Protein Help

MDH3 / YDL078C 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
malate dehydrogenase MDH3
Feature Type
ORF , Verified
EC Number
1.1.1.37

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-life8.8 hrChristiano R, et al. (2014)

Protein Abundance

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Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
4300SDuntreatedconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
5073SD0.2 M hydroxyurea160 minconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
3241SD200 ng/ml sirolimus700 minconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
7214YEPDuntreatedflow cytometry evidenceS288CDavidson GS, et al. (2011)Ho B, et al. (2018)
3908YEPDcell quiescence7 dflow cytometry evidenceS288CDavidson GS, et al. (2011)Ho B, et al. (2018)
Showing 1 to 5 of 26 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.


MDH3ΔSKL | mdh3-Δ

View all MDH3 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 MVKVAILGAS GGVGQPLSLL LKLSPYVSEL ALYDIRAAEG IGKDLSHINT NSSCVGYDKD
61 SIENTLSNAQ VVLIPAGVPR KPGLTRDDLF KMNAGIVKSL VTAVGKFAPN ARILVISNPV
121 NSLVPIAVET LKKMGKFKPG NVMGVTNLDL VRAETFLVDY LMLKNPKIGQ EQDKTTMHRK
181 VTVIGGHSGE TIIPIITDKS LVFQLDKQYE HFIHRVQFGG DEIVKAKQGA GSATLSMAFA
241 GAKFAEEVLR SFHNEKPETE SLSAFVYLPG LKNGKKAQQL VGDNSIEYFS LPIVLRNGSV
301 VSIDTSVLEK LSPREEQLVN TAVKELRKNI EKGKSFILDS SKL*

* 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.

10 entries for 9 sites

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SiteModificationModifierReference
K106ubiquitinylated lysineSwaney DL, et al. (2013) PMID: 23749301
K106monoacetylated residueHenriksen P, et al. (2012) PMID: 22865919
K138ubiquitinylated lysineSwaney DL, et al. (2013) PMID: 23749301
K167ubiquitinylated lysineSwaney DL, et al. (2013) PMID: 23749301
K174ubiquitinylated lysineSwaney DL, et al. (2013) PMID: 23749301
K225ubiquitinylated lysineSwaney DL, et al. (2013) PMID: 23749301
K256ubiquitinylated lysineSwaney DL, et al. (2013) PMID: 23749301
K324ubiquitinylated lysineSwaney DL, et al. (2013) PMID: 23749301
S335phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S341phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
Showing 1 to 10 of 10 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
A236.71
C10.29
D154.37
E205.83
F133.79
G288.16
H61.75
I236.71
K319.04
L3811.08
M72.04
N174.96
P154.37
Q113.21
R113.21
S288.16
T164.66
V339.62
W00.00
Y72.04

Physical Details

Length (a.a): 343
Molecular Weight (Da): 37193.6
Isoelectric Point (pl): 9.79
Formula: C1668H2732N447O493S8
Aliphatic Index: 102.28
Instability Index: 30.78

Coding Region Translation Calculations

Codon Bias: 0.18
Codon Adaptation Index: 0.15
Frequence of Optimal Codons: 0.53
Hydropathicity of Protein: -0.02
Aromaticity Score: 0.06

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 10430.0
NO Cys residues appear as half cystines: 10430.0

Atomic 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.

Atom Frequency Percentage

Data not found or not available for  S288C

External Identifiers

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

18 entries for 8 sources


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External IDSource
orf19.5323CGD
6473DIP
1.1.1.37ExPASy
2506850GenBank/EMBL/DDBJ
AAA34767.1GenBank/EMBL/DDBJ
171918GenBank/EMBL/DDBJ
1431096GenBank/EMBL/DDBJ
Z74126GenBank/EMBL/DDBJ
M98763GenBank/EMBL/DDBJ
6320125GenBank/EMBL/DDBJ
Showing 1 to 10 of 18 entries

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