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protein coding gene - pdb1 (SPBC30D10.13c) - pyruvate dehydrogenase e1 component beta subunit Pdb1

Gene summary

Standard name
pdb1
Systematic ID
SPBC30D10.13c
Product
pyruvate dehydrogenase e1 component beta subunit Pdb1
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
agg1
UniProt ID
Q09171
ORFeome ID
39/39E10
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome II: 3070467..3072018 forward strand

Annotation

PBO:0002875 - 1.2.4.1

Disease association

MONDO:0019169 - pyruvate dehydrogenase deficiency

References:

MONDO:0013580 - pyruvate dehydrogenase E1-beta deficiency

References:

GO biological process

GO:0006086 - pyruvate decarboxylation to acetyl-CoA

References:

GO cellular component

GO:0005759 - mitochondrial matrix

References:

GO:0005739 - mitochondrion

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GO:0045254 - pyruvate dehydrogenase complex

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GO molecular function

GO:0004739 - pyruvate dehydrogenase (acetyl-transferring) activity

References:

Modification

MOD:00046 - O-phospho-L-serine

References:

MOD:00696 - phosphorylated residue

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Protein sequence feature

SO:0001808 - mitochondrial_targeting_signal

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Qualitative gene expression

PomGeneEx:0000019 - protein level decreased

References:

PomGeneEx:0000012 - RNA level decreased

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PomGeneEx:0000011 - RNA level increased

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Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0000983 - decreased glutamate dehydrogenase (NADP+) activity

References:

Genotypes:

FYPO:0000708 - decreased mating efficiency

References:

Genotypes:

FYPO:0000470 - decreased mating type switching

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Genotypes:

FYPO:0000916 - decreased pyruvate dehydrogenase activity

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Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0008128 - decreased vegetative cell population growth on low glucose

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Genotypes:

FYPO:0009007 - decreased vegetative cell population viability

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Genotypes:

FYPO:0000035 - growth auxotrophic for arginine

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Genotypes:

FYPO:0000921 - increased aconitate hydratase activity

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Genotypes:

FYPO:0005261 - increased cell population growth on galactose carbon source

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Genotypes:

FYPO:0009094 - increased cell population growth on lysine and proline nitrogen source

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Genotypes:

FYPO:0009072 - increased cell population growth on lysine nitrogen source

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Genotypes:

FYPO:0009074 - increased cell population growth on serine nitrogen source

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Genotypes:

FYPO:0000919 - increased citrate (Si)-synthase activity

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Genotypes:

FYPO:0000923 - increased isocitrate dehydrogenase (NAD+) activity

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Genotypes:

FYPO:0009008 - increased vegetative cell population viability

References:

Genotypes:

FYPO:0001309 - increased viability in stationary phase

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Genotypes:

FYPO:0004163 - increased viability upon glucose starvation

References:

Genotypes:

FYPO:0002379 - inviable after spore germination, without cell division, with elongated germ tube

References:

Genotypes:

FYPO:0000981 - normal glutamate dehydrogenase (NAD+) activity

References:

Genotypes:

FYPO:0000914 - normal glutamate-ammonia ligase activity

References:

Genotypes:

FYPO:0001357 - normal vegetative cell population growth

References:

Genotypes:

FYPO:0000073 - resistance to caffeine

References:

Genotypes:

FYPO:0000764 - resistance to cycloheximide

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Genotypes:

FYPO:0009038 - resistance to egtazic acid

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Genotypes:

FYPO:0001453 - resistance to ethanol

References:

Genotypes:

FYPO:0009034 - resistance to ethylenediaminetetraacetic acid

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Genotypes:

FYPO:0001103 - resistance to hydrogen peroxide

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Genotypes:

FYPO:0002578 - resistance to hydroxyurea

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Genotypes:

FYPO:0009087 - resistance to magnesium chloride and sodium dodecyl sulfate

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Genotypes:

FYPO:0000725 - resistance to methyl methanesulfonate

References:

Genotypes:

FYPO:0001097 - sensitive to amitrole

References:

Genotypes:

FYPO:0000440 - sensitive to antimycin A

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Genotypes:

FYPO:0000095 - sensitive to bleomycin

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Genotypes:

FYPO:0000096 - sensitive to cadmium

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Genotypes:

FYPO:0000842 - sensitive to ethanol during vegetative growth

References:

Genotypes:

FYPO:0000785 - sensitive to formamide

References:

Genotypes:

FYPO:0000089 - sensitive to methyl methanesulfonate

References:

Genotypes:

FYPO:0009082 - sensitive to potassium chloride and methyl methanesulfonate

References:

Genotypes:

FYPO:0000797 - sensitive to tert-butyl hydroperoxide

References:

Genotypes:

FYPO:0003656 - sensitive to vanadate

References:

Genotypes:

FYPO:0002060 - viable vegetative cell population

References:

Genotypes:

FYPO:0001510 - viable vegetative cell, abnormal cell shape, normal cell size

References:

Genotypes:

Taxonomic conservation

PBO:0011067 - conserved in bacteria

PBO:0011065 - conserved in eukaryotes

PBO:0011064 - conserved in fungi

PBO:0011069 - conserved in metazoa

PBO:0011070 - conserved in vertebrates

PBO:0006222 - predominantly single copy (one to one)

Protein features

IDNameInterPro nameDB name
PF02779Transket_pyrTransketolase-like_Pyr-bdPfam
PF02780Transketolase_CTransketolase_CPfam
cd07036TPP_PYR_E1-PDHc-beta_likeCDD
SM00861Transket_pyrTransketolase-like_Pyr-bdSMART
G3DSA:3.40.50.920:FF:000001CATH-FunFam
G3DSA:3.40.50.970:FF:000006CATH-FunFam
G3DSA:3.40.50.920Transketo_C/PFOR_IICATH-Gene3D
G3DSA:3.40.50.970THDP-bindingCATH-Gene3D
SSF52518THDP-bindingSUPERFAMILY
SSF52922Transketo_C/PFOR_IISUPERFAMILY
PTHR11624PDHB_mito-typePANTHER
NF006667PRK09212.1NCBIFAM
NF008854PRK11892.1NCBIFAM

Orthologs

References / Literature

GO_REF:0000111 - Gene Ontology annotations Inferred by Curator (IC) using at least one Inferred by Sequence Similarity (ISS) annotation to support the inference
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:22540037 - Predicting the fission yeast protein interaction network.
Pancaldi V et al. G3 (Bethesda) 2012 Apr;2(4):453-67
PMID:39367033 - Quantitative proteomics and phosphoproteomics profiling of meiotic divisions in the fission yeast Schizosaccharomyces pombe.
Sivakova B et al. Sci Rep 2024 Oct 04;14(1):23105
PMID:23640107 - Screening for long-lived genes identifies Oga1, a guanine-quadruplex associated protein that affects the chronological lifespan of the fission yeast Schizosaccharomyces pombe.
Ohtsuka H et al. Mol Genet Genomics 2013 Jun;288(5-6):285-95
PMID:27984744 - Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs.
Joh RI et al. Mol Cell 2016 Dec 15;64(6):1088-1101
PMID:34984977 - Functional profiling of long intergenic non-coding RNAs in fission yeast.
Rodriguez-Lopez M et al. Elife 2022 Jan 05;11
PMID:25720772 - Quantitative phosphoproteomics reveals pathways for coordination of cell growth and division by the conserved fission yeast kinase pom1.
Kettenbach AN et al. Mol Cell Proteomics 2015 May;14(5):1275-87
PMID:37859837 - In fission yeast, 65 non-essential mitochondrial proteins related to respiration and stress become essential in low-glucose conditions.
Mori A et al. R Soc Open Sci 2023 Oct;10(10):230404
PMID:22119525 - SIN-inhibitory phosphatase complex promotes Cdc11p dephosphorylation and propagates SIN asymmetry in fission yeast.
Singh NS et al. Curr Biol 2011 Dec 06;21(23):1968-78
PMID:36478272 - Translation-complex profiling of fission yeast cells reveals dynamic rearrangements of scanning ribosomal subunits upon nutritional stress.
Duncan CDS et al. Nucleic Acids Res 2022 Dec 09;50(22):13011-13025
PMID:37787768 - Broad functional profiling of fission yeast proteins using phenomics and machine learning.
Rodríguez-López M et al. Elife 2023 Oct 03;12
PMID:16823372 - ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.
Matsuyama A et al. Nat Biotechnol 2006 Jul;24(7):841-7
PMID:7828917 - Cloning and sequence of a gene encoding the pyruvate dehydrogenase E1 beta subunit of Schizosaccharomyces pombe.
Cavan G et al. Gene 1995 Jan 11;152(1):117-20
PMID:40849408 - A repurposed AMP binding domain reveals mitochondrial protein AMPylation as a regulator of cellular metabolism.
Gonzalez A et al. Nat Commun 2025 Aug 23;16(1):7863
PMID:28281664 - Genetic interactions and functional analyses of the fission yeast gsk3 and amk2 single and double mutants defective in TORC1-dependent processes.
Rallis C et al. Sci Rep 2017 Mar 10;7:44257
PMID:26098123 - Promoter nucleosome dynamics regulated by signalling through the CTD code.
Materne P et al. Elife 2015 Jun 22;4:e09008
PMID:34496258 - Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription.
Heo DH et al. Cell Rep 2021 Sep 07;36(10):109671
PMID:23950735 - Global analysis of fission yeast mating genes reveals new autophagy factors.
Sun LL et al. PLoS Genet 2013;9(8):e1003715
PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.
Kim DU et al. Nat Biotechnol 2010 Jun;28(6):617-623
PMID:23101633 - Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.
Marguerat S et al. Cell 2012 Oct 26;151(3):671-83
PMID:24763107 - Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).
Carpy A et al. Mol Cell Proteomics 2014 Aug;13(8):1925-36
PMID:28218250 - Chromatin remodeller Fun30 Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation.
Lee J et al. Nat Commun 2017 Feb 20;8:14527
PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.
Hayles J et al. Open Biol 2013 May 22;3(5):130053
PMID:30726745 - Fission Yeast NDR/LATS Kinase Orb6 Regulates Exocytosis via Phosphorylation of the Exocyst Complex.
Tay YD et al. Cell Rep 2019 Feb 05;26(6):1654-1667.e7
PMID:30355493 - Expanded Interactome of the Intrinsically Disordered Protein Dss1.
Schenstrøm SM et al. Cell Rep 2018 Oct 23;25(4):862-870
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
PMID:36408920 - UniProt: the Universal Protein Knowledgebase in 2023.
UniProt Consortium Nucleic Acids Res 2023 Jan 06;51(D1):D523-D531
PB_REF:0000003 - Disease Association Curation
PMID:19547744 - Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.
Beltrao P et al. PLoS Biol 2009 Jun 16;7(6):e1000134
PMID:29852001 - New insights into donor directionality of mating-type switching in Schizosaccharomyces pombe.
Maki T et al. PLoS Genet 2018 May;14(5):e1007424
PMID:7851743 - Mutations which reduce levels of pyruvate dehydrogenase in Schizosaccharomyces pombe cause a requirement for arginine or glutamine.
Cavan G et al. FEMS Microbiol Lett 1994 Dec 15;124(3):361-5
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:25963819 - Nucleocytoplasmic transport in the midzone membrane domain controls yeast mitotic spindle disassembly.
Lucena R et al. J Cell Biol 2015 May 11;209(3):387-402
PMID:21386897 - Systematic two-hybrid and comparative proteomic analyses reveal novel yeast pre-mRNA splicing factors connected to Prp19.
Ren L et al. PLoS One 2011 Feb 28;6(2):e16719