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8  structures 1569  species 0  interactions 3824  sequences 65  architectures

Family: HYPK_UBA (PF19026)

Summary: HYPK UBA domain

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

HYPK UBA domain Provide feedback

This entry represents the UBA domain [1] found at the C-terminus of the HYPK protein and its homologues. This domain in HYPK mediates a protein interaction with the Naa15 C-terminus [1].

Literature references

  1. Gottlieb L, Marmorstein R;, Structure. 2018;26:925-935.: Structure of Human NatA and Its Regulation by the Huntingtin Interacting Protein HYPK. PUBMED:29754825 EPMC:29754825


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR044034

In eukaryotes, the Nascent polypeptide-Associated Complex (NAC) is a heterodimeric cytosolic protein complex composed of alpha and beta subunits. NAC binds reversibly to the ribosome where it is in contact with nascent chains as they emerge from the ribosome and protects them against inappropriate interaction with cytosolic factors. However, the cellular function of NAC seems to be much more diverse as it is also involved in transcription regulation and mitochondrial translocation [ PUBMED:12475173 ]. Alpha and beta NACs share homology with each other, both contain a NAC A/B domain, responsible for the complex dimerisation. In archaea no beta NAC proteins are found; the complex is an homodimer of NAC alpha [ PUBMED:10413400 , PUBMED:15665334 ]. These proteins have an additional ubiquitin-associated (UBA) domain which suggests the involvement of NAC in the cellular protein quality control system via the ubiquitination pathway [ PUBMED:15665334 ].

This entry represents the UBA domain found at the C-terminal of the Nascent polypeptide-Associated Complex (NAC) subunit alpha. This domain is also found in HYPK (Huntingtin-interacting protein K) in which mediates a constitutively protein interaction with Naa15 auxiliary subunit from N-terminal acetyltransferase NatA. NatA associates with the ribosome and nascent polypeptides, suggesting that HYPK also interacts with these polypeptides possibly to facilitate Nt-acetylation fidelity [ PUBMED:29754825 ].

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 UBA (CL0214), which has the following description:

This superfamily includes domains related to the UBA domain. These domains are often involved in ubiquitin binding.

The clan contains the following 21 members:

CRAL_TRIO_N CUE DMA DUF1421 E3_UbLigase_EDD E3_UbLigase_RBR GIP1_N HBS1_N HOIP-UBA HYPK_UBA Regnase_1_C RuvA_C TAP_C UBA UBA_2 UBA_3 UBA_4 UBA_5 UBA_6 Ubiq-assoc WIYLD

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

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
(37)
Full
(3824)
Representative proteomes UniProt
(7605)
RP15
(711)
RP35
(1795)
RP55
(3077)
RP75
(4259)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(37)
Full
(3824)
Representative proteomes UniProt
(7605)
RP15
(711)
RP35
(1795)
RP55
(3077)
RP75
(4259)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(37)
Full
(3824)
Representative proteomes UniProt
(7605)
RP15
(711)
RP35
(1795)
RP55
(3077)
RP75
(4259)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: ECOD:6c95_D
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 37
Number in full: 3824
Average length of the domain: 40.40 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 14.20 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 41
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 HYPK_UBA domain has been found. There are 8 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0R0EWX9 View 3D Structure Click here
A0A1D6K372 View 3D Structure Click here
A0A1D6MC00 View 3D Structure Click here
A0A1D6N700 View 3D Structure Click here
A4HS72 View 3D Structure Click here
A4HS73 View 3D Structure Click here
A4HVZ4 View 3D Structure Click here
B1WB51 View 3D Structure Click here
B4FL79 View 3D Structure Click here
B6SU89 View 3D Structure Click here
C6KT55 View 3D Structure Click here
C6T3N4 View 3D Structure Click here
E7EZQ7 View 3D Structure Click here
E9PAV3 View 3D Structure Click here
F1M6E5 View 3D Structure Click here
F1M8A5 View 3D Structure Click here
G5ECC1 View 3D Structure Click here
I1JMZ3 View 3D Structure Click here
I1JMZ4 View 3D Structure Click here
I1JYG6 View 3D Structure Click here
I1JYG7 View 3D Structure Click here
I1KB25 View 3D Structure Click here
I1KB26 View 3D Structure Click here
I1L0Q5 View 3D Structure Click here
I1MGE4 View 3D Structure Click here
I1MRR2 View 3D Structure Click here
I1N8M4 View 3D Structure Click here
K7VIA7 View 3D Structure Click here
M0R9L0 View 3D Structure Click here
O15069 View 3D Structure Click here
P38879 View 3D Structure Click here
P70670 View 3D Structure Click here
P87147 View 3D Structure Click here
Q4DHW9 View 3D Structure Click here
Q54U07 View 3D Structure Click here
Q57728 View 3D Structure Click here
Q5ANP2 View 3D Structure Click here
Q5SWP3 View 3D Structure Click here
Q6ICZ8 View 3D Structure Click here
Q7XXR8 View 3D Structure Click here
Q7Y139 View 3D Structure Click here
Q86S66 View 3D Structure Click here
Q8JIU7 View 3D Structure Click here
Q8LGC6 View 3D Structure Click here
Q8LMR3 View 3D Structure Click here
Q8RUI4 View 3D Structure Click here
Q94518 View 3D Structure Click here
Q94JX9 View 3D Structure Click here
Q9C901 View 3D Structure Click here
Q9CR41 View 3D Structure Click here
Q9H009 View 3D Structure Click here
Q9LHG9 View 3D Structure Click here
Q9NX55 View 3D Structure Click here
Q9SZY1 View 3D Structure Click here
Q9VFN9 View 3D Structure Click here