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66  structures 1494  species 0  interactions 17692  sequences 650  architectures

Family: U-box (PF04564)

Summary: U-box domain

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U-box domain Provide feedback

The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process [1-3]. This domain is related to the Ring finger PF00097 but lacks the zinc binding residues [4].

Literature references

  1. Nordquist KA, Dimitrova YN, Brzovic PS, Ridenour WB, Munro KA, Soss SE, Caprioli RM, Klevit RE, Chazin WJ;, Biochemistry. 2010;49:347-355.: Structural and functional characterization of the monomeric U-box domain from E4B. PUBMED:20017557 EPMC:20017557

  2. Hatakeyama S, Yada M, Matsumoto M, Ishida N, Nakayama KI;, J Biol Chem. 2001;276:33111-33120.: U box proteins as a new family of ubiquitin-protein ligases. PUBMED:11435423 EPMC:11435423

  3. Wiborg J, O'Shea C, Skriver K;, Biochem J. 2008;413:447-457.: Biochemical function of typical and variant Arabidopsis thaliana U-box E3 ubiquitin-protein ligases. PUBMED:18393940 EPMC:18393940

  4. Aravind L, Koonin EV; , Curr Biol 2000;10:132-134.: The U box is a modified RING finger - a common domain in ubiquitination. PUBMED:10704423 EPMC:10704423


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003613

This entry represents the U-box domain.

The molecular mechanism underlying the transfer of ubiquitin (Ub) to a substrate consists of three key enzymatic steps. First, ubiquitin itself is adenylated at its C-terminal glycine residue by an activating enzyme (E1). Second, the adenylated Ub forms a covalent linkage to a conjugating enzyme (E2). Finally, a ligating enzyme (E3) recruits both the Ub-charged E2 species and the target protein. There are three classes of E3 enzymes- HECT, RING, and U-box, which are distinguished on the basis of their E2-recruiting domains.

The U-box and RING classes of E3 ligases act as scaffolding molecules that recruit and colocalize both a Ub-charged E2 and the substrate concomitantly. The recruitement of substrate in these proteins involves protein interaction modules such as a WD-40 repeat, TPR, and armadillo repeat domains. In addition to a common organisation, the architecture of U-box and RING domains are similar. Both contain a central alpha-helix flanked by two surface-exposed loops arranged in a cross-brace formation. the structure of RING domains is built around two zinc binding sites that are critical to its stability. In contrast, U-boxes do not bind zinc but have evolved instead networks of hydrogen bonds and salt bridges in corresponding location in the structure. Other similarities between these two domains include an antiparallel beta-sheet type arrangement involving the first surface exposed loop and the central alpha helix. The beta-sheet is stabilised by highly conserved hydrophobic residues responsible for the core packing and stability of the molecule. Most U-box and RING domain structures also contain an elongated C-terminal helix. The physical basis and physiological rationale for evolving distinct U-box and RING E3 ligases are not yet known [ PUBMED:20017557 , PUBMED:11435423 , PUBMED:18393940 ].

The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha-fold typical of U-box and RING domains (see PDB:2QIZ). The central alpha helix is flanked by two prominent surface-exposed loop regions. The characteristic network of hydrogen bonds within each loop stabilises the overall structure. The U-box protein appear to catalyze their own ubiquitination as well as that of heterologous substrate [ PUBMED:20017557 , PUBMED:11435423 , PUBMED:18393940 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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...

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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
(16)
Full
(17692)
Representative proteomes UniProt
(33461)
RP15
(2909)
RP35
(9208)
RP55
(14763)
RP75
(19412)
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PP/heatmap 1            

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

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

Format an alignment

  Seed
(16)
Full
(17692)
Representative proteomes UniProt
(33461)
RP15
(2909)
RP35
(9208)
RP55
(14763)
RP75
(19412)
Alignment:
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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
(16)
Full
(17692)
Representative proteomes UniProt
(33461)
RP15
(2909)
RP35
(9208)
RP55
(14763)
RP75
(19412)
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: Pfam-B_2801 (release 7.5)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Chuguransky S
Number in seed: 16
Number in full: 17692
Average length of the domain: 71.00 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 10.52 %

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 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 73
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 U-box domain has been found. There are 66 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
A0A0P0V0T6 View 3D Structure Click here
A0A0P0VAX7 View 3D Structure Click here
A0A0P0VBB5 View 3D Structure Click here
A0A0P0VGD5 View 3D Structure Click here
A0A0P0VGG2 View 3D Structure Click here
A0A0P0VMV4 View 3D Structure Click here
A0A0P0VPF1 View 3D Structure Click here
A0A0P0VRD5 View 3D Structure Click here
A0A0P0VS27 View 3D Structure Click here
A0A0P0VYX0 View 3D Structure Click here
A0A0P0W983 View 3D Structure Click here
A0A0P0WAA1 View 3D Structure Click here
A0A0P0WNR0 View 3D Structure Click here
A0A0P0WV49 View 3D Structure Click here
A0A0P0WV73 View 3D Structure Click here
A0A0P0X147 View 3D Structure Click here
A0A0P0XFL3 View 3D Structure Click here
A0A0P0XX00 View 3D Structure Click here
A0A0P0XX95 View 3D Structure Click here
A0A0P0Y7A8 View 3D Structure Click here
A0A0R0D606 View 3D Structure Click here
A0A0R0E2R0 View 3D Structure Click here
A0A0R0EYL4 View 3D Structure Click here
A0A0R0F179 View 3D Structure Click here
A0A0R0FC26 View 3D Structure Click here
A0A0R0FN30 View 3D Structure Click here
A0A0R0GT27 View 3D Structure Click here
A0A0R0H3F3 View 3D Structure Click here
A0A0R0HUX5 View 3D Structure Click here
A0A0R0J4K3 View 3D Structure Click here
A0A0R0JU54 View 3D Structure Click here
A0A0R0KJN7 View 3D Structure Click here
A0A0R0KXK1 View 3D Structure Click here
A0A0R0L8N7 View 3D Structure Click here
A0A1D6DSN6 View 3D Structure Click here
A0A1D6E1J9 View 3D Structure Click here
A0A1D6E1T3 View 3D Structure Click here
A0A1D6E3I1 View 3D Structure Click here
A0A1D6E7T1 View 3D Structure Click here
A0A1D6EA92 View 3D Structure Click here
A0A1D6EPI6 View 3D Structure Click here
A0A1D6G927 View 3D Structure Click here
A0A1D6GWR9 View 3D Structure Click here
A0A1D6H4M4 View 3D Structure Click here
A0A1D6H6B7 View 3D Structure Click here
A0A1D6H8A2 View 3D Structure Click here
A0A1D6HA26 View 3D Structure Click here
A0A1D6HA67 View 3D Structure Click here
A0A1D6HJN5 View 3D Structure Click here
A0A1D6I0E4 View 3D Structure Click here
A0A1D6I421 View 3D Structure Click here
A0A1D6IAU7 View 3D Structure Click here
A0A1D6ITH7 View 3D Structure Click here
A0A1D6IUH4 View 3D Structure Click here
A0A1D6JY56 View 3D Structure Click here
A0A1D6K5Z2 View 3D Structure Click here
A0A1D6K803 View 3D Structure Click here
A0A1D6K831 View 3D Structure Click here
A0A1D6KB93 View 3D Structure Click here
A0A1D6KE36 View 3D Structure Click here
A0A1D6KHR4 View 3D Structure Click here
A0A1D6KPJ0 View 3D Structure Click here
A0A1D6LDT6 View 3D Structure Click here
A0A1D6LII0 View 3D Structure Click here
A0A1D6M516 View 3D Structure Click here
A0A1D6M6J3 View 3D Structure Click here
A0A1D6MF38 View 3D Structure Click here
A0A1D6MKS4 View 3D Structure Click here
A0A1D6MU43 View 3D Structure Click here
A0A1D6MWU2 View 3D Structure Click here
A0A1D6N4C7 View 3D Structure Click here
A0A1D6N5E0 View 3D Structure Click here
A0A1D6N6H8 View 3D Structure Click here
A0A1D6N848 View 3D Structure Click here
A0A1D6NR05 View 3D Structure Click here
A0A1D6NUQ7 View 3D Structure Click here
A0A1D6NVT3 View 3D Structure Click here
A0A1D6NYN3 View 3D Structure Click here
A0A1D6P8K6 View 3D Structure Click here
A0A1D6PX27 View 3D Structure Click here
A0A1D6PXB6 View 3D Structure Click here
A0A1D6Q0X7 View 3D Structure Click here
A0A1D6Q2Y9 View 3D Structure Click here
A0A1D6Q4X5 View 3D Structure Click here
A0A1D6Q6L6 View 3D Structure Click here
A0A1D6Q9G7 View 3D Structure Click here
A0A1D6QAK9 View 3D Structure Click here
A0A1D6QPZ2 View 3D Structure Click here
A0A1X7YE91 View 3D Structure Click here
A0A1X7YII5 View 3D Structure Click here
A0A368UGC3 View 3D Structure Click here
A0AUS0 View 3D Structure Click here
A4HSU3 View 3D Structure Click here
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B4FVL5 View 3D Structure Click here
B4G159 View 3D Structure Click here
B4G225 View 3D Structure Click here
B6SRZ6 View 3D Structure Click here
B6SV52 View 3D Structure Click here
B6SV72 View 3D Structure Click here
B6SWJ0 View 3D Structure Click here
B6TTC2 View 3D Structure Click here
B7EPT4 View 3D Structure Click here
B7F9Y0 View 3D Structure Click here
B7FA87 View 3D Structure Click here
B8A203 View 3D Structure Click here
C0H4Y0 View 3D Structure Click here
C0PG49 View 3D Structure Click here
C0PJJ1 View 3D Structure Click here
C0PK51 View 3D Structure Click here
C4IZ35 View 3D Structure Click here
C4JBY4 View 3D Structure Click here
C7IYS0 View 3D Structure Click here
D4A4T0 View 3D Structure Click here
E7EXE9 View 3D Structure Click here
E7F6E1 View 3D Structure Click here
E7FEA3 View 3D Structure Click here
E9Q735 View 3D Structure Click here
F1M8V2 View 3D Structure Click here
F1Q8K3 View 3D Structure Click here
F1R6T8 View 3D Structure Click here
F4HZI0 View 3D Structure Click here
F4K964 View 3D Structure Click here
G3V953 View 3D Structure Click here
G5ECY6 View 3D Structure Click here
I1J504 View 3D Structure Click here
I1J7N4 View 3D Structure Click here
I1J9E6 View 3D Structure Click here
I1J9G1 View 3D Structure Click here
I1JC18 View 3D Structure Click here
I1JCP2 View 3D Structure Click here
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I1JE03 View 3D Structure Click here
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I1JX38 View 3D Structure Click here
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I1K429 View 3D Structure Click here
I1K4X0 View 3D Structure Click here
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I1K885 View 3D Structure Click here
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I1KM13 View 3D Structure Click here
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I1KS03 View 3D Structure Click here
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I1L423 View 3D Structure Click here
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I1LCX7 View 3D Structure Click here
I1LEJ9 View 3D Structure Click here
I1LH60 View 3D Structure Click here
I1LK32 View 3D Structure Click here
I1LLV0 View 3D Structure Click here
I1LMA2 View 3D Structure Click here
I1LNA0 View 3D Structure Click here
I1LQR1 View 3D Structure Click here
I1LRL5 View 3D Structure Click here
I1LU00 View 3D Structure Click here
I1LU01 View 3D Structure Click here
I1LWP5 View 3D Structure Click here
I1M1P9 View 3D Structure Click here
I1M2F3 View 3D Structure Click here
I1M491 View 3D Structure Click here
I1M492 View 3D Structure Click here
I1M8V2 View 3D Structure Click here
I1MBT5 View 3D Structure Click here
I1MDF7 View 3D Structure Click here
I1ME75 View 3D Structure Click here
I1MEV7 View 3D Structure Click here
I1MNE6 View 3D Structure Click here
I1MPA0 View 3D Structure Click here
I1MSE8 View 3D Structure Click here
I1MTI6 View 3D Structure Click here
I1MXG4 View 3D Structure Click here
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I1N1W6 View 3D Structure Click here
I1N3T8 View 3D Structure Click here
I1NAU2 View 3D Structure Click here
I1NAU9 View 3D Structure Click here
I1NCF7 View 3D Structure Click here
I1ND65 View 3D Structure Click here
I1NHI3 View 3D Structure Click here
I1NIK5 View 3D Structure Click here
K7K4C9 View 3D Structure Click here
K7KAB1 View 3D Structure Click here
K7KAW8 View 3D Structure Click here
K7KC17 View 3D Structure Click here
K7KFF3 View 3D Structure Click here
K7KLG1 View 3D Structure Click here
K7KPI2 View 3D Structure Click here
K7KR67 View 3D Structure Click here
K7KUU8 View 3D Structure Click here
K7KV13 View 3D Structure Click here
K7KXQ3 View 3D Structure Click here
K7L464 View 3D Structure Click here
K7L4R9 View 3D Structure Click here
K7LAW2 View 3D Structure Click here
K7LBJ3 View 3D Structure Click here
K7LG44 View 3D Structure Click here
K7LKD4 View 3D Structure Click here
K7LL16 View 3D Structure Click here
K7LN26 View 3D Structure Click here
K7LNF7 View 3D Structure Click here
K7LPP0 View 3D Structure Click here
K7LVI4 View 3D Structure Click here
K7LXC7 View 3D Structure Click here
K7M3E1 View 3D Structure Click here
K7MER9 View 3D Structure Click here
K7MPA0 View 3D Structure Click here
K7MQ50 View 3D Structure Click here
K7MQ92 View 3D Structure Click here
K7MUA7 View 3D Structure Click here
K7MVL4 View 3D Structure Click here
K7MVX7 View 3D Structure Click here
K7N3S5 View 3D Structure Click here
K7TM26 View 3D Structure Click here
K7TP91 View 3D Structure Click here
K7U4K7 View 3D Structure Click here
K7UHK0 View 3D Structure Click here
K7UVS5 View 3D Structure Click here
K7V5S2 View 3D Structure Click here
K7VD57 View 3D Structure Click here
K7W7S8 View 3D Structure Click here
O22193 View 3D Structure Click here
O23225 View 3D Structure Click here
O44007 View 3D Structure Click here
O48700 View 3D Structure Click here
O80742 View 3D Structure Click here
O81902 View 3D Structure Click here
O94941 View 3D Structure Click here
O95155 View 3D Structure Click here
P0C6E7 View 3D Structure Click here
P54860 View 3D Structure Click here
P97868 View 3D Structure Click here
Q058P4 View 3D Structure Click here
Q09349 View 3D Structure Click here
Q0DEQ5 View 3D Structure Click here
Q0DR28 View 3D Structure Click here
Q0E0I9 View 3D Structure Click here
Q0IMG9 View 3D Structure Click here
Q0IZG9 View 3D Structure Click here
Q0IZH1 View 3D Structure Click here
Q0WUF6 View 3D Structure Click here
Q10051 View 3D Structure Click here
Q10FT0 View 3D Structure Click here
Q10NB2 View 3D Structure Click here
Q10PB1 View 3D Structure Click here
Q10PI9 View 3D Structure Click here
Q14139 View 3D Structure Click here
Q2QU07 View 3D Structure Click here
Q2QU09 View 3D Structure Click here
Q336S5 View 3D Structure Click here
Q336U1 View 3D Structure Click here
Q336U5 View 3D Structure Click here
Q33BK6 View 3D Structure Click here
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Q3T1H9 View 3D Structure Click here
Q4D029 View 3D Structure Click here
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Q4DHT9 View 3D Structure Click here
Q4DW87 View 3D Structure Click here
Q54C21 View 3D Structure Click here
Q54RD2 View 3D Structure Click here
Q54SX5 View 3D Structure Click here
Q55AK6 View 3D Structure Click here
Q59R98 View 3D Structure Click here
Q5ADV1 View 3D Structure Click here
Q5AND8 View 3D Structure Click here
Q5FVN8 View 3D Structure Click here
Q5N8V2 View 3D Structure Click here
Q5PNY6 View 3D Structure Click here
Q5VMW9 View 3D Structure Click here
Q5VMX1 View 3D Structure Click here
Q5VMX4 View 3D Structure Click here
Q5VRH9 View 3D Structure Click here
Q5WA76 View 3D Structure Click here
Q5XEZ8 View 3D Structure Click here
Q5Z7K5 View 3D Structure Click here
Q67VB9 View 3D Structure Click here
Q67VC1 View 3D Structure Click here
Q681N2 View 3D Structure Click here
Q683D5 View 3D Structure Click here
Q69Y81 View 3D Structure Click here
Q6DBN5 View 3D Structure Click here
Q6ER82 View 3D Structure Click here
Q6ETF7 View 3D Structure Click here
Q6EUK7 View 3D Structure Click here
Q6H4P2 View 3D Structure Click here
Q6H593 View 3D Structure Click here
Q6K762 View 3D Structure Click here
Q6P7A2 View 3D Structure Click here
Q6Z250 View 3D Structure Click here
Q6Z2G6 View 3D Structure Click here
Q6Z2K3 View 3D Structure Click here
Q6ZC56 View 3D Structure Click here
Q6ZGX9 View 3D Structure Click here
Q75HW6 View 3D Structure Click here
Q75I67 View 3D Structure Click here
Q7X741 View 3D Structure Click here
Q7XLZ8 View 3D Structure Click here
Q7XTM1 View 3D Structure Click here
Q7XV59 View 3D Structure Click here
Q7Z6E9 View 3D Structure Click here
Q7ZV92 View 3D Structure Click here
Q84TG3 View 3D Structure Click here
Q8GUG9 View 3D Structure Click here
Q8GUH1 View 3D Structure Click here
Q8GWV5 View 3D Structure Click here
Q8GXQ7 View 3D Structure Click here
Q8GZ84 View 3D Structure Click here
Q8H333 View 3D Structure Click here
Q8IC12 View 3D Structure Click here
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Q8VZ40 View 3D Structure Click here
Q925F4 View 3D Structure Click here
Q94A51 View 3D Structure Click here
Q99KP6 View 3D Structure Click here
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Q9FL17 View 3D Structure Click here
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Q9HE05 View 3D Structure Click here
Q9JMJ4 View 3D Structure Click here
Q9LF41 View 3D Structure Click here
Q9LM76 View 3D Structure Click here
Q9LQ92 View 3D Structure Click here
Q9LSA6 View 3D Structure Click here
Q9LT79 View 3D Structure Click here
Q9LU47 View 3D Structure Click here
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Q9SF15 View 3D Structure Click here
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Q9SNC6 View 3D Structure Click here
Q9SRS9 View 3D Structure Click here
Q9SRT0 View 3D Structure Click here
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Q9SVC6 View 3D Structure Click here
Q9SW11 View 3D Structure Click here
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Q9UMS4 View 3D Structure Click here
Q9UNE7 View 3D Structure Click here
Q9VA79 View 3D Structure Click here
Q9VK44 View 3D Structure Click here
Q9WUD1 View 3D Structure Click here
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Q9ZV31 View 3D Structure Click here