CARKD

From Wikipedia, the free encyclopedia
Jump to: navigation, search
Carbohydrate kinase domain containing
Identifiers
Symbols CARKD ; LP3298
External IDs MGI1913353 HomoloGene6333 GeneCards: CARKD Gene
EC number 4.2.1.93
Protein domains
CARKDschematic.jpg
Orthologs
Species Human Mouse
Entrez 55739 69225
Ensembl ENSG00000213995 ENSMUSG00000031505
UniProt Q8IW45 Q9CZ42
RefSeq (mRNA) NM_001242881 NM_001190357
RefSeq (protein) NP_001229810 NP_001177286
Location (UCSC) Chr 13:
111.27 – 111.29 Mb
Chr 8:
11.5 – 11.51 Mb
PubMed search [1] [2]
Carbohydrate kinase
Carbohydrate kinase 1KYH.png
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
SUPERFAMILY 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.

Gene[edit]

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

  • COL4A2: A2 Subunit of type IV collagen
  • RAB20: Potential regulator of Connexin 43 trafficking.
  • CARS2: Mitochondrial Cystienyl-tRNA Synthetase 2
  • ING1: Tumor-Suppressor Protein

Protein[edit]

Structure[edit]

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[edit]

The following properties of CARKD were predicted using bioinformatic analysis:

Tissue distribution[edit]

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[edit]

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 significance[edit]

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[edit]

  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. 
  2. ^ "UCSC Genome Browser: CARKD". 
  3. ^ a b "CDD: Conserved Domain Database (NCBI)". 
  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. 
  5. ^ a b "PI Program (Isoelectric Point Prediction)". 
  6. ^ a b "UniProt Database". 
  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". 
  9. ^ "Unigene (EST profile viewer) Mouse CARKD". 
  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. 
  11. ^ "STRING: Known and Predicted Protein-Protein Interactions". 
  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. 
  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.