Human Gene LCMT1 (uc002dnx.1) Description and Page Index
  Description: Homo sapiens leucine carboxyl methyltransferase 1 (LCMT1), transcript variant 1, mRNA.
RefSeq Summary (NM_016309): LCMT1 catalyzes the methylation of the carboxyl group of the C-terminal leucine residue (leu309) of the catalytic subunit of protein phosphatase-2A (PPP2CA; MIM 176915) (De Baere et al., 1999 [PubMed 10600115]).[supplied by OMIM, Mar 2008].
Transcript (Including UTRs)
   Position: hg19 chr16:25,123,047-25,189,551 Size: 66,505 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr16:25,123,205-25,189,344 Size: 66,140 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:25,123,047-25,189,551)mRNA (may differ from genome)Protein (334 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: LCMT1_HUMAN
DESCRIPTION: RecName: Full=Leucine carboxyl methyltransferase 1; EC=2.1.1.233; AltName: Full=Protein-leucine O-methyltransferase; AltName: Full=[Phosphatase 2A protein]-leucine-carboxy methyltransferase 1;
FUNCTION: Methylates the carboxyl group of the C-terminal leucine residue of protein phosphatase 2A catalytic subunits to form alpha-leucine ester residues.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + [phosphatase 2A protein]-leucine = S-adenosyl-L-homocysteine + [phosphatase 2A protein]-leucine methyl ester.
BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=0.1 uM for PP2AD; KM=1.3 uM for AdoMet;
INTERACTION: P51116:FXR2; NbExp=2; IntAct=EBI-747632, EBI-740459;
SIMILARITY: Belongs to the methyltransferase superfamily. LCMT family.

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 23.67 RPKM in Testis
Total median expression: 602.04 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 -62.90158-0.398 Picture PostScript Text
3' UTR -58.82207-0.284 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
IPR007213 - LCM_MeTrfase
IPR021121 - LCM_MeTrfase_euk
IPR016651 - Leu_CO_MeTrfase_LCTM1

Pfam Domains:
PF04072 - Leucine carboxyl methyltransferase

SCOP Domains:
53335 - S-adenosyl-L-methionine-dependent methyltransferases

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

3IEI
- X-ray MuPIT

3O7W
- X-ray MuPIT

3P71
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9UIC8
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003880 protein C-terminal carboxyl O-methyltransferase activity
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008276 protein methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0016740 transferase activity
GO:0018423 protein C-terminal leucine carboxyl O-methyltransferase activity

Biological Process:
GO:0000086 G2/M transition of mitotic cell cycle
GO:0006464 cellular protein modification process
GO:0006479 protein methylation
GO:0006481 C-terminal protein methylation
GO:0010906 regulation of glucose metabolic process
GO:0031333 negative regulation of protein complex assembly
GO:0032259 methylation
GO:0042981 regulation of apoptotic process
GO:0090266 regulation of mitotic cell cycle spindle assembly checkpoint

Cellular Component:
GO:0005654 nucleoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  HQ448264 - Synthetic construct Homo sapiens clone IMAGE:100071666; CCSB007303_03 leucine carboxyl methyltransferase 1 (LCMT1) gene, encodes complete protein.
AK223364 - Homo sapiens mRNA for leucine carboxyl methyltransferase variant, clone: FCC101G05.
AF151826 - Homo sapiens CGI-68 protein mRNA, complete cds.
BC001214 - Homo sapiens leucine carboxyl methyltransferase 1, mRNA (cDNA clone MGC:682 IMAGE:3533656), complete cds.
AK025884 - Homo sapiens cDNA: FLJ22231 fis, clone HRC01949.
AK225271 - Homo sapiens mRNA for leucine carboxyl methyltransferase 1 isoform a variant, clone: DMC05571.
AK291885 - Homo sapiens cDNA FLJ76357 complete cds, highly similar to Homo sapiens leucine carboxyl methyltransferase 1 (LCMT1), mRNA.
AK314409 - Homo sapiens cDNA, FLJ95189, highly similar to Homo sapiens leucine carboxyl methyltransferase 1 (LCMT1), mRNA.
BC014217 - Homo sapiens leucine carboxyl methyltransferase 1, mRNA (cDNA clone MGC:20616 IMAGE:3959936), complete cds.
AF037601 - Homo sapiens leucine carboxyl methyltransferase (LCMT) mRNA, complete cds.
CU674610 - Synthetic construct Homo sapiens gateway clone IMAGE:100018982 5' read LCMT1 mRNA.
KJ893916 - Synthetic construct Homo sapiens clone ccsbBroadEn_03310 LCMT1 gene, encodes complete protein.
AL137283 - Homo sapiens mRNA; cDNA DKFZp434C0816 (from clone DKFZp434C0816); partial cds.
CU676933 - Synthetic construct Homo sapiens gateway clone IMAGE:100017088 5' read LCMT1 mRNA.
KJ902593 - Synthetic construct Homo sapiens clone ccsbBroadEn_11987 LCMT1 gene, encodes complete protein.
JD528190 - Sequence 509214 from Patent EP1572962.
JD050533 - Sequence 31557 from Patent EP1572962.
JD469479 - Sequence 450503 from Patent EP1572962.
JD294488 - Sequence 275512 from Patent EP1572962.
JD044385 - Sequence 25409 from Patent EP1572962.
JD462988 - Sequence 444012 from Patent EP1572962.
JD053038 - Sequence 34062 from Patent EP1572962.
JD112927 - Sequence 93951 from Patent EP1572962.
JD133416 - Sequence 114440 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00340 - Histidine metabolism
hsa00350 - Tyrosine metabolism
hsa00450 - Selenoamino acid metabolism

Reactome (by CSHL, EBI, and GO)

Protein Q9UIC8 (Reactome details) participates in the following event(s):

R-HSA-8856945 PP2A methylation by LCMT1
R-HSA-69273 Cyclin A/B1/B2 associated events during G2/M transition
R-HSA-69275 G2/M Transition
R-HSA-453274 Mitotic G2-G2/M phases
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: A6NL89, A8K770, CGI-68, LCMT, LCMT1_HUMAN, NM_016309, NP_057393, Q53FC5, Q96CI5, Q9H6I9, Q9NTG4, Q9UIC8, Q9Y378
UCSC ID: uc002dnx.1
RefSeq Accession: NM_016309
Protein: Q9UIC8 (aka LCMT1_HUMAN or LCM1_HUMAN)
CCDS: CCDS45445.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016309.2
exon count: 11CDS single in 3' UTR: no RNA size: 1374
ORF size: 1005CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2190.00frame shift in genome: no % Coverage: 99.71
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.