Human Gene PCCB (ENST00000251654.9_6) from GENCODE V47lift37
  Description: propionyl-CoA carboxylase subunit beta, transcript variant 1 (from RefSeq NM_000532.5)
Gencode Transcript: ENST00000251654.9_6
Gencode Gene: ENSG00000114054.14_10
Transcript (Including UTRs)
   Position: hg19 chr3:135,969,182-136,049,011 Size: 79,830 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr3:135,969,218-136,048,868 Size: 79,651 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:135,969,182-136,049,011)mRNA (may differ from genome)Protein (539 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PCCB_HUMAN
DESCRIPTION: RecName: Full=Propionyl-CoA carboxylase beta chain, mitochondrial; Short=PCCase subunit beta; EC=6.4.1.3; AltName: Full=Propanoyl-CoA:carbon dioxide ligase subunit beta; Flags: Precursor;
CATALYTIC ACTIVITY: ATP + propanoyl-CoA + HCO(3)(-) = ADP + phosphate + (S)-methylmalonyl-CoA.
PATHWAY: Metabolic intermediate metabolism; propanoyl-CoA degradation; succinyl-CoA from propanoyl-CoA: step 1/3.
SUBUNIT: Probably a dodecamer composed of six biotin-containing alpha subunits and six beta subunits.
SUBCELLULAR LOCATION: Mitochondrion matrix.
DISEASE: Defects in PCCB are the cause of propionic acidemia type II (PA-2) [MIM:606054]. PA-2 is a life-threatening disease characterized by episodic vomiting, lethargy and ketosis, neutropenia, periodic thrombocytopenia, hypogammaglobulinemia, developmental retardation, and intolerance to protein.
SIMILARITY: Belongs to the AccD/PCCB family.
SIMILARITY: Contains 1 carboxyltransferase domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PCCB";

-  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: PCCB
Diseases sorted by gene-association score: propionicacidemia* (1119), pccb-related propionic acidemia* (100), biotinidase deficiency (13), multiple carboxylase deficiency (10), biotin deficiency (8), organic acidemia (7), amino acid metabolic disorder (6), leigh syndrome (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 45.24 RPKM in Adrenal Gland
Total median expression: 517.24 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 -15.3036-0.425 Picture PostScript Text
3' UTR -17.90143-0.125 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

SCOP Domains:
52096 - ClpP/crotonase
53697 - SIS domain

ModBase Predicted Comparative 3D Structure on P05166
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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004658 propionyl-CoA carboxylase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016421 CoA carboxylase activity
GO:0016874 ligase activity

Biological Process:
GO:0006768 biotin metabolic process
GO:0009062 fatty acid catabolic process

Cellular Component:
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AB209009 - Homo sapiens mRNA for Propionyl Coenzyme A carboxylase, beta polypeptide variant protein.
AL831978 - Homo sapiens mRNA; cDNA DKFZp451E113 (from clone DKFZp451E113).
X73424 - Homo sapiens gene for propionyl-CoA carboxylase a subunit.
S67325 - propionyl CoA carboxylase beta subunit [human, liver, placenta, HL1008, mRNA, 1791 nt].
BC005909 - Homo sapiens propionyl Coenzyme A carboxylase, beta polypeptide, mRNA (cDNA clone IMAGE:4133623).
BC013768 - Homo sapiens propionyl Coenzyme A carboxylase, beta polypeptide, mRNA (cDNA clone MGC:9104 IMAGE:3919091), complete cds.
BC053661 - Homo sapiens propionyl Coenzyme A carboxylase, beta polypeptide, mRNA (cDNA clone MGC:61502 IMAGE:6054692), complete cds.
AK295312 - Homo sapiens cDNA FLJ54352 complete cds, highly similar to Propionyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.3).
AK130359 - Homo sapiens cDNA FLJ26849 fis, clone PRS07953, highly similar to Propionyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.3).
AK303079 - Homo sapiens cDNA FLJ53115 complete cds, highly similar to Propionyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.3).
AK225733 - Homo sapiens mRNA for propionyl Coenzyme A carboxylase, beta polypeptide variant, clone: TST01956.
AK225215 - Homo sapiens mRNA for propionyl Coenzyme A carboxylase, beta polypeptide variant, clone: COL09126.
CU680676 - Synthetic construct Homo sapiens gateway clone IMAGE:100020306 5' read PCCB mRNA.
JF432277 - Synthetic construct Homo sapiens clone IMAGE:100073449 propionyl Coenzyme A carboxylase, beta polypeptide (PCCB) gene, encodes complete protein.
KJ891756 - Synthetic construct Homo sapiens clone ccsbBroadEn_01150 PCCB gene, encodes complete protein.
KR709412 - Synthetic construct Homo sapiens clone CCSBHm_00001987 PCCB (PCCB) mRNA, encodes complete protein.
KR709413 - Synthetic construct Homo sapiens clone CCSBHm_00001989 PCCB (PCCB) mRNA, encodes complete protein.
KR709414 - Synthetic construct Homo sapiens clone CCSBHm_00001992 PCCB (PCCB) mRNA, encodes complete protein.
KR709415 - Synthetic construct Homo sapiens clone CCSBHm_00002007 PCCB (PCCB) mRNA, encodes complete protein.
AK302522 - Homo sapiens cDNA FLJ50917 complete cds, highly similar to Propionyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.3).
AF217984 - Homo sapiens clone PP1591 unknown mRNA.
M13573 - Human propionyl-CoA carboxylase beta chain mRNA.
BC018013 - Homo sapiens, clone IMAGE:4284020, mRNA, partial cds.
JD157215 - Sequence 138239 from Patent EP1572962.
JD555791 - Sequence 536815 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PROPIONMET-PWY - propanoyl CoA degradation I
PWY-5130 - 2-oxobutanoate degradation
PWY-5328 - superpathway of methionine degradation

Reactome (by CSHL, EBI, and GO)

Protein P05166 (Reactome details) participates in the following event(s):

R-HSA-2993447 HLCS biotinylates 6x(PCCA:PCCB)
R-HSA-71031 propionyl-CoA + CO2 + ATP <=> D-methylmalonyl-CoA + ADP + orthophosphate
R-HSA-196780 Biotin transport and metabolism
R-HSA-3371599 Defective HLCS causes multiple carboxylase deficiency
R-HSA-196849 Metabolism of water-soluble vitamins and cofactors
R-HSA-3323169 Defects in biotin (Btn) metabolism
R-HSA-71032 Propionyl-CoA catabolism
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-3296482 Defects in vitamin and cofactor metabolism
R-HSA-77289 Mitochondrial Fatty Acid Beta-Oxidation
R-HSA-1430728 Metabolism
R-HSA-5668914 Diseases of metabolism
R-HSA-8978868 Fatty acid metabolism
R-HSA-1643685 Disease
R-HSA-556833 Metabolism of lipids

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z2Z4, ENST00000251654.1, ENST00000251654.2, ENST00000251654.3, ENST00000251654.4, ENST00000251654.5, ENST00000251654.6, ENST00000251654.7, ENST00000251654.8, NM_000532, P05166, PCCB , PCCB_HUMAN, Q16813, Q96CX0, uc317fey.1, uc317fey.2
UCSC ID: ENST00000251654.9_6
RefSeq Accession: NM_000532.5
Protein: P05166 (aka PCCB_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PCCB:
propionic-a (Propionic Acidemia)

-  Gene Model Information
  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.