Human Gene SDS (uc001tvg.3) Description and Page Index
  Description: Homo sapiens serine dehydratase (SDS), mRNA.
RefSeq Summary (NM_006843): This gene encodes one of three enzymes that are involved in metabolizing serine and glycine. L-serine dehydratase converts L-serine to pyruvate and ammonia and requires pyridoxal phosphate as a cofactor. The encoded protein can also metabolize threonine to NH4+ and 2-ketobutyrate. The encoded protein is found predominantly in the liver. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR3476690.600160.1, SRR5189664.1638.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000257549.9/ ENSP00000257549.4 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr12:113,830,251-113,841,692 Size: 11,442 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr12:113,830,746-113,837,513 Size: 6,768 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:113,830,251-113,841,692)mRNA (may differ from genome)Protein (328 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SDHL_HUMAN
DESCRIPTION: RecName: Full=L-serine dehydratase/L-threonine deaminase; Short=SDH; EC=4.3.1.17; AltName: Full=L-serine deaminase; AltName: Full=L-threonine dehydratase; Short=TDH; EC=4.3.1.19;
CATALYTIC ACTIVITY: L-serine = pyruvate + NH(3).
CATALYTIC ACTIVITY: L-threonine = 2-oxobutanoate + NH(3).
COFACTOR: Pyridoxal phosphate.
BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=23 mM for serine; KM=31 mM for threonine;
PATHWAY: Carbohydrate biosynthesis; gluconeogenesis.
SUBUNIT: Homodimer.
SUBCELLULAR LOCATION: Cytoplasm.
SIMILARITY: Belongs to the serine/threonine dehydratase family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SDS
CDC HuGE Published Literature: SDS

-  MalaCards Disease Associations
  MalaCards Gene Search: SDS
Diseases sorted by gene-association score: autosomal dominant nonsyndromic deafness 69 (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 204.11 RPKM in Liver
Total median expression: 310.29 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -28.45122-0.233 Picture PostScript Text
3' UTR -173.50495-0.351 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000634 - Ser/Thr_deHydtase_PyrdxlP-BS
IPR001926 - Trp_syn_b_sub_like_PLP_eny_SF

Pfam Domains:
PF00291 - Pyridoxal-phosphate dependent enzyme

SCOP Domains:
53686 - Tryptophan synthase beta subunit-like PLP-dependent enzymes

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1P5J
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P20132
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003941 L-serine ammonia-lyase activity
GO:0004794 L-threonine ammonia-lyase activity
GO:0016829 lyase activity
GO:0016836 hydro-lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0006094 gluconeogenesis
GO:0006520 cellular amino acid metabolic process
GO:0006565 L-serine catabolic process
GO:0019518 L-threonine catabolic process to glycine
GO:0042866 pyruvate biosynthetic process

Cellular Component:
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK124290 - Homo sapiens cDNA FLJ42296 fis, clone TLIVE2008712.
AK292760 - Homo sapiens cDNA FLJ75824 complete cds, highly similar to Homo sapiens serine dehydratase (SDS), mRNA.
J05037 - Human serine dehydratase mRNA, complete cds.
JD382473 - Sequence 363497 from Patent EP1572962.
JD230362 - Sequence 211386 from Patent EP1572962.
JD565825 - Sequence 546849 from Patent EP1572962.
JD323748 - Sequence 304772 from Patent EP1572962.
JD421018 - Sequence 402042 from Patent EP1572962.
JD391006 - Sequence 372030 from Patent EP1572962.
JD139404 - Sequence 120428 from Patent EP1572962.
JD454897 - Sequence 435921 from Patent EP1572962.
AB529149 - Synthetic construct DNA, clone: pF1KB5210, Homo sapiens SDS gene for serine dehydratase, without stop codon, in Flexi system.
BC020750 - Homo sapiens serine dehydratase, mRNA (cDNA clone MGC:22597 IMAGE:4662951), complete cds.
CU676692 - Synthetic construct Homo sapiens gateway clone IMAGE:100022109 5' read SDS mRNA.
KJ902183 - Synthetic construct Homo sapiens clone ccsbBroadEn_11577 SDS gene, encodes complete protein.
JD248114 - Sequence 229138 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00260 - Glycine, serine and threonine metabolism
hsa00270 - Cysteine and methionine metabolism
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
PWY-3661 - glycine betaine degradation
SERDEG-PWY - L-serine degradation

Reactome (by CSHL, EBI, and GO)

Protein P20132 (Reactome details) participates in the following event(s):

R-HSA-9014627 SDS dimers:PXLP dehydrate L-Thr to 2AA
R-HSA-8849175 Threonine catabolism
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A8K9P5, NM_006843, NP_006834, P20132, SDH, SDHL_HUMAN
UCSC ID: uc001tvg.3
RefSeq Accession: NM_006843
Protein: P20132 (aka SDHL_HUMAN)
CCDS: CCDS9169.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006843.2
exon count: 8CDS single in 3' UTR: no RNA size: 1620
ORF size: 987CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2174.00frame shift in genome: no % Coverage: 99.01
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.