Human Gene BDH2 (ENST00000296424.9) from GENCODE V46 (2024)

Human Gene BDH2 (ENST00000296424.9) from GENCODE V46

Description: hom*o sapiens 3-hydroxybutyrate dehydrogenase 2 (BDH2), mRNA. (from RefSeq NM_020139)
Gencode Transcript: ENST00000296424.9
Gencode Gene: ENSG00000164039.15
Transcript (Including UTRs)
Position:hg38 chr4:103,077,592-103,099,834Size:22,243Total Exon Count:10Strand:-
Coding Region
Position:hg38 chr4:103,079,702-103,096,254Size:16,553Coding Exon Count:9

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	RNA-Seq Expression
Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations	mRNA Descriptions
Pathways	Other Names	Methods

Data last updated at UCSC:2024-06-17 15:45:33

Sequence and Links to Tools and Databases

Genomic Sequence (chr4:103,077,592-103,099,834)			mRNA (may differ from genome)		Protein (245 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	Gencode	GeneCards
HGNC	Lynx	Malacards	MGI	neXtProt	PubMed
Reactome	UniProtKB	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: BDH2_HUMAN DESCRIPTION: RecName: Full=3-hydroxybutyrate dehydrogenase type 2; EC=1.1.1.-; EC=1.1.1.30; AltName: Full=Dehydrogenase/reductase SDR family member 6; AltName: Full=Oxidoreductase UCPA; AltName: Full=R-beta-hydroxybutyrate dehydrogenase; FUNCTION: Dehydrogenase that mediates the formation of 2,5- dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin and associates with LCN2, thereby playing a key role in iron homeostasis and transport. Also acts as a 3-hydroxybutyrate dehydrogenase (By similarity). CATALYTIC ACTIVITY: (R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH. BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=60 uM for NAD; KM=10 mM for R-hydroxybutyrate; Vmax=82 nmol/min/mg enzyme (at 30 degrees Celsius); pH dependence: Optimum pH is 7.5-9.0; PATHWAY: Siderophore biosynthesis. SUBUNIT: homotetramer. SUBCELLULAR LOCATION:* Cytoplasm. SIMILARITY: Belongs to the short-chain dehydrogenases/reductases (SDR) family.

Primer design for this transcript


	Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA. Click here to load the transcript sequence and exon structure into Primer3Plus Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence. Click here to open Exonprimer with this transcript To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D016604Aflatoxin B1 D013749Tetrachlorodibenzodioxin C0284741,4-bis(2-(3,5-dichloropyridyloxy))benzene C0164032,4-dinitrotoluene C0235142,6-dinitrotoluene D0151237,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide C547126AZM551248 D000082Acetaminophen D000393Air Pollutants D002945Cisplatin more ... click here to view the complete list

RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 54.34 RPKM in Kidney - Cortex Total median expression: 1029.99 RPKM View in GTEx track of Genome BrowserView at GTEx portalView GTEx Body Map

Highest median expression: 54.34 RPKM in Kidney - Cortex
Total median expression: 1029.99 RPKM

View in GTEx track of Genome BrowserView at GTEx portalView GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-12.50	72	-0.174	Picture	PostScript	Text
3' UTR	-513.30	2110	-0.243	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
IPR002198 - DH_sc/Rdtase_SDR
IPR002347 - Glc/ribitol_DH
IPR016040 - NAD(P)-bd_dom
IPR020904 - Sc_DH/Rdtase_CS

Protein Data Bank (PDB) 3-D Structure

MuPIT help

2AG5 - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q9BUT1


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
Genome Browser	Genome Browser	Genome Browser	No ortholog	No ortholog	No ortholog
Gene Details
Gene Sorter
MGI	RGD	Ensembl
Protein Sequence	Protein Sequence	Protein Sequence
Alignment	Alignment	Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0003858 3-hydroxybutyrate dehydrogenase activity GO:0016491 oxidoreductase activity GO:0016628 oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor GO:0051287 NAD binding Biological Process: GO:0006635 fatty acid beta-oxidation GO:0019290 siderophore biosynthetic process GO:0030855 epithelial cell differentiation GO:0042168 heme metabolic process GO:0046951 ketone body biosynthetic process GO:0055072 iron ion homeostasis GO:0055114 oxidation-reduction process Cellular Component: GO:0005737 cytoplasm GO:0005829 cytosol GO:0070062 extracellular exosome GO:0005739 mitochondrion

Molecular Function:
GO:0003858 3-hydroxybutyrate dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016628 oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding

Biological Process:
GO:0006635 fatty acid beta-oxidation
GO:0019290 siderophore biosynthetic process
GO:0030855 epithelial cell differentiation
GO:0042168 heme metabolic process
GO:0046951 ketone body biosynthetic process
GO:0055072 iron ion homeostasis
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome
GO:0005739 mitochondrion

Descriptions from all associated GenBank mRNAs


	BC095414 - homo sapiens 3-hydroxybutyrate dehydrogenase, type 2, mRNA (cDNA clone MGC:110919 IMAGE:5284436), complete cds. JD179490 - Sequence 160514 from Patent EP1572962. JD029242 - Sequence 10266 from Patent EP1572962. BC001953 - homo sapiens 3-hydroxybutyrate dehydrogenase, type 2, mRNA (cDNA clone MGC:4385 IMAGE:2905279), complete cds. AK300626 - homo sapiens cDNA FLJ57796 complete cds, highly similar to Dehydrogenase/reductase SDR family member 6 precursor (EC 1.1.-.-). AF164790 - homo sapiens oxidoreductase UCPA mRNA, complete cds. AK023323 - homo sapiens cDNA FLJ13261 fis, clone OVARC1000885, weakly similar to OXIDOREDUCTASE UCPA (EC 1.-.-.-). AY358841 - homo sapiens clone DNA171771 GRLD6308 (UNQ6308) mRNA, complete cds. AK128463 - homo sapiens cDNA FLJ46606 fis, clone THYMU3047891, highly similar to Dehydrogenase/reductase SDR family member 6 precursor (EC 1.1.-.-). BC037277 - homo sapiens 3-hydroxybutyrate dehydrogenase, type 2, mRNA (cDNA clone MGC:32990 IMAGE:4838679), complete cds. AK290160 - homo sapiens cDNA FLJ76235 complete cds, highly similar to homo sapiens dehydrogenase/reductase (SDR family) member 6 (DHRS6),mRNA. JD154590 - Sequence 135614 from Patent EP1572962. JD552095 - Sequence 533119 from Patent EP1572962. JD292082 - Sequence 273106 from Patent EP1572962. KJ899262 - Synthetic construct homo sapiens clone ccsbBroadEn_08656 BDH2 gene, encodes complete protein. AK291335 - homo sapiens cDNA FLJ78346 complete cds, highly similar to homo sapiens 3-hydroxybutyrate dehydrogenase, type 2, mRNA. CR457309 - homo sapiens full open reading frame cDNA clone RZPDo834E089D for gene DHRS6, dehydrogenase/reductase (SDR family) member 6; complete cds, incl. stopcodon. JD526552 - Sequence 507576 from Patent EP1572962.

Biochemical and Signaling Pathways


	KEGG - Kyoto Encyclopedia of Genes and Genomes hsa00072 - Synthesis and degradation of ketone bodies hsa00650 - Butanoate metabolism hsa01100 - Metabolic pathways BioCyc Knowledge Library PWY66-367 - ketogenesis PWY66-368 - ketolysis Reactome (by CSHL, EBI, and GO) Protein Q9BUT1 (Reactome details) participates in the following event(s): R-HSA-5696457 BDH2 dehydrogenates 3HBA R-HSA-77111 Synthesis of Ketone Bodies R-HSA-74182 Ketone body metabolism R-HSA-556833 Metabolism of lipids R-HSA-1430728 Metabolism

KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00072 - Synthesis and degradation of ketone bodies
hsa00650 - Butanoate metabolism
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
PWY66-367 - ketogenesis
PWY66-368 - ketolysis

Reactome (by CSHL, EBI, and GO)

Protein Q9BUT1 (Reactome details) participates in the following event(s):

R-HSA-5696457 BDH2 dehydrogenates 3HBA
R-HSA-77111 Synthesis of Ketone Bodies
R-HSA-74182 Ketone body metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

Other Names for This Gene


	Alternate Gene Symbols: A8K295, B4DUF6, BDH2 , DHRS6 , DHRS6_HUMAN, ENST00000296424.1, ENST00000296424.2, ENST00000296424.3, ENST00000296424.4, ENST00000296424.5, ENST00000296424.6, ENST00000296424.7, ENST00000296424.8, NM_020139, Q503A0, Q6IA46, Q6UWD3, Q9BUT1, Q9H8S8, Q9NRX8, SDR15C1, uc003hwz.1, uc003hwz.2, uc003hwz.3, uc003hwz.4, uc003hwz.5, UNQ6308/PRO20933 UCSC ID: ENST00000296424.9 RefSeq Accession: NM_020139 Protein: Q9BUT1 (aka BDH2_HUMAN) CCDS: CCDS3663.1

Methods, Credits, and Use Restrictions


	Click here for details on how this gene model was made and data restrictions if any.

Human Gene BDH2 (ENST00000296424.9) from GENCODE V46 (2024)

References