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YDR466W Gene in Saccharomyces cerevisiae  

Introduction

    The YDR466W gene in Saccharomyces cerevisiae encodes for a protein that is still unknown both in structure and function.  However, it is located on chromosome 4, near other important genes (such as MRPL28), and could be very important to the study of gene location in the genome and the relationship that occurs when genes are closely located on the same chromosome.

Nucleotide Information

    The YDR466W gene is found on chromosome 4 in Saccharomyces cerevisiae .  It is a gene with a length of 2697 base pairs.   The sequence for this gene is very lengthy, but can be viewed at this URL .  The location of the gene on chromosome 4 is shown in this map, obtained from the Saccharomyces Genome Database :  

                   
                                                                                                        (permission to use image pending from  Saccharomyces Genome Database )


    The nucleotide sequence for the YDR466W gene was compared with a BLAST search at the National Center for Biotechnology Information webpage, and it was found that there are several very similar nucleotide sequences in different organisms.  However, the only sequence that matched with E-values of less than 1.0 was from Saccharomyces cerevisiae. With this unknown gene, and nothing to compare it to, speculating on the function of the gene is difficult.

Protein Information

    The YDR466W gene in Saccharomyces cerevisiae codes for an unknown protein with a length of 898 amino acids.  This protein has not been crystallized yet, and thus there is not a chime file showing the 3D structure of the protein.  When a BLAST search was performed, it was found that the most similar protein is the cAMP-dependent protein kinase catalytic subunit in Rattus norvegicus .  Therefore, it could be assumed that this unknown protein has some function in the protein kinase cell pathway in Saccharomyces cerevisiae.  An attempt in Swiss-Model to determine similar 3D structures did not produce any documented proteins with a 3D stucture similar to YDR466W with an E-value of <0.0001.  A PREDATOR search reveals that the protein is made up of  18.15% alpha-helices, 68.04% random coils, and 13.81% extended strand.  A hydropathy plot was then conducted, and it was found that the protein had no region where the protein would exceed the value of statistical significance (2.0) for hydrophobic regions.  The amino acid sequence for the YDR466W protein is displayed below:  

                mtsrkrsphd fifkeelghg systvfkald kkspnkiyai kvcskkhiik eakvkyvtie
         kntmnllaqk hhagiiklyy tfhdeenlyf vldfapggel lsllhkmgtf ndiwtrhfta
         qlidalefih shgiihrdlk penvlldrdg rlmitdfgaa atidpslsgd sakfnsdsng
         skdnqncasf vgtaeyvspe lllynqcgyg sdiwalgcmi yqfvqgqppf rgenelktfe
         kivaldypwg pnnrinnsts pinplvinlv qkilvievne risleqikrh pyfskvdwnd
         kikiwrgiwq sqgqslqqtt lglpnipqni lptrqlhvid tparsiqitk qkrkkptkis
         nttssivvwr krlgistgkd dlgtvpsttp avtapndtnv ltntaahsta nialppnsqs
         nqvkraqlva pnrippkvpv indnvrnksi prtkpnvppl qtssipqkls tssassalsa
         psteirnqdl thtldgrnsi dihvlkqdyv fiygipyehe gpamslnsyn kidndlitsl
         vaqhkeelkn sesflqvltl kksgmlsykn tvmegnddqe nkehqmanie dtdlsmydfe
         fneltrkgfl ilekyknriw fislpsystl skipfnavks stinnnenwv dcffrarqll
         eekqildkis nvsfdskass epsspppisr kerplsignn vttlsytakn gsqnnapqnd
         nvgeekpfri psstkdrpga nstpssrhpr vlssnnaget pkkmngrlpn sapstntytn
         gsvpafnhrp stnvgnnkhn iltskkqgss vfspsssttk pqikttgyrq ptpspplpqm
         efpttrekys apsnmvisss ryevlhtlnn sqtnfdreia srgasaafrs lqkskkkk


Phenotype Information

    The structure, function, and variations of this gene have not been documented, and thus the effects of variation in this gene are unknown at this time.  However, variations in the gene would likely have some effect on the intracellular protein kinase pathway, due to a great similarity in amino acid sequence with other protein kinases.

Conclusions

    The study of related genes on a chromosome is a very important one, as this is the central theme of the study of genomics.  It has been discovered that the distance between genes on a chromosome plays a vital role in how they interact.  Therefore, the YDR466W gene must continue to be studied, which may reveal an important relationship between known genes in the future.


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This page was created by:
Peter Lowry
pelowry@davidson.edu
Davidson College