shm1 (SPAC24C9.12c)


Gene Standard Nameshm1 Characterisation Statusbiological_role_inferred
Systematic IDSPAC24C9.12c Feature Typeprotein coding
Synonyms Name Description
Productserine hydroxymethyltransferase Shm1 (predicted) Product Size467aa, 51.86 kDa
Genomic Location Chromosome I, 3071192-3069322 (1871nt); CDS:3071017-3069614 (1404nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
glycine hydroxymethyltransferase activity2
Annotation ExtensionEvidenceWith/FromReference
pyridoxal phosphate binding26
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
glycine metabolic process8
Annotation ExtensionEvidenceWith/FromReference
L-serine metabolic process11
Annotation ExtensionEvidenceWith/FromReference
one-carbon metabolic process10
Annotation ExtensionEvidenceWith/FromReference
tetrahydrofolate interconversion7
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytoplasm4208
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Viable

Population Phenotype

Term NameAlleleExpressionCount
slow vegetative cell population growthshm1ΔNull321
viable vegetative cell populationshm1ΔNull3792

Cell Phenotype

Term NameAlleleExpressionCount
viable vegetative cell with normal cell morphologyshm1ΔNull3092
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons3071192..3069322
mRNA3071192..3069322
5' UTR3071192..3071018PMID:21511999
CDS3071017..3069614
3' UTR3069613..3069322AU013689
Protein Features

Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID Database InterPro Description Start End Count
PF00464 Pfam IPR001085 Serine hydroxymethyltransferase 12 410 2
PS00096 Prosite Patterns IPR019798 Serine hydroxymethyltransferase, pyridoxal phosphate binding site 235 251 2
PTHR11680:SF5 HMMPANTHER 1 463 1
PTHR11680 HMMPANTHER IPR001085 Serine hydroxymethyltransferase 1 463 2
3.90.1150.10 Gene3D IPR015422 Pyridoxal phosphate-dependent transferase, major region, subdomain 2 310 464 25
3.40.640.10 Gene3D IPR015421 Pyridoxal phosphate-dependent transferase, major region, subdomain 1 41 309 31
SSF53383 SuperFamily IPR015424 Pyridoxal phosphate-dependent transferase 8 464 31
MF_00051 hamap IPR001085 Serine hydroxymethyltransferase 11 465 2
PIRSF000412 PIRSF IPR001085 Serine hydroxymethyltransferase 3 466 2

View domain organization at Pfam

Protein Properties

Ave. residue weight 111.05 Da
Charge 7.00
Isoelectric point 7.94
Molecular weight 51.86 kDa
Number of residues 467
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serineS6 1672
Annotation ExtensionEvidenceResidueReference
experimental evidence S6 PMID:24763107
O-phospho-L-threonineT10 698
Annotation ExtensionEvidenceResidueReference
experimental evidence T10 PMID:24763107
phosphorylated residue 1926
Annotation ExtensionEvidenceResidueReference
IDA PMID:19547744
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
444690during GO:0000080PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
455806during GO:0000084PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
459910during GO:0000085PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
453003during GO:0000087PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
457986during GO:0072690PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
184036.17during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633
56511.76during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
82during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633
7.9during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
conserved in fungi4604
conserved in eukaryotes4516
conserved in bacteria1000
conserved in metazoa3430
conserved in vertebrates3405
conserved in archaea237
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity captured bycbf11CBF1/Su(H)/LAG-1 family transcription factor Cbf11 Affinity Capture-MSPMID:22540037
affinity captured byddb1damaged DNA binding protein Ddb1 Affinity Capture-MSPMID:18794354
affinity captured byhhp1serine/threonine protein kinase Hhp1 Affinity Capture-MSPMID:24055157
affinity captured byhhp2serine/threonine protein kinase Hhp2 Affinity Capture-MSPMID:24055157
affinity captured bynak1PAK-related kinase Nak1 Affinity Capture-MSPMID:23462181
affinity captured bytea1cell end marker Tea1 Affinity Capture-MSPMID:21652630
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
positive genetic interaction withatb2tubulin alpha 2 Positive GeneticPMID:22681890
negative genetic interaction withcph1Clr6 histone deacetylase associated PHD protein-1 Cph1 Negative GeneticPMID:22681890
negative genetic interaction withdsc3Golgi Dsc E3 ligase complex subunit Dsc3 Negative GeneticPMID:21504829
positive genetic interaction withelp2elongator complex subunit Elp2 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withelp3elongator complex subunit Elp3 (predicted) Positive GeneticPMID:22681890
negative genetic interaction withers1RNA-silencing factor Ers1 Negative GeneticPMID:22681890
negative genetic interaction withhrr1Helicase Required for RNAi-mediated heterochromatin assembly Hrr1 Negative GeneticPMID:22681890
positive genetic interaction withpef1Pho85/PhoA-like cyclin-dependent kinase Pef1 Positive GeneticPMID:22681890
negative genetic interaction withphp3CCAAT-binding factor complex subunit Php3 Negative GeneticPMID:22681890
negative genetic interaction withphp5CCAAT-binding factor complex subunit Php5 Negative GeneticPMID:22681890
negative genetic interaction withprp4serine/threonine protein kinase Prp4 Negative GeneticPMID:22681890
negative genetic interaction withpst2Clr6 histone deacetylase complex subunit Pst2 Negative GeneticPMID:22681890
negative genetic interaction withptc1protein phosphatase 2C Ptc1 Negative GeneticPMID:22681890
negative genetic interaction withrxt2histone deacetylase complex subunit Rxt2 Negative GeneticPMID:22681890
positive genetic interaction withsep1forkhead transcription factor Sep1 Positive GeneticPMID:22681890
negative genetic interaction withsfp1transcription factor Sfp1 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withSPAC19B12.11czinc finger protein, human ZNF593 ortholog Positive GeneticPMID:22681890
positive genetic interaction withSPBC31F10.10czf-MYND type zinc finger protein Positive GeneticPMID:22681890
negative genetic interaction withspf1Set1C PHD Finger protein Spf1 Negative GeneticPMID:22681890
negative genetic interaction withsty1MAP kinase Sty1 Negative GeneticPMID:22681890
negative genetic interaction withtrt1telomerase reverse transcriptase 1 protein Trt1 Negative GeneticPMID:22681890
negative genetic interaction withvps35retromer complex subunit Vps35 Negative GeneticPMID:22681890
negative genetic interaction withypa1protein phosphatase type 2A regulator, PTPA family Ypa1 Negative GeneticPMID:22681890
External References
Database Identifier Description
NBRP SPAC24C9.12c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC24C9.12c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC24C9.12c BioGRID Interaction Datasets
Expression Viewer SPAC24C9.12c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC24C9.12c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC24C9.12c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC24C9.12c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC24C9.12c Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC24C9.12c Transcriptome Viewer (Bähler Lab)
Cyclebase SPAC24C9.12c Cell Cycle Data
GEO SPAC24C9.12c GEO profiles
PInt SPAC24C9.12c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAC24C9.12c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPAC24C9.12c Fission yeast phenotypic data & analysis
IntEnz2.1.2.1Integrated relational Enzyme database
Rhea2.1.2.1Annotated reactions database
SPD / RIKEN21/21G01Orfeome Localization Data
KEGGMAP00460KEGG Pathway Database
KEGGMAP00670KEGG Pathway Database
KEGGMAP00260KEGG Pathway Database
KEGGMAP00680KEGG Pathway Database
KEGGMAP00310KEGG Pathway Database
UniProtKB/SwissProtO13972Probable serine hydroxymethyltransferase, cytosolic
ModBaseO13972Database of comparative protein structure models
STRINGO13972Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_594037glycine hydroxymethyltransferase (predicted)
RefSeq mRNANM_001019462972h- glycine hydroxymethyltransferase (predicted) (SPAC24C9.12c), mRNA
European Nucleotide ArchiveCAB11269.1ENA Protein Mapping
MetaCycPWY-1622Formaldehyde assimilation I (serine pathway)
MetaCycPWY-181Photorespiration
MetaCycPWY-2161Folate polyglutamylation
MetaCycPWY-2201Folate transformations I
MetaCycPWY-3661Glycine betaine degradation
MetaCycPWY-3661-1Glycine betaine degradation II (mammalian)
MetaCycPWY-3841Folate transformations II
MetaCycPWY-5497Purine nucleobases degradation II (anaerobic)
KEGG_Enzyme00260+2.1.2.1Glycine, serine and threonine metabolism
KEGG_Enzyme00460+2.1.2.1Cyanoamino acid metabolism
KEGG_Enzyme00630+2.1.2.1Glyoxylate and dicarboxylate metabolism
KEGG_Enzyme00670+2.1.2.1One carbon pool by folate
KEGG_Enzyme00680+2.1.2.1Methane metabolism
UniParcUPI000012B893UniProt Archive
UniPathwayUPA00193One-carbon metabolism; tetrahydrofolate interconversion
UniPathwayUPA00288Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1

Literature for shm1

Search: Europe PMC or PubMed

Release Version: PomBase:25_50 - 10 Mar 2015