CARKD

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NAXD
Identifiers
Aliases NAXD, LP3298, CARKD, NAD(P)HX dehydratase
External IDs MGI: 1913353 HomoloGene: 6333 GeneCards: NAXD
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001242881
NM_001242882
NM_001242883
NM_018210

NM_001190357
NM_001293661
NM_026995

RefSeq (protein)

NP_001229810
NP_001229811
NP_001229812
NP_060680

NP_001177286.1
NP_081271.2
NP_001177286
NP_001280590
NP_081271

Location (UCSC) Chr 13: 110.62 – 110.64 Mb Chr 8: 11.5 – 11.51 Mb
PubMed search [1] [2]
Wikidata
View/Edit Human View/Edit Mouse
Carbohydrate kinase
Carbohydrate kinase 1KYH.png
Crystallographic structure of a putative Bacillus subtilis carbohydrate kinase (rainbow colored, N-terminus = blue, C-terminus = red).[3]
Identifiers
Symbol Carb_kinase
Pfam PF01256
Pfam clan CL0118
InterPro IPR000631
PROSITE PDOC00806
SCOP 1kyh
SUPERFAMILY 1kyh

Carbohydrate kinase domain containing protein (abbreviated as CARKD), encoded by CARKD gene, is a human protein of unknown function. The CARKD gene encodes proteins with a predicted mitochondrial propeptide (mCARKD), a signal peptide (spCARKD) or neither of them (cCARKD). Confocal microscopy analysis of transfected CHO (Chinese-hamster ovary) cells indicated that cCARKD remains in the cytosol, whereas mCARKD and spCARKD are targeted to the mitochondria and the endoplasmic reticulum respectively.[4] The protein is conserved throughout many species, and has predicted orthologs through eukaryotes, bacteria, and archea.

Structure[edit]

Gene[edit]

Human CARKD gene has 10 exons and resides on Chromosome 13 at q34. The following genes are near CARKD on the chromosome:[5]

  • 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]

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.[6] CARKD contains a carbohydrate kinase domain (Pfam PF01256).[6] 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:

Function[edit]

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.[11][12] 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.[13]

Binding partners[edit]

The human protein apolipoprotein A-1 binding precursor (APOA1BP) was predicted to be a binding partner for CARKD.[14] 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,[15] 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.[16] In addition, microarray data indicates that CARKD is up-regulated in Glioblastoma multiforme tumors.[17]

References[edit]

  1. ^ "Human PubMed Reference:". 
  2. ^ "Mouse PubMed Reference:". 
  3. ^ 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 2793413Freely accessible. PMID 12457846. 
  4. ^ Marbaix, AY; Tyteca, D; Niehaus, TD; Hanson, AD; Linster, CL; Van Schaftingen, E (15 May 2014). "Occurrence and subcellular distribution of the NADPHX repair system in mammals.". The Biochemical Journal. 460 (1): 49–58. doi:10.1042/bj20131482. PMID 24611804. 
  5. ^ "UCSC Genome Browser: CARKD". 
  6. ^ a b "CDD: Conserved Domain Database (NCBI)". 
  7. ^ 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 48584Freely accessible. PMID 1549558. 
  8. ^ a b "PI Program (Isoelectric Point Prediction)". 
  9. ^ a b "UniProt Database". 
  10. ^ 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. 
  11. ^ "Unigene (EST profile viewer) Human CARKD". 
  12. ^ "Unigene (EST profile viewer) Mouse CARKD". 
  13. ^ 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 1613258Freely accessible. PMID 17005852. 
  14. ^ "STRING: Known and Predicted Protein-Protein Interactions". 
  15. ^ Date SV (2008). "The Rosetta stone method". Methods Mol Biol. 453: 169–80. 
  16. ^ 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 2612957Freely accessible. PMID 18997001. 
  17. ^ 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 1592108Freely accessible. PMID 17002787. 

External links[edit]