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36  structures 4216  species 2  interactions 4484  sequences 18  architectures

Family: Carb_kinase (PF01256)

Summary: Carbohydrate kinase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "CARKD". More...

CARKD Edit Wikipedia article

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. 

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Carbohydrate kinase Provide feedback

This family is related to PF02110 and PF00294 implying that it also is a carbohydrate kinase. (personal obs Yeats C).

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000631

This family is related to Hydroxyethylthiazole kinase INTERPRO and PfkB carbohydrate kinase INTERPRO implying that it also a carbohydrate kinase.

Several uncharacterised proteins have been shown to share regions of similarities, including yeast chromosome XI hypothetical protein YKL151c; Caenorhabditis elegans hypothetical protein R107.2; Escherichia coli hypothetical protein yjeF; Bacillus subtilis hypothetical protein yxkO; Helicobacter pylori hypothetical protein HP1363; Mycobacterium tuberculosis hypothetical protein MtCY77.05c; Mycobacterium leprae hypothetical protein B229_C2_201; Synechocystis sp. (strain PCC 6803) hypothetical protein sll1433; and Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical protein MJ1586. These are proteins of about 30 to 40 kDa whose central region is well conserved.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Ribokinase (CL0118), which has the following description:

All of these enzymes are phosphotransferases that have an alcohol group as an acceptor (EC:2.7.1.-). However, 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMPP kinase) catalyses two phosphorylation reactions: one to a hydroxymethyl group of hydroxymethyl pyrimidine (HMP) and the second to the phosphomethyl group of HMPP [1]. The common structural feature for the enzymes in this superfamily is a central eight-stranded sheet that is flanked by eight structurally conserved helices, five on one side and three on the other [1]. The active site is located in a shallow groove along one edge of the sheet, with the phosphate acceptor hydroxyl group and -phosphate of ATP close together in the middle of the groove, and substrate and ATP binding at the ends [1].

The clan contains the following 6 members:

ADP_PFK_GK Aldolase_2 Carb_kinase HK PfkB Phos_pyr_kin

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(9)
Full
(4484)
Representative proteomes NCBI
(6104)
Meta
(1631)
RP15
(429)
RP35
(805)
RP55
(1066)
RP75
(1246)
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  Seed
(9)
Full
(4484)
Representative proteomes NCBI
(6104)
Meta
(1631)
RP15
(429)
RP35
(805)
RP55
(1066)
RP75
(1246)
Alignment:
Format:
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Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(9)
Full
(4484)
Representative proteomes NCBI
(6104)
Meta
(1631)
RP15
(429)
RP35
(805)
RP55
(1066)
RP75
(1246)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: UPF0031; carb_kinase;
Type: Family
Author: Finn RD, Bateman A, Yeats C
Number in seed: 9
Number in full: 4484
Average length of the domain: 239.10 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 56.40 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 242
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Carb_kinase YjeF_N

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Carb_kinase domain has been found. There are 36 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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