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XYLB xylulokinase [ Homo sapiens (human) ]

Gene ID: 9942, updated on 11-Apr-2024

Summary

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Official Symbol
XYLBprovided by HGNC
Official Full Name
xylulokinaseprovided by HGNC
Primary source
HGNC:HGNC:12839
See related
Ensembl:ENSG00000093217 MIM:604049; AllianceGenome:HGNC:12839
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
The protein encoded by this gene shares 22% sequence identity with Hemophilus influenzae xylulokinase, and even higher identity to other gene products in C.elegans (45%) and yeast (31-35%), which are thought to belong to a family of enzymes that include fucokinase, gluconokinase, glycerokinase and xylulokinase. These proteins play important roles in energy metabolism. [provided by RefSeq, Aug 2009]
Expression
Broad expression in liver (RPKM 5.0), kidney (RPKM 3.6) and 18 other tissues See more
Orthologs
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Genomic context

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Location:
3p22.2
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (38346785..38453041)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (38352536..38459118)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (38388276..38468677)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 22 member 14 Neighboring gene RNA, U6 small nuclear 235, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38358039-38358575 Neighboring gene DLEC1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38388053-38388884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38388885-38389716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38415461-38415962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38447285-38447785 Neighboring gene MPRA-validated peak4613 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38494963-38495462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14212 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38496067-38496650 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:38496651-38497235 Neighboring gene ACVR2B antisense RNA 1 Neighboring gene activin A receptor type 2B Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:38518043-38518542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19686 Neighboring gene exo/endonuclease G Neighboring gene D-dopachrome tautomerase pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Use of a repetitive seeding protocol to obtain diffraction-quality crystals of a putative human D-xylulokinase. Bunker RD, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2012 Oct 1. PMID 23027762, Free PMC Article
  2. Genomic structure of a novel human gene (XYLB) on chromosome 3p22-->p21.3 encoding a xylulokinase-like protein. Tamari M, et al. Cytogenet Cell Genet, 1998. PMID 9763671
  3. Structure and function of human xylulokinase, an enzyme with important roles in carbohydrate metabolism. Bunker RD, et al. J Biol Chem, 2013 Jan 18. PMID 23179721, Free PMC Article
  4. Pooled genetic analysis reveals an association of SNPs of only a few genes with risk predisposition to ischemic stroke in a Chinese population. Zhang Z, et al. IUBMB Life, 2015 Mar. PMID 25855559
  5. Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae. Smith JG, et al. Heart Rhythm, 2009 May. PMID 19389651, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Single nucleotide polymorphisms in nNOS, renalase, MTHFR, CELSR1 and XYLB genes were found significantly associated with ischemic stroke in Chinese patients.
    Title: Pooled genetic analysis reveals an association of SNPs of only a few genes with risk predisposition to ischemic stroke in a Chinese population.
  2. Xylulose binds to domain-I and ADP to domain-II, but in an open form of D-xylulokinase they are 10 A apart, implying that a large scale conformational change is required for catalysis.
    Title: Structure and function of human xylulokinase, an enzyme with important roles in carbohydrate metabolism.
  3. crystals of D-xylulokinase proved to be trigonal, with point-group symmetry 3 and unit-cell parameters a = b = 101.87, c = 158.85 A degrees
    Title: Use of a repetitive seeding protocol to obtain diffraction-quality crystals of a putative human D-xylulokinase.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetic determinants of P wave duration and PR segment.
EBI GWAS Catalog
Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10343, FLJ12539, FLJ22075

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables D-xylulokinase activity EXP
Inferred from Experiment
more info
 PubMed 
enables D-xylulokinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables D-xylulokinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in D-xylose metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in carbohydrate metabolic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in carbohydrate phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in generation of precursor metabolites and energy TAS
Traceable Author Statement
more info
 PubMed 
involved_in glucuronate catabolic process to xylulose 5-phosphate TAS
Traceable Author Statement
more info
  
involved_in phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in xylulose catabolic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in xylulose metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in xylulose metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
xylulose kinase
Names
D-xylulokinase
xylulokinase homolog (H. influenzae)
NP_001336107.1
NP_001336108.1
NP_001336109.1
NP_005099.2
XP_011532627.1
XP_011532629.1
XP_011532630.1
XP_011532631.1
XP_011532632.1
XP_016863085.1
XP_016863086.1
XP_024309618.1
XP_047305337.1
XP_047305338.1
XP_047305339.1
XP_047305340.1
XP_054204638.1
XP_054204639.1
XP_054204640.1
XP_054204641.1
XP_054204642.1
XP_054204643.1
XP_054204644.1
XP_054204645.1
XP_054204646.1
XP_054204647.1
XP_054204648.1
XP_054204649.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001349178.2 → NP_001336107.1  xylulose kinase isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AP006191, AP006193
    UniProtKB/TrEMBL
    A0A3B3IRM4
    Conserved Domains (1) summary
    cd07776
    Location:9 → 479
    FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases

  2. NM_001349179.2 → NP_001336108.1  xylulose kinase isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two alternate 5' exons and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus and has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AP006191, AP006193
    Conserved Domains (1) summary
    cl17037
    Location:1 → 342
    NBD_sugar-kinase_HSP70_actin; Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily

  3. NM_001349180.2 → NP_001336109.1  xylulose kinase isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an alternate exon in place of most of the 3' exons compared to variant 1. The resulting isoform (4) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AP006193
    Consensus CDS
    CCDS87062.1
    UniProtKB/TrEMBL
    C9J0N9
    Related
    ENSP00000412282.1, ENST00000427323.5
    Conserved Domains (1) summary
    cl17037
    Location:9 → 62
    NBD_sugar-kinase_HSP70_actin; Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily

  4. NM_005108.4 → NP_005099.2  xylulose kinase isoform 2

    See identical proteins and their annotated locations for NP_005099.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AP006191, AP006193
    Consensus CDS
    CCDS2678.1
    UniProtKB/Swiss-Prot
    B2RAW4, B4DDT2, B9EH64, O75191
    UniProtKB/TrEMBL
    A0A3B3IRM4
    Related
    ENSP00000207870.3, ENST00000207870.8
    Conserved Domains (2) summary
    PLN02669
    Location:11 → 535
    PLN02669; xylulokinase
    cd07776
    Location:9 → 479
    FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases

RNA

  1. NR_146068.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two alternate 5' exons compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AP006191, AP006193

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    38346785..38453041
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534327.3 → XP_011532629.1  xylulose kinase isoform X5

    UniProtKB/TrEMBL
    A0A3B3IRM4
    Conserved Domains (2) summary
    cd07776
    Location:9 → 479
    FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases
    COG1070
    Location:10 → 504
    XylB; Sugar (pentulose or hexulose) kinase [Carbohydrate transport and metabolism]

  2. XM_011534329.3 → XP_011532631.1  xylulose kinase isoform X7

    UniProtKB/TrEMBL
    A0A3B3IRM4
    Conserved Domains (2) summary
    cd07776
    Location:9 → 479
    FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases
    COG1070
    Location:10 → 520
    XylB; Sugar (pentulose or hexulose) kinase [Carbohydrate transport and metabolism]

  3. XM_011534328.4 → XP_011532630.1  xylulose kinase isoform X6

    UniProtKB/TrEMBL
    A0A3B3IRM4
    Conserved Domains (2) summary
    cd07776
    Location:9 → 479
    FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases
    COG1070
    Location:10 → 504
    XylB; Sugar (pentulose or hexulose) kinase [Carbohydrate transport and metabolism]

  4. XM_011534330.4 → XP_011532632.1  xylulose kinase isoform X8

    UniProtKB/TrEMBL
    A0A3B3IRM4
    Conserved Domains (2) summary
    PLN02669
    Location:11 → 516
    PLN02669; xylulokinase
    cd07776
    Location:9 → 479
    FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases

  5. XM_011534325.4 → XP_011532627.1  xylulose kinase isoform X1

    Conserved Domains (5) summary
    cd05482
    Location:678 → 764
    HIV_retropepsin_like; Retropepsins, pepsin-like aspartate proteases
    smart00443
    Location:789 → 822
    G_patch; glycine rich nucleic binding domain
    cd07776
    Location:9 → 479
    FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases
    COG1070
    Location:10 → 504
    XylB; Sugar (pentulose or hexulose) kinase [Carbohydrate transport and metabolism]
    cl00493
    Location:582 → 658
    trimeric_dUTPase; Trimeric dUTP diphosphatases

  6. XM_047449383.1 → XP_047305339.1  xylulose kinase isoform X9

    Related
    ENSP00000496840.1, ENST00000650590.1

  7. XM_047449384.1 → XP_047305340.1  xylulose kinase isoform X11

  8. XM_024453850.2 → XP_024309618.1  xylulose kinase isoform X10

    Conserved Domains (1) summary
    cd07776
    Location:1 → 413
    FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases

  9. XM_017007596.2 → XP_016863085.1  xylulose kinase isoform X2

  10. XM_047449382.1 → XP_047305338.1  xylulose kinase isoform X3

  11. XM_047449381.1 → XP_047305337.1  xylulose kinase isoform X2

  12. XM_017007597.2 → XP_016863086.1  xylulose kinase isoform X4

RNA

  1. XR_001740394.3 RNA Sequence

  2. XR_001740393.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    38352536..38459118
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348668.1 → XP_054204643.1  xylulose kinase isoform X5

  2. XM_054348670.1 → XP_054204645.1  xylulose kinase isoform X7

  3. XM_054348669.1 → XP_054204644.1  xylulose kinase isoform X6

  4. XM_054348671.1 → XP_054204646.1  xylulose kinase isoform X8

  5. XM_054348663.1 → XP_054204638.1  xylulose kinase isoform X1

  6. XM_054348672.1 → XP_054204647.1  xylulose kinase isoform X9

  7. XM_054348674.1 → XP_054204649.1  xylulose kinase isoform X11

  8. XM_054348673.1 → XP_054204648.1  xylulose kinase isoform X10

  9. XM_054348666.1 → XP_054204641.1  xylulose kinase isoform X2

  10. XM_054348665.1 → XP_054204640.1  xylulose kinase isoform X3

  11. XM_054348664.1 → XP_054204639.1  xylulose kinase isoform X2

  12. XM_054348667.1 → XP_054204642.1  xylulose kinase isoform X4

RNA

  1. XR_008486878.1 RNA Sequence

  2. XR_008486877.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75191.3 GenPept UniProtKB/Swiss-Prot:O75191

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