protein that localizes to the nucleus and to membranes of early endosomes. RUFY2 protein contains no signal peptide, no DNA/RNA binding sites, no mitochondrial targeting motifs and no peroxisomal targeting signal in the C-terminus. There is no transmembrane domain in RUFY2.

Domains

RUN domain The RUN domain is between amino acids 45...168 and consists of the RPIP8, UNC-14, and NESCA proteins. The RUN domain has been shown to have interacting functions with GTPases in the Rap and Rab signal transduction pathways and endosomal membrane trafficking.

DUF972 Domain of unknown function that is part of a family of hypothetical bacterial sequences pfam06156. It make be linked to the YabA initiation control protein which functions as the chromosomal replication initiation control in bacteria.

PspA/IM30 The PspA/IM30 family is a negative regulator of sigma54 transcription initiation factor in bacteria.

FYVE domain FYVE domain consists of Fab-1, YGL023, Vps27, and EEA1 proteins. Within the FYVE domain there are Zinc finger binding sites that interact with phosphatidylinositol-3-phosphate, to bring target proteins to membrane lipids.

Protein interactions The proline rich motif in the FYVE domain of RUFY2 has been shown to have binding activity with the SH3 domain of EPHA3 (Etk) in signal transduction pathways.

Post-translational modifications

RUFY2 possibly has 6 phosphorylation sites and are located mainly in the DUF972 region. RUFY2 also has 6 protein kinase C phosphorylation sites that are located mainly within the FYVE domain.

Other notable modification sites within the protein 4 Lysine acetylation sites 4 N-myristolation sites 3 N-glycosylation sites

Homology and evolution RUFY2 has 4 paralogs: RUFY3, RUFY1, RUNDC3A, RUNDC3B. There are 60 orthologs of RUFY2 that have been identified including mammals, some birds, reptiles and fish. RUFY2 is highly conserved among its orthologs but is not present in plants, bacteria, archea or protist.

Species distribution The following table lists the homologs of RUFY2.

Clinical significance Certain neurodegenerative diseases such as Alzheimer's have been found to have defective endosomal trafficking. Therefore, the involvement of RUFY2 protein domains, RUN and FYVE, may possibly play a role in neurodegenerative diseases such as Alzheimer's.

Expression RUFY2 protein has been shown to mainly be expressed in the brain, lung, and testes while microarray expression shows RUFY2 ubiquitous expression.

References

Illustrations

Worked examples

Example 1 — a first encounter with RUFY2

Start with the simplest possible case. Write down what RUFY2 claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to RUFY2 before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about RUFY2 ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of RUFY2

In research: RUFY2 appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses RUFY2 in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: RUFY2 is common in secondary-school and first-year university syllabi. It links to neighbouring topics Genes on human chromosome 10, Protein domains, so understanding it makes those chapters shorter.
In everyday life: Look for RUFY2 outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study RUFY2 in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what RUFY2 means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain RUFY2 out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is RUFY2 in simple terms?

RUN and FYVE domain containing 2 (RUFY2) is a protein that in humans is encoded by the RUFY2 gene. The RUFY2 gene is named for two of its domains, the RUN domain and FYVE domains.

Why does RUFY2 matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study RUFY2?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on RUFY2.