NAA60 N-alpha-acetyltransferase 60, NatF catalytic subunit [Homo sapiens (human)] - Gene

Summary

Official Symbol: NAA60provided by HGNC
Official Full Name: N-alpha-acetyltransferase 60, NatF catalytic subunitprovided by HGNC
Primary source: HGNC:HGNC:25875
See related: Ensembl:ENSG00000122390 MIM:614246; AllianceGenome:HGNC:25875
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: HAT4; NatF; IBGC9; NAT15; hNaa60
Summary: This gene encodes an enzyme that localizes to the Golgi apparatus, where it transfers an acetyl group to the N-terminus of free proteins. This enzyme acts on histones, and its activity is important for chromatin assembly and chromosome integrity. Alternative splicing and the use of alternative promoters results in multiple transcript variants. The upstream promoter is located in a differentially methylated region (DMR) and undergoes imprinting; transcript variants originating from this position are expressed from the maternal allele. [provided by RefSeq, Nov 2015]
Expression: Ubiquitous expression in kidney (RPKM 15.2), duodenum (RPKM 14.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p13.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (3443611..3486963)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (3470880..3514228)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (3493611..3536963)

Chromosome 16 - NC_000016.10 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Biallelic NAA60 variants with impaired n-terminal acetylation capacity cause autosomal recessive primary familial brain calcifications.
Title: Biallelic NAA60 variants with impaired n-terminal acetylation capacity cause autosomal recessive primary familial brain calcifications.
NAA60 (HAT4): the newly discovered bi-functional Golgi member of the acetyltransferase family.
Title: NAA60 (HAT4): the newly discovered bi-functional Golgi member of the acetyltransferase family.
Results from a study on gene expression variability markers in early-stage human embryos shows that NAA60 (NAT15) is a putative expression variability marker for the 3-day, 8-cell embryo stage.
Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
The hNaa60 protein contains an amphipathic helix following its GNAT domain that may contribute to Golgi localization of hNaa60, and the beta7-beta8 hairpin adopted different conformations in the hNaa60(1-242) and hNaa60(1-199) crystal structures.
Title: Structure and function of human Naa60 (NatF), a Golgi-localized bi-functional acetyltransferase.
analysis of the mode of cytosolic Naa60 anchoring to the Golgi apparatus, most likely occurring post-translationally and specifically facilitating post-translational N-terminal acetylation of many transmembrane proteins
Title: Molecular determinants of the N-terminal acetyltransferase Naa60 anchoring to the Golgi membrane.
Knockdown of the N-terminal acetyltransferase Naa60 compromises Golgi ribbon integrity.
Title: Holding it together: Naa60 at the Golgi.
The first crystal structure of the N-terminal acetyltransferase Naa60 reveals two elongated loops important for substrate-specific binding not found in other NAT structures.
Title: Crystal Structure of the Golgi-Associated Human Nα-Acetyltransferase 60 Reveals the Molecular Determinants for Substrate-Specific Acetylation.
Naa60 is necessary for maintenance of the Golgi ribbon through its Nt-acetylation of substrate protein(s) that is/are involved in Golgi ribbon structural and/or functional organization.
Title: An organellar nα-acetyltransferase, naa60, acetylates cytosolic N termini of transmembrane proteins and maintains Golgi integrity.
Naa60 is an N-terminal acetyltransferase defined as NatF. Human and Drosophila melanogaster Naa60 acetylate Met-Lys- and other Met-starting N-termini. In Drosophila cells, NAA60 knockdown induced chromosomal segregation defects.
Title: NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation.
HAT4 is an important player in the organization and function of the genome and may contribute to the diversity and complexity of higher eukaryotic organisms [HAT4]
Title: HAT4, a Golgi apparatus-anchored B-type histone acetyltransferase, acetylates free histone H4 and facilitates chromatin assembly.

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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
Genome-wide association study of ancestry-specific TB risk in the South African Coloured population. 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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables histone H2AK5 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AK9 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BK12 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BK5 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K122 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K14 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K18 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K23 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K27 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K36 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K56 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H4 acetyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H4K12 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H4K16 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H4K5 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H4K8 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone acetyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables peptide alpha-N-acetyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables peptide alpha-N-acetyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables peptide-methionine-alpha-N-acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in N-terminal peptidyl-methionine acetylation	IDA Inferred from Direct Assay more info	PubMed
involved_in N-terminal protein amino acid acetylation	IDA Inferred from Direct Assay more info	PubMed
involved_in cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromosome segregation	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromosome segregation	ISS Inferred from Sequence or Structural Similarity more info
involved_in nucleosome assembly	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in Golgi membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: N-alpha-acetyltransferase 60

Names: N-acetyltransferase 15 (GCN5-related, putative); N-alpha-acetyltransferase F; epididymis secretory sperm binding protein; histone acetyltransferase type B protein 4

NP_001077069.1

EC 2.3.1.259

EC 2.3.1.48

NP_001077070.1

EC 2.3.1.259

EC 2.3.1.48

NP_001304022.1

EC 2.3.1.259

EC 2.3.1.48

NP_001304023.1

EC 2.3.1.259

EC 2.3.1.48

NP_001304024.1

EC 2.3.1.259

EC 2.3.1.48

NP_001304025.1

EC 2.3.1.259

EC 2.3.1.48

NP_001304026.1

EC 2.3.1.259

EC 2.3.1.48

NP_001304027.1

EC 2.3.1.259

EC 2.3.1.48

NP_079121.1

EC 2.3.1.259

EC 2.3.1.48

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.

Genomic

NG_045230.1 RefSeqGene

Range

5070..48343

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1067

mRNA and Protein(s)

NM_001083600.3 → NP_001077069.1 N-alpha-acetyltransferase 60 isoform a

See identical proteins and their annotated locations for NP_001077069.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents use of an alternate promoter and differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same isoform (a).

Source sequence(s)

AC004224, AC025283, AK130792, BC011267, BG472911, DC339939

Consensus CDS

CCDS45396.1

UniProtKB/Swiss-Prot

B3KRQ0, B4DLZ0, B4DPZ8, B4DYC4, D3DUC2, E7EQ65, Q6IA31, Q6UX26, Q9H7X0

UniProtKB/TrEMBL

A0A384NYU5

Related

ENSP00000458667.1, ENST00000575076.5

Conserved Domains (1) summary

pfam00583
Location:23 → 155

Acetyltransf_1; Acetyltransferase (GNAT) family
NM_001083601.3 → NP_001077070.1 N-alpha-acetyltransferase 60 isoform a

See identical proteins and their annotated locations for NP_001077070.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. This variant may be expressed predominantly from the maternal allele (PMID:21593219). Variants 1, 2, and 3 encode the same isoform (a).

Source sequence(s)

AC004224, AL833594, BC011267, BG472911, DC401343

Consensus CDS

CCDS45396.1

UniProtKB/Swiss-Prot

B3KRQ0, B4DLZ0, B4DPZ8, B4DYC4, D3DUC2, E7EQ65, Q6IA31, Q6UX26, Q9H7X0

UniProtKB/TrEMBL

A0A384NYU5

Related

ENSP00000385903.4, ENST00000407558.9

Conserved Domains (1) summary

pfam00583
Location:23 → 155

Acetyltransf_1; Acetyltransferase (GNAT) family
NM_001317093.1 → NP_001304022.1 N-alpha-acetyltransferase 60 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains multiple differences in the 5' coding region and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded isoform (b) has a longer, distinct N-terminus compared to isoform a.

Source sequence(s)

AC004224, AK297219, BC011267, BG472911, DC401343

Consensus CDS

CCDS81937.1

UniProtKB/Swiss-Prot

Q9H7X0

Related

ENSP00000401237.2, ENST00000424546.6

Conserved Domains (2) summary

COG0456
Location:44 → 173

RimI; Ribosomal protein S18 acetylase RimI and related acetyltransferases [Translation, ribosomal structure and biogenesis]

pfam00583
Location:86 → 163

Acetyltransf_1; Acetyltransferase (GNAT) family
NM_001317094.2 → NP_001304023.1 N-alpha-acetyltransferase 60 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (5) represents use of an alternate promoter and contains multiple differences in both UTRs and in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (c) is shorter than isoform a.

Source sequence(s)

AC004224, AK311524, BC011267, DC339939

Consensus CDS

CCDS81940.1

UniProtKB/TrEMBL

I3L153

Related

ENSP00000461703.1, ENST00000576916.5
NM_001317095.2 → NP_001304024.1 N-alpha-acetyltransferase 60 isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (6) represents use of an alternate promoter and contains multiple differences in both UTRs and in the coding region, compared to variant 1. It initiates translation at a downstream start codon. The encoded isoform (d) has a shorter N-terminus than isoform a.

Source sequence(s)

AC004224, AK092005, BC011267, BU501490

Consensus CDS

CCDS81941.1

UniProtKB/Swiss-Prot

Q9H7X0

Related

ENSP00000354108.5, ENST00000360862.9

Conserved Domains (1) summary

pfam00583
Location:12 → 90

Acetyltransf_1; Acetyltransferase (GNAT) family
NM_001317096.2 → NP_001304025.1 N-alpha-acetyltransferase 60 isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (7) represents use of an alternate promoter and contains multiple differences in both UTRs and in the coding region, resulting in a frameshift, compared to variant 1. The encoded isoform (e) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AC004224, AK298566, BC011267, BU501490, DC339939

Consensus CDS

CCDS81938.1

UniProtKB/Swiss-Prot

Q9H7X0

Related

ENSP00000405873.3, ENST00000421765.7
NM_001317097.2 → NP_001304026.1 N-alpha-acetyltransferase 60 isoform f

Status: REVIEWED

Description

Transcript Variant: This variant (8) represents use of an alternate promoter and contains multiple differences in both UTRs and in the coding region, resulting in a frameshift, compared to variant 1. The encoded isoform (f) has a distinct C-terminus and is shorter than isoform a. Variants 8 and 9 encode the same isoform (f).

Source sequence(s)

AC004224, AK302361, BC011267, BU501490, DC339939

Consensus CDS

CCDS81939.1

UniProtKB/Swiss-Prot

Q9H7X0

Related

ENSP00000461730.1, ENST00000572942.5
NM_001317098.2 → NP_001304027.1 N-alpha-acetyltransferase 60 isoform f

Status: REVIEWED

Description

Transcript Variant: This variant (9) represents use of an alternate promoter and contains multiple differences in the 5' UTR and the coding region, resulting in a frameshift, compared to variant 1. The encoded isoform (f) has a distinct C-terminus and is shorter than isoform a. Variants 8 and 9 encode the same isoform (f).

Source sequence(s)

AC004224, BC011267, BG472911, BG822206, DC339939

Consensus CDS

CCDS81939.1

UniProtKB/Swiss-Prot

Q9H7X0

Related

ENSP00000460763.1, ENST00000570819.5
NM_024845.4 → NP_079121.1 N-alpha-acetyltransferase 60 isoform a

See identical proteins and their annotated locations for NP_079121.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) represents use of an alternate promoter, differs in the 5' UTR, and uses an alternate splice site in the 3' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same isoform (a).

Source sequence(s)

AC004224, AK024216, BC011267, BU501490, DC339939

Consensus CDS

CCDS45396.1

UniProtKB/Swiss-Prot

B3KRQ0, B4DLZ0, B4DPZ8, B4DYC4, D3DUC2, E7EQ65, Q6IA31, Q6UX26, Q9H7X0

UniProtKB/TrEMBL

A0A384NYU5

Related

ENSP00000393224.2, ENST00000414063.6

Conserved Domains (1) summary

pfam00583
Location:23 → 155

Acetyltransf_1; Acetyltransferase (GNAT) family