CARKD

Carbohydrate kinase domain containing
Identifiers
Symbols CARKD; FLJ10769; FLJ34548; FLJ52550; LP3298
External IDs MGI: 1913353 HomoloGene: 6333 GeneCards: CARKD Gene
Protein domains
Orthologs
Species Human Mouse
Entrez 55739 69225
Ensembl ENSG00000213995 ENSMUSG00000031505
UniProt Q8IW45 Q9CZ42
RefSeq (mRNA) NM_018210 NM_026995
RefSeq (protein) NP_060680 NP_081271
Location (UCSC) Chr 13:
111.27 – 111.29 Mb		 Chr 8:
11.5 – 11.51 Mb
PubMed search [1] [2]
Carbohydrate kinase
Crystallographic structure of a putative Bacillus subtilis carbohydrate kinase (rainbow colored, N-terminus = blue, C-terminus = red).[1]
Identifiers
Symbol Carb_kinase
Pfam PF01256
Pfam clan CL0118
InterPro IPR000631
PROSITE PDOC00806
SCOP 1kyh

Carbohydrate kinase domain containing protein, also known as CARKD, is a human protein of unknown function. The protein is conserved throughout many species, and has predicted orthologs through eukaryotes, bacteria, and archea.

Contents

Gene

CARKD is located on Chromosome 13 in humans. The following genes are near CARKD on the chromosome:[2]

Protein

Structure

This protein is part of the phosphomethylpyrimidine kinase: ribokinase / pfkB superfamily. This family is characterized by the presence of a domain shared by the family.[3] CARKD contains a carbohydrate kinase domain (Pfam PF01256).[3] This family is related to Pfam PF02210 and Pfam PF00294 implying that it also is a carbohydrate kinase.

Predicted properties

The following properties of CARKD were predicted using bioinformatic analysis:

Tissue distribution

CARKD appears to be ubiquitously expressed at high levels. Expression data in the human protein, and the mouse ortholog, indicate its expression in almost all tissues.[8][9] One peculiar expression pattern of CARKD is its differential expression through the development of oligodendrocytes. Its expression is lower in oligodendrocyte progenitor cells than in mature oligodendrocytes.[10]

Binding partners

The human protein apolipoprotein A-1 binding precursor (APOA1BP) was predicted to be a binding partner for CARKD.[11] This prediction is based on co-occurrence across genomes and co-expression. In addition to these data, the orthologs of CARKD in E. coli contain a domain similar to APOA1BP. This indicates that the two proteins are likely to have originated from a common evolutionary ancestor and, according to Rosetta stone analysis theory,[12] are likely interaction partners even in species such as humans where the two proteins are not produced as a single polypeptide.

Clinical signficance

Based on allele-specific expression of CARKD, CARKD may play a role in acute lymphoblastic leukemia.[13] In addition, microarray data indicates that CARKD is up-regulated in Glioblastoma multiforme tumors.[14]

References

  1. ^ PDB 1kyh; Zhang RG, Grembecka J, Vinokour E, Collart F, Dementieva I, Minor W, Joachimiak A (September 2002). "Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase". Journal of Structural Biology 139 (3): 161–70. doi:10.1016/S1047-8477(02)00532-4. PMC 2793413. PMID 12457846. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2793413. 
  2. ^ "UCSC Genome Browser: CARKD". http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr13:110066009-110090343&hgsid=130989312&refGene=pack&hgFind.matches=NM_018210,. 
  3. ^ a b "CDD: Conserved Domain Database (NCBI)". http://www.ncbi.nlm.nih.gov/sites/entrez?itool=gene_full_report&DbFrom=gene&Cmd=Link&LinkName=gene_cdd&IdsFromResult=55739. 
  4. ^ Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S (March 1992). "Methods and algorithms for statistical analysis of protein sequences". Proceedings of the National Academy of Sciences of the United States of America 89 (6): 2002–6. doi:10.1073/pnas.89.6.2002. PMC 48584. PMID 1549558. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=48584. 
  5. ^ a b "PI Program (Isoelectric Point Prediction)". http://www.embl-heidelberg.de/cgi/pi-wrapper.pl. 
  6. ^ a b "UniProt Database". http://www.uniprot.org/uniprot/Q8IW45. 
  7. ^ Bendtsen JD, Nielsen H, von Heijne G, Brunak S (July 2004). "Improved prediction of signal peptides: SignalP 3.0". Journal of Molecular Biology 340 (4): 783–95. doi:10.1016/j.jmb.2004.05.028. PMID 15223320. 
  8. ^ "Unigene (EST profile viewer) Human CARKD". http://www.ncbi.nlm.nih.gov/UniGene/ESTProfileViewer.cgi?uglist=Hs.408324. 
  9. ^ "Unigene (EST profile viewer) Mouse CARKD". http://www.ncbi.nlm.nih.gov/UniGene/ESTProfileViewer.cgi?uglist=Mm.64911. 
  10. ^ Nielsen JA, Maric D, Lau P, Barker JL, Hudson LD (September 2006). "Identification of a novel oligodendrocyte cell adhesion protein using gene expression profiling". Journal of Neuroscience 26 (39): 9881–91. doi:10.1523/JNEUROSCI.2246-06.2006. PMC 1613258. PMID 17005852. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1613258. 
  11. ^ "STRING: Known and Predicted Protein-Protein Interactions". http://string.embl.de/. 
  12. ^ The Rosetta stone method, Date SV. Methods Mol Biol. 2008;453:169-80.
  13. ^ Milani L, Lundmark A, Nordlund J, Kiialainen A, Flaegstad T, Jonmundsson G, Kanerva J, Schmiegelow K, Gunderson KL, Lönnerholm G, Syvänen AC (January 2009). "Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation". Genome Research 19 (1): 1–11. doi:10.1101/gr.083931.108. PMC 2612957. PMID 18997001. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2612957. 
  14. ^ Ruano Y, Mollejo M, Ribalta T, Fiaño C, Camacho FI, Gómez E, de Lope AR, Hernández-Moneo JL, Martínez P, Meléndez B (2006). "Identification of novel candidate target genes in amplicons of Glioblastoma multiforme tumors detected by expression and CGH microarray profiling". Molecular Cancer 5 (1): 39. doi:10.1186/1476-4598-5-39. PMC 1592108. PMID 17002787. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1592108.