Human Gene MCCC2 (ENST00000340941.11) from GENCODE V44
  Description: Homo sapiens methylcrotonoyl-CoA carboxylase 2 (MCCC2), transcript variant 1, mRNA; nuclear gene for mitochondrial product. (from RefSeq NM_022132)
RefSeq Summary (NM_022132): This gene encodes the small subunit of 3-methylcrotonyl-CoA carboxylase. This enzyme functions as a heterodimer and catalyzes the carboxylation of 3-methylcrotonyl-CoA to form 3-methylglutaconyl-CoA. Mutations in this gene are associated with 3-Methylcrotonylglycinuria, an autosomal recessive disorder of leucine catabolism. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, May 2018].
Gencode Transcript: ENST00000340941.11
Gencode Gene: ENSG00000131844.17
Transcript (Including UTRs)
   Position: hg38 chr5:71,587,340-71,658,706 Size: 71,367 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg38 chr5:71,587,426-71,656,860 Size: 69,435 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:71,587,340-71,658,706)mRNA (may differ from genome)Protein (563 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MCCB_HUMAN
DESCRIPTION: RecName: Full=Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial; Short=MCCase subunit beta; EC=6.4.1.4; AltName: Full=3-methylcrotonyl-CoA carboxylase 2; AltName: Full=3-methylcrotonyl-CoA carboxylase non-biotin-containing subunit; AltName: Full=3-methylcrotonyl-CoA:carbon dioxide ligase subunit beta; Flags: Precursor;
CATALYTIC ACTIVITY: ATP + 3-methylcrotonoyl-CoA + HCO(3)(-) = ADP + phosphate + 3-methylglutaconyl-CoA.
PATHWAY: Amino-acid degradation; L-leucine degradation; (S)-3- hydroxy-3-methylglutaryl-CoA from 3-isovaleryl-CoA: step 2/3.
SUBUNIT: Probably a dodecamer composed of six biotin-containing alpha subunits and six beta subunits.
SUBCELLULAR LOCATION: Mitochondrion matrix.
DISEASE: Defects in MCCC2 are the cause of methylcrotonoyl-CoA carboxylase 2 deficiency (MCC2D) [MIM:210210]. An autosomal recessive disorder of leucine catabolism. The phenotype is variable, ranging from neonatal onset with severe neurological involvement to asymptomatic adults. There is a characteristic organic aciduria with massive excretion of 3-hydroxyisovaleric acid and 3-methylcrotonylglycine, usually in combination with a severe secondary carnitine deficiency.
SIMILARITY: Belongs to the AccD/PCCB family.
SIMILARITY: Contains 1 carboxyltransferase domain.
SEQUENCE CAUTION: Sequence=AAH14897.1; Type=Frameshift; Positions=359;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/MCCC2";

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: MCCC2
Diseases sorted by gene-association score: 3-methylcrotonyl-coa carboxylase 2 deficiency* (1200), 3-methylcrotonyl-coa carboxylase deficiency* (267), mccc2-related 3-methylcrotonyl-coa carboxylase deficiency* (100), multiple carboxylase deficiency (11), ketothiolase deficiency (8), biotinidase deficiency (6), 3-methylglutaconic aciduria (5)
* = Manually curated disease association

-  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: 26.41 RPKM in Adrenal Gland
Total median expression: 492.02 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 -36.3086-0.422 Picture PostScript Text
3' UTR -451.501846-0.245 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
IPR000022 - Carboxyl_trans
IPR011763 - COA_CT_C
IPR011762 - COA_CT_N

Pfam Domains:
PF01039 - Carboxyl transferase domain

ModBase Predicted Comparative 3D Structure on Q9HCC0
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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 BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsemblWormBase 
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 
AlignmentAlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004485 methylcrotonoyl-CoA carboxylase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity

Biological Process:
GO:0006552 leucine catabolic process
GO:0006768 biotin metabolic process
GO:0015936 coenzyme A metabolic process
GO:0051291 protein heterooligomerization

Cellular Component:
GO:0002169 3-methylcrotonyl-CoA carboxylase complex, mitochondrial
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol
GO:1905202 methylcrotonoyl-CoA carboxylase complex


-  Descriptions from all associated GenBank mRNAs
  KJ904848 - Synthetic construct Homo sapiens clone ccsbBroadEn_14242 MCCC2 gene, encodes complete protein.
KJ899435 - Synthetic construct Homo sapiens clone ccsbBroadEn_08829 MCCC2 gene, encodes complete protein.
KR711133 - Synthetic construct Homo sapiens clone CCSBHm_00020602 MCCC2 (MCCC2) mRNA, encodes complete protein.
KR711134 - Synthetic construct Homo sapiens clone CCSBHm_00020615 MCCC2 (MCCC2) mRNA, encodes complete protein.
KR711135 - Synthetic construct Homo sapiens clone CCSBHm_00020623 MCCC2 (MCCC2) mRNA, encodes complete protein.
KR711136 - Synthetic construct Homo sapiens clone CCSBHm_00020628 MCCC2 (MCCC2) mRNA, encodes complete protein.
BC014897 - Homo sapiens methylcrotonoyl-Coenzyme A carboxylase 2 (beta), mRNA (cDNA clone MGC:10207 IMAGE:3910739), complete cds.
HM005569 - Homo sapiens clone HTL-S-29 testicular secretory protein Li 29 mRNA, complete cds.
AF310971 - Homo sapiens 3-methylcrotonyl-CoA carboxylase beta subunit (MCCB) mRNA, complete cds.
AB050049 - Homo sapiens mccb mRNA for non-biotin containing subunit of 3-methylcrotonyl-CoA carboxylase, complete cds.
AF301000 - Homo sapiens 3-methylcrotonyl-CoA carboxylase beta subunit (MCCB) mRNA, complete cds.
AK310194 - Homo sapiens cDNA, FLJ17236.
JD463465 - Sequence 444489 from Patent EP1572962.
AF261884 - Homo sapiens 3-methylcrotonyl-CoA carboxylase subunit MCCB (MCCB) mRNA, complete cds.
BC065027 - Homo sapiens methylcrotonoyl-Coenzyme A carboxylase 2 (beta), mRNA (cDNA clone MGC:74816 IMAGE:6043576), complete cds.
JD067727 - Sequence 48751 from Patent EP1572962.
CU688004 - Synthetic construct Homo sapiens gateway clone IMAGE:100021795 5' read MCCC2 mRNA.
KU178741 - Homo sapiens methylcrotonoyl-CoA carboxylase 2 isoform 1 (MCCC2) mRNA, partial cds, alternatively spliced.
KU178742 - Homo sapiens methylcrotonoyl-CoA carboxylase 2 isoform 2 (MCCC2) mRNA, partial cds, alternatively spliced.
AK090834 - Homo sapiens cDNA FLJ33515 fis, clone BRAMY2005662, highly similar to Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.4).
AX746643 - Sequence 168 from Patent EP1308459.
AK025591 - Homo sapiens cDNA: FLJ21938 fis, clone HEP04471, highly similar to HST000014 Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 195423.
AL079298 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 195423.
AK094987 - Homo sapiens cDNA FLJ37668 fis, clone BRHIP2011838.
JD559983 - Sequence 541007 from Patent EP1572962.
JD292813 - Sequence 273837 from Patent EP1572962.
JD249259 - Sequence 230283 from Patent EP1572962.
JD146663 - Sequence 127687 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00280 - Valine, leucine and isoleucine degradation
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
LEU-DEG2-PWY - L-leucine degradation

Reactome (by CSHL, EBI, and GO)

Protein Q9HCC0 (Reactome details) participates in the following event(s):

R-HSA-2993799 HLCS biotinylates 6xMCCC1:6xMCCC2
R-HSA-70773 beta-methylcrotonyl-CoA + ATP + CO2 <=> beta-methylglutaconyl-CoA + ADP + orthophosphate + H2O [MCCA]
R-HSA-508308 beta-methylglutaconyl-CoA + ADP + orthophosphate + H2O <=> beta-methylcrotonyl-CoA + ATP + CO2 [MCCA]
R-HSA-196780 Biotin transport and metabolism
R-HSA-3371599 Defective HLCS causes multiple carboxylase deficiency
R-HSA-70895 Branched-chain amino acid catabolism
R-HSA-196849 Metabolism of water-soluble vitamins and cofactors
R-HSA-3323169 Defects in biotin (Btn) metabolism
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-3296482 Defects in vitamin and cofactor metabolism
R-HSA-1430728 Metabolism
R-HSA-5668914 Diseases of metabolism
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: A6NIY9, ENST00000340941.1, ENST00000340941.10, ENST00000340941.2, ENST00000340941.3, ENST00000340941.4, ENST00000340941.5, ENST00000340941.6, ENST00000340941.7, ENST00000340941.8, ENST00000340941.9, MCCB, MCCB_HUMAN, NM_022132, Q96C27, Q9HCC0, Q9Y4L7, uc003kbs.1, uc003kbs.2, uc003kbs.3, uc003kbs.4, uc003kbs.5, uc003kbs.6
UCSC ID: ENST00000340941.11
RefSeq Accession: NM_022132
Protein: Q9HCC0 (aka MCCB_HUMAN)
CCDS: CCDS34184.1

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