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TCD2 / YKL027W Protein

Protein abundance data, domains, shared domains with other proteins, protein sequence retrieval for various strains, sequence-based physico-chemical properties, protein modification sites, and external identifiers for the protein.

Protein Product
tRNA threonylcarbamoyladenosine dehydratase
Feature Type
ORF , Verified
Paralog
TCD1 4

AlphaFold Protein Structure

AlphaFold, developed by DeepMind, is an AI program that accurately predicts protein structures from amino acid sequences, enabling visualization of protein conformations. The predicted structures can be accessed through the Protein Data Bank (PDB) and AlphaFold Protein Structure Database.

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Model Confidence

Very high
Confident
Low
Very low

Experimental Data

Contains experimentally-derived protein half-life data obtained using stable isotope labeling by amino acids (SILAC) coupled with mass spectrometry. This section also contains protein abundance data for both untreated and treated cells obtained from over 20 studies. These data have been normalized and converted to a common unit of molecules per cell.

Protein Half Life

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ExperimentResultReference
half-life9.3 hrChristiano R, et al. (2014)

Protein Abundance

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Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
4873SDuntreatedconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
3072SD2 mM 1,4-dithiothreitol2 hr0.63confocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
4415SD1 mM hydrogen peroxide1 hrconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
1405SD minus nitrogencellular response to nitrogen starvation15 hr0.29confocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
4618SDuntreatedconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
Showing 1 to 5 of 29 entries

Domains and Classification - S288C

Collection of computationally identified domains and motifs, as determined by InterProScan analysis; includes protein coordinates for the domain, a domain Description, a Source and corresponding accession ID, and the number of S. cerevisiae genes that share the same domain.

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Gene Protein Coordinates Accession ID Description Source No. of Genes with Domain

Domain Locations

Visual representation of the locations of the domains within the protein, as listed in the Domains and Classification table. Each row displays the domain(s) derived from a different Source, with domains color-coded according to this Source.

Scroll over a domain to view its exact coordinates and its Description.

Shared Domains

This diagram displays domains (colored squares) shared between the given protein (yellow circle) and other proteins (gray circles); the domains are color-coded according to their source, as displayed in the Domain Locations table, above.

Reset

Click on a gene or domain name to go to its specific page within SGD; drag any of the gene or domain objects around within the visualization for easier viewing; click “Reset” to automatically redraw the diagram.

Alleles

Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.

tcd2-P351S | tcd2-Δ

View all TCD2 alleles in SGD search

Sequence

Protein sequence for the given gene in S288C and other strains, when available. Use the pull-down menu under "Strain" to select the sequence for a specific strain. The displayed sequence can be downloaded in FASTA format as a .txt file. Amino acids displayed in blue represent modification sites. More detailed evidence for these modification sites is presented in the Post-translational Modifications table, located just below the protein sequence. 

  1 MVEKDTWKLI TATALFTVAV TTITDYAWTS WQAQKQVIAQ QKNKNKGGQT KSDTDKYHQY 
 61 DEQFIRQSLK NNVEFLGEDT IEKLSNQYVV VVGAGGVGSW VVNSLVRSGC RKIRVVDFDQ 
121 VSLSSLNRHS CAILNDVGTP KVECLRRHMR EIAPWCEIDP INELWTLQNG ERLTLGNGTP 
181 DFIVDCIDNI DTKVDLLEFA YNHGIKVISS MGASAKSDPT KLNVGDLATT EEDPLARVVR 
241 RKLKKRGILS GIPVVFSAEK PDPKKAKLLP LPDEEYERGK VDELSALKDF RVRILPVLGT 
301 MPSLFGLTIT TWILSNISDK PLEPVEGKNR IKVYDGIYQS LAGQMSRVGI PSQRIPLALK 
361 DVSYLVEEVF KGKSPISGIS TRLTLTKWDP SKPISLQNVV VLTKNEQKVH EDRVLKGKES 
421 LQDVYDAKVL KLVSQRFREE AYYSQFR*

* Blue amino acids indicate modification sites. More information below.

Post-translational Modifications - S288C

Modification sites for the protein in the selected strain, based on the presence of a residue in the specific strain, as inferred from experimental evidence.

8 entries for 5 sites

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SiteModificationModifierReference
S52phosphorylated residueHolt LJ, et al. (2009) PMID: 19779198
S52phosphorylated residueMacGilvray ME, et al. (2020) PMID: 32597660
S52phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
T54phosphorylated residueMacGilvray ME, et al. (2020) PMID: 32597660
T54phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S122phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S124phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
K221ubiquitinylated lysineSwaney DL, et al. (2013) PMID: 23749301
Showing 1 to 8 of 8 entries

Sequence-Based Physico-chemical Properties - S288C

Calculated protein properties, including amino acid composition, length, coding region calculations, and atomic composition.

Amino Acid Composition

Sort table using the arrow to the right of a column header to sort by that column; download all properties as a .txt file using the "Download Properties" button.

Amino AcidFrequencyPercentage
A214.70
C51.12
D296.49
E276.04
F122.68
G276.04
H51.12
I286.26
K398.72
L449.84
M51.12
N184.03
P204.47
Q204.47
R245.37
S337.38
T276.04
V439.62
W81.79
Y122.68

Physical Details

Length (a.a): 447
Molecular Weight (Da): 50273.3
Isoelectric Point (pl): 9.16
Formula: C2246H3627N614O670S10
Aliphatic Index: 90.76
Instability Index: 30.88

Coding Region Translation Calculations

Codon Bias: 0.09
Codon Adaptation Index: 0.15
Frequence of Optimal Codons: 0.48
Hydropathicity of Protein: -0.33
Aromaticity Score: 0.07

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 62130.0
NO Cys residues appear as half cystines: 61880.0

Atomic Composition

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Atom Frequency Percentage

Data not found or not available for  S288C

External Identifiers

List of external identifiers for the protein from various database sources.

19 entries for 9 sources

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External IDSource
AN4714AspGD
orf19.2115CGD
6322825GenBank/EMBL/DDBJ
CAA81862.1GenBank/EMBL/DDBJ
AAT92710.1GenBank/EMBL/DDBJ
Z28027GenBank/EMBL/DDBJ
AY692691GenBank/EMBL/DDBJ
549663GenBank/EMBL/DDBJ
51012833GenBank/EMBL/DDBJ
486025GenBank/EMBL/DDBJ
Showing 1 to 10 of 19 entries

Resources

Homologs

AGD | AnalogYeast | AspGD | BLASTP at NCBI | CGD | FungiDB | PhylomeDB | PomBase | YGOB | YOGY

Protein Databases

AlphaFold Protein Structure | GPMDB | ModelArchive | Pfam domains | SUPERFAMILY | TopologYeast | UniProtKB

Localization

CYCLoPs | dHITS | LoQAtE | YeastGFP | YeastRC Public Images | YeastRGB | YPL+

Post-translational Modifications

CoSMoS.c. | PhosphoGRID | PhosphoPep