CARKD

Last updated
NAXD
Identifiers
Aliases NAXD , LP3298, CARKD, NAD(P)HX dehydratase, PEBEL2
External IDs OMIM: 615910 MGI: 1913353 HomoloGene: 6333 GeneCards: NAXD
Orthologs
SpeciesHumanMouse
Entrez

55739

69225

Ensembl

ENSG00000213995

ENSMUSG00000031505

UniProt

Q8IW45

Q9CZ42

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
NP_001280590
NP_081271
NP_001389565

Location (UCSC) Chr 13: 110.62 – 110.64 Mb Chr 8: 11.55 – 11.56 Mb
PubMed search [3] [4]
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). [5]
Identifiers
SymbolCarb_kinase
Pfam PF01256
Pfam clan CL0118
InterPro IPR000631
PROSITE PDOC00806
SCOP2 1kyh / SCOPe / SUPFAM
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
PDB 1kyh ​, 2ax3 ​

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. [6] The protein is conserved throughout many species, and has predicted orthologs through eukaryotes, bacteria, and archea.

Contents

Structure

Gene

Human CARKD gene has 10 exons and resides on Chromosome 13 at q34. The following genes are near CARKD on the chromosome: [7]

Protein

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. [8] CARKD contains a carbohydrate kinase domain (Pfam PF01256). [8] 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:

Function

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. [13] [14] 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. [15]

Binding partners

The human protein apolipoprotein A-1 binding precursor (APOA1BP) was predicted to be a binding partner for CARKD. [16] 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, [17] are likely interaction partners even in species such as humans where the two proteins are not produced as a single polypeptide.

Clinical significance

Based on allele-specific expression of CARKD, CARKD may play a role in acute lymphoblastic leukemia. [18] In addition, microarray data indicates that CARKD is up-regulated in Glioblastoma multiforme tumors. [19]

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References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000213995 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000031505 - Ensembl, May 2017
  3. ↑ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ↑ 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.
  6. ↑ 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.
  7. ↑ "UCSC Genome Browser: CARKD".
  8. 1 2 "CDD: Conserved Domain Database (NCBI)".
  9. ↑ 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. Bibcode:1992PNAS...89.2002B. doi: 10.1073/pnas.89.6.2002 . PMC   48584 . PMID   1549558.
  10. 1 2 "PI Program (Isoelectric Point Prediction)". Archived from the original on 2008-10-26.
  11. 1 2 "UniProt Database".
  12. ↑ 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. CiteSeerX   10.1.1.165.2784 . doi:10.1016/j.jmb.2004.05.028. PMID   15223320.
  13. ↑ "Unigene (EST profile viewer) Human CARKD".
  14. ↑ "Unigene (EST profile viewer) Mouse CARKD".
  15. ↑ 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.
  16. ↑ "STRING: Known and Predicted Protein-Protein Interactions".
  17. ↑ Date SV (2008). "The Rosetta Stone Method". Bioinformatics. Methods in Molecular Biology. Vol. 453. Totowa, NJ: Humana Press. pp. 169–80. doi:10.1007/978-1-60327-429-6_7. ISBN   978-1-60327-428-9. PMID   18712302.
  18. ↑ 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.
  19. ↑ 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.
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