XYLB xylulokinase [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 3p22.2

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (38346785..38453041)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (38352536..38459118)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (38388276..38468677)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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 EBI GWAS CatalogPubMed
Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S3639 (e-PCR)
- UniSTS:45827

D8S2279 (e-PCR)
- UniSTS:473907

D3S1260 (e-PCR), detects polymorphism
- UniSTS:13680

D11S3114 (e-PCR)
- UniSTS:152207

D3S1260 (e-PCR), detects polymorphism
- UniSTS:35729

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-glucuronate catabolic process to D-xylulose 5-phosphate	TAS Traceable Author Statement more info
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 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

EC 2.7.1.17

NP_001336108.1

EC 2.7.1.17

NP_001336109.1

EC 2.7.1.17

NP_005099.2

EC 2.7.1.17

XP_011532627.1

EC 2.7.1.17

XP_011532629.1

EC 2.7.1.17

XP_011532630.1

EC 2.7.1.17

XP_011532631.1

EC 2.7.1.17

XP_011532632.1

EC 2.7.1.17

XP_016863085.1

EC 2.7.1.17

XP_016863086.1

EC 2.7.1.17

XP_024309618.1

EC 2.7.1.17

XP_047305337.1

EC 2.7.1.17

XP_047305338.1

EC 2.7.1.17

XP_047305339.1

EC 2.7.1.17

XP_047305340.1

EC 2.7.1.17

XP_054204638.1

EC 2.7.1.17

XP_054204639.1

EC 2.7.1.17

XP_054204640.1

EC 2.7.1.17

XP_054204641.1

EC 2.7.1.17

XP_054204642.1

EC 2.7.1.17

XP_054204643.1

EC 2.7.1.17

XP_054204644.1

EC 2.7.1.17

XP_054204645.1

EC 2.7.1.17

XP_054204646.1

EC 2.7.1.17

XP_054204647.1

EC 2.7.1.17

XP_054204648.1

EC 2.7.1.17

XP_054204649.1

EC 2.7.1.17

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)

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
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
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
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

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

38346785..38453041

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Related

ENSP00000496840.1, ENST00000650590.1
XM_047449384.1 → XP_047305340.1 xylulose kinase isoform X11
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
XM_017007596.2 → XP_016863085.1 xylulose kinase isoform X2
XM_047449382.1 → XP_047305338.1 xylulose kinase isoform X3
XM_047449381.1 → XP_047305337.1 xylulose kinase isoform X2
XM_017007597.2 → XP_016863086.1 xylulose kinase isoform X4