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PSMB9 proteasome 20S subunit beta 9 [ Homo sapiens (human) ]

Gene ID: 5698, updated on 10-Dec-2024

Summary

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Official Symbol
PSMB9provided by HGNC
Official Full Name
proteasome 20S subunit beta 9provided by HGNC
Primary source
HGNC:HGNC:9546
See related
Ensembl:ENSG00000240065 MIM:177045; AllianceGenome:HGNC:9546
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
Also known as
LMP2; PRAAS3; PRAAS6; PSMB6i; RING12; beta1i
Summary
The proteasome is a multicatalytic proteinase complex with a highly ordered ring-shaped 20S core structure. The core structure is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a member of the proteasome B-type family, also known as the T1B family, that is a 20S core beta subunit. This gene is located in the class II region of the MHC (major histocompatibility complex). Expression of this gene is induced by gamma interferon and this gene product replaces catalytic subunit 1 (proteasome beta 6 subunit) in the immunoproteasome. Proteolytic processing is required to generate a mature subunit. [provided by RefSeq, Mar 2010]
Expression
Broad expression in spleen (RPKM 72.3), lymph node (RPKM 60.9) and 24 other tissues See more
Orthologs
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Genomic context

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See PSMB9 in Genome Data Viewer
Location:
6p21.32
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32854192..32859851)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (32675567..32681226)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32821969..32827628)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene PSMB8 antisense RNA 1 (head to head) Neighboring gene proteasome 20S subunit beta 8 Neighboring gene transporter 1, ATP binding cassette subfamily B member Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 2 pseudogene 1 Neighboring gene uncharacterized LOC100294145 Neighboring gene major histocompatibility complex, class I, Z (pseudogene)

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. Transcriptome-wide association study identifies PSMB9 as a susceptibility gene for coal workers' pneumoconiosis. Yuan J, et al. Environ Toxicol, 2022 Aug. PMID 35506645
  2. C-terminal domain of the Epstein-Barr virus LMP2A membrane protein contains a clustering signal. Matskova L, et al. J Virol, 2001 Nov. PMID 11602734, Free PMC Article
  3. A novel diagnostic biomarker for human uterine leiomyosarcoma: PSMB9/β1i. Hayashi T, et al. Chin Clin Oncol, 2017 Apr. PMID 28482675
  4. Association of MHC region SNPs with irritant susceptibility in healthcare workers. Yucesoy B, et al. J Immunotoxicol, 2016 Sep. PMID 27258892, Free PMC Article
  5. LMP2, a novel immunohistochemical marker to distinguish renal oncocytoma from the eosinophilic variant of chromophobe renal cell carcinoma. Zheng G, et al. Exp Mol Pathol, 2013 Feb. PMID 22705098, Free PMC Article

See all (130) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Deciphering the tumor-suppressive role of PSMB9 in melanoma through multi-omics and single-cell transcriptome analyses.
    Title: Deciphering the tumor-suppressive role of PSMB9 in melanoma through multi-omics and single-cell transcriptome analyses.
  2. Immunohistochemical Identification and Assessment of the Location of Immunoproteasome Subunits LMP2 and LMP7 in Acquired Cholesteatoma.
    Title: Immunohistochemical Identification and Assessment of the Location of Immunoproteasome Subunits LMP2 and LMP7 in Acquired Cholesteatoma.
  3. Immunoproteasome-specific subunit PSMB9 induction is required to regulate cellular proteostasis upon mitochondrial dysfunction.
    Title: Immunoproteasome-specific subunit PSMB9 induction is required to regulate cellular proteostasis upon mitochondrial dysfunction.
  4. Variants in PSMB9 and FGR differentially affect Parkinson's disease risk in GBA and LRRK2 mutation carriers.
    Title: Variants in PSMB9 and FGR differentially affect Parkinson's disease risk in GBA and LRRK2 mutation carriers.
  5. Increased expression of the immunoproteasome subunits PSMB8 and PSMB9 by cancer cells correlate with better outcomes for triple-negative breast cancers.
    Title: Increased expression of the immunoproteasome subunits PSMB8 and PSMB9 by cancer cells correlate with better outcomes for triple-negative breast cancers.
  6. Identification of PSMB9 and CXCL13 as Immune-related Diagnostic Markers for Rheumatoid Arthritis by Machine Learning.
    Title: Identification of PSMB9 and CXCL13 as Immune-related Diagnostic Markers for Rheumatoid Arthritis by Machine Learning.
  7. Transcriptome-wide association study identifies PSMB9 as a susceptibility gene for coal workers' pneumoconiosis.
    Title: Transcriptome-wide association study identifies PSMB9 as a susceptibility gene for coal workers' pneumoconiosis.
  8. Heterozygous missense variant of the proteasome subunit beta-type 9 causes neonatal-onset autoinflammation and immunodeficiency.
    Title: Heterozygous missense variant of the proteasome subunit β-type 9 causes neonatal-onset autoinflammation and immunodeficiency.
  9. Successful treatment of a novel type I interferonopathy due to a de novo PSMB9 gene mutation with a Janus kinase inhibitor.
    Title: Successful treatment of a novel type I interferonopathy due to a de novo PSMB9 gene mutation with a Janus kinase inhibitor.
  10. The dominant model of LMP2 CfoI might be a risk factor for IDDM in Asian population. Whereas, the allelic and dominant models of LMP7 G37360T might be protective factors for IDDM in Caucasian population
    Title: The genetic association between LMP2 and LMP7 polymorphisms and susceptibility of insulin dependent diabetes mellitus: A meta-analysis.
Submit: New GeneRIF Correction See all GeneRIFs (54)

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

Associated conditions

Description Tests
Proteasome-associated autoinflammatory syndrome 3
MedGen: C4747850 OMIM: 617591 GeneReviews: Not available
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EBI GWAS Catalog

Description
A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population.
EBI GWAS Catalog
Genome-wide association study identifies susceptibility loci for IgA nephropathy.
EBI GWAS Catalog
Novel genetic variants associated with lumbar disc degeneration in northern Europeans: a meta-analysis of 4600 subjects.
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)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat represses transcription of the LMP2 gene by competing with STAT1 (signal transducer and activator of transcription 1) for binding to IRF-1 (interferon-regulatory factor-1) at the LMP2 promoter PubMed
tat HIV-1 Tat binds to the alpha2, alpha4, alpha6, alpha7, beta1, beta2, beta3, beta5, beta6, beta7, LMP7/beta5i, and MECL1/beta2i subunits of the proteasome 20 S core structure and can inhibit cellular proteasome function PubMed
tat HIV-1 Tat slightly enhances the activity of the purified 26 S proteasome PubMed
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human proteasome (prosome, macropain) subunit, beta type, 9 (PSMB9) at amino acid residues 25-26 by the HIV-1 protease PubMed

Go to the HIV-1, Human Interaction Database

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

  • MGC70470

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables threonine-type endopeptidase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in immune system process IEA
Inferred from Electronic Annotation
more info
  
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of cysteine-type endopeptidase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of proteasome complex TAS
Traceable Author Statement
more info
 PubMed 
part_of proteasome core complex ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of proteasome core complex, beta-subunit complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of proteasome core complex, beta-subunit complex ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of spermatoproteasome complex ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
proteasome subunit beta type-9
Names
large multifunctional peptidase 2
low molecular mass protein 2
macropain chain 7
multicatalytic endopeptidase complex chain 7
proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional peptidase 2)
proteasome catalytic subunit 1i
proteasome chain 7
proteasome subunit beta 6i
proteasome subunit beta 9
proteasome subunit beta-1i
proteasome subunit beta1i
proteasome-related gene 2
really interesting new gene 12 protein
NP_002791.1

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_002800.5 → NP_002791.1  proteasome subunit beta type-9 precursor

    See identical proteins and their annotated locations for NP_002791.1

    Status: REVIEWED

    Source sequence(s)
    AI310206, BC065513, BF513693
    Consensus CDS
    CCDS4759.1
    UniProtKB/Swiss-Prot
    B0V0T1, P28065, Q16523, Q5JNW4
    UniProtKB/TrEMBL
    A0A1U9X8D7, A0A1U9X8E2, A0A1U9X8E3
    Related
    ENSP00000363993.2, ENST00000374859.3
    Conserved Domains (1) summary
    cd03762
    Location:21 → 207
    proteasome_beta_type_6; proteasome beta type-6 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that ...

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

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    32854192..32859851
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    4159057..4164713
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    4266391..4272052
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    4097762..4103421
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    4273545..4279205
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    4153261..4158917
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    4048480..4054140
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    4253444..4259100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    32675567..32681226
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_148954.2: Suppressed sequence

    Description
    NM_148954.2: This RefSeq was permanently suppressed because it represents a poorly supported variant with non-consensus splice sites.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P28065.2 GenPept UniProtKB/Swiss-Prot:P28065

Gene LinkOut

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