Human Gene BHMT2 (ENST00000521567.1) from GENCODE V44
  Description: Homo sapiens betaine--homocysteine S-methyltransferase 2 (BHMT2), transcript variant 2, mRNA. (from RefSeq NM_001178005)
RefSeq Summary (NM_001178005): Homocysteine is a sulfur-containing amino acid that plays a crucial role in methylation reactions. Transfer of the methyl group from betaine to homocysteine creates methionine, which donates the methyl group to methylate DNA, proteins, lipids, and other intracellular metabolites. The protein encoded by this gene is one of two methyl transferases that can catalyze the transfer of the methyl group from betaine to homocysteine. Anomalies in homocysteine metabolism have been implicated in disorders ranging from vascular disease to neural tube birth defects such as spina bifida. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010].
Gencode Transcript: ENST00000521567.1
Gencode Gene: ENSG00000132840.10
Transcript (Including UTRs)
   Position: hg38 chr5:79,069,767-79,089,195 Size: 19,429 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg38 chr5:79,069,783-79,088,574 Size: 18,792 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:79,069,767-79,089,195)mRNA (may differ from genome)Protein (299 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: BHMT2_HUMAN
DESCRIPTION: RecName: Full=S-methylmethionine--homocysteine S-methyltransferase BHMT2; Short=SMM-hcy methyltransferase; EC=2.1.1.5; AltName: Full=Betaine--homocysteine S-methyltransferase 2;
FUNCTION: Involved in the regulation of homocysteine metabolism. Converts homocysteine to methionine using S-methylmethionine (SMM) as a methyl donor.
CATALYTIC ACTIVITY: Trimethylammonioacetate + L-homocysteine = dimethylglycine + L-methionine.
COFACTOR: Binds 1 zinc ion per subunit.
PATHWAY: Amine and polyamine degradation; betaine degradation; sarcosine from betaine: step 1/2.
PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (BhmT route): step 1/1.
SUBUNIT: Homotetramer (By similarity). May interact with PRNP.
TISSUE SPECIFICITY: Expressed in liver and kidney and at reduced levels in the brain, heart, and skeletal muscle.
SIMILARITY: Contains 1 Hcy-binding domain.
SEQUENCE CAUTION: Sequence=BAA90880.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

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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           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 127.18 RPKM in Liver
Total median expression: 469.91 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -1.3016-0.081 Picture PostScript Text
3' UTR -141.70621-0.228 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
IPR017226 - Betaine-hCys_S-MeTrfase_BHMT
IPR003726 - S_MeTrfase

Pfam Domains:
PF02574 - Homocysteine S-methyltransferase

ModBase Predicted Comparative 3D Structure on Q9H2M3
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008168 methyltransferase activity
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0046872 metal ion binding
GO:0061627 S-methylmethionine-homocysteine S-methyltransferase activity
GO:0047150 betaine-homocysteine S-methyltransferase activity

Biological Process:
GO:0000096 sulfur amino acid metabolic process
GO:0009086 methionine biosynthetic process
GO:0032259 methylation
GO:0033477 S-methylmethionine metabolic process
GO:0046500 S-adenosylmethionine metabolic process
GO:0071267 L-methionine salvage
GO:0006577 amino-acid betaine metabolic process

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


-  Descriptions from all associated GenBank mRNAs
  AF257473 - Homo sapiens betaine-homocysteine methyltransferase 2 (BHMT2) mRNA, complete cds.
JD121360 - Sequence 102384 from Patent EP1572962.
AK298298 - Homo sapiens cDNA FLJ52714 complete cds, highly similar to Homo sapiens betaine-homocysteine methyltransferase 2 (BHMT2), mRNA.
AK315520 - Homo sapiens cDNA, FLJ96586, highly similar to Homo sapiens betaine-homocysteine methyltransferase 2 (BHMT2), mRNA.
BC020665 - Homo sapiens betaine-homocysteine methyltransferase 2, mRNA (cDNA clone MGC:22349 IMAGE:4722608), complete cds.
DQ894550 - Synthetic construct Homo sapiens clone IMAGE:100009010; FLH176296.01L; RZPDo839B09121D betaine-homocysteine methyltransferase 2 (BHMT2) gene, encodes complete protein.
DQ891370 - Synthetic construct clone IMAGE:100004000; FLH176300.01X; RZPDo839B09122D betaine-homocysteine methyltransferase 2 (BHMT2) gene, encodes complete protein.
AB590411 - Synthetic construct DNA, clone: pFN21AE1448, Homo sapiens BHMT2 gene for betaine-homocysteine methyltransferase 2, without stop codon, in Flexi system.
CU676622 - Synthetic construct Homo sapiens gateway clone IMAGE:100022250 5' read BHMT2 mRNA.
KJ893443 - Synthetic construct Homo sapiens clone ccsbBroadEn_02837 BHMT2 gene, encodes complete protein.
AK000008 - Homo sapiens cDNA FLJ20001 fis, clone ADKA01273.
JD326678 - Sequence 307702 from Patent EP1572962.
JD433692 - Sequence 414716 from Patent EP1572962.
JD169973 - Sequence 150997 from Patent EP1572962.
JD131519 - Sequence 112543 from Patent EP1572962.
JD163091 - Sequence 144115 from Patent EP1572962.
JD521240 - Sequence 502264 from Patent EP1572962.
JD271097 - Sequence 252121 from Patent EP1572962.
JD236992 - Sequence 218016 from Patent EP1572962.
JD367483 - Sequence 348507 from Patent EP1572962.
JD437000 - Sequence 418024 from Patent EP1572962.
JD403589 - Sequence 384613 from Patent EP1572962.
JD083061 - Sequence 64085 from Patent EP1572962.
JD460557 - Sequence 441581 from Patent EP1572962.
JD404592 - Sequence 385616 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9H2M3 (Reactome details) participates in the following event(s):

R-HSA-5696838 BHMT2 tetramer transfers CH3 group from SMM to LHCYS
R-HSA-1614635 Sulfur amino acid metabolism
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z516, BHMT2_HUMAN, NM_001178005, Q9H2M3, Q9NXX7, uc011cth.1, uc011cth.2, uc011cth.3
UCSC ID: ENST00000521567.1
RefSeq Accession: NM_001178005
Protein: Q9H2M3 (aka BHMT2_HUMAN)
CCDS: CCDS54871.1

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