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61  structures 2475  species 0  interactions 12322  sequences 243  architectures

Family: zf-UBP (PF02148)

Summary: Zn-finger in ubiquitin-hydrolases and other protein

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Zn-finger in ubiquitin-hydrolases and other protein Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001607

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [ PUBMED:10529348 , PUBMED:15963892 , PUBMED:15718139 , PUBMED:17210253 , PUBMED:12665246 ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [ PUBMED:11179890 ]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [ PUBMED:9759494 , PUBMED:9409543 ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties.

Some of the proteins containing an UBP zinc finger include:

  • Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD)
  • Human deubiquitinating enzyme 5 (UBP5)
  • Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA)
  • Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8)
  • Yeast deubiquitinating enzyme 14 (UBP14)

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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Pfam Clan

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
(149)
Full
(12322)
Representative proteomes UniProt
(24567)
RP15
(1863)
RP35
(5097)
RP55
(10388)
RP75
(14773)
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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
(149)
Full
(12322)
Representative proteomes UniProt
(24567)
RP15
(1863)
RP35
(5097)
RP55
(10388)
RP75
(14773)
Alignment:
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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
(149)
Full
(12322)
Representative proteomes UniProt
(24567)
RP15
(1863)
RP35
(5097)
RP55
(10388)
RP75
(14773)
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: IPR001607
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mian N , Bateman A
Number in seed: 149
Number in full: 12322
Average length of the domain: 68.40 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 11.27 %

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 22.7 22.7
Trusted cut-off 22.7 22.7
Noise cut-off 22.6 22.6
Model length: 64
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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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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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 zf-UBP domain has been found. There are 61 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
A0A0B4KHR2 View 3D Structure Click here
A0A0G2K4S7 View 3D Structure Click here
A0A1D6DW81 View 3D Structure Click here
A0A1D6DW87 View 3D Structure Click here
A0A1D6ESQ1 View 3D Structure Click here
A0A1D6GTX8 View 3D Structure Click here
A0A1D6H2Q8 View 3D Structure Click here
A0A1D6JS92 View 3D Structure Click here
A0A1D6LFE8 View 3D Structure Click here
A0A1D6MXX1 View 3D Structure Click here
A0A1D6MXY3 View 3D Structure Click here
A0A1D8PFY2 View 3D Structure Click here
A0A1D8PGI9 View 3D Structure Click here
A0A1D8PGM1 View 3D Structure Click here
A0A1D8PIP6 View 3D Structure Click here
A3KQ59 View 3D Structure Click here
A4HRG6 View 3D Structure Click here
A4I4U4 View 3D Structure Click here
A4IA95 View 3D Structure Click here
A5PMR2 View 3D Structure Click here
A5PN09 View 3D Structure Click here
A6H8I0 View 3D Structure Click here
A8HAL1 View 3D Structure Click here
B1AY15 View 3D Structure Click here
B2GV41 View 3D Structure Click here
B7F7L1 View 3D Structure Click here
B9GDC7 View 3D Structure Click here
C0PCY1 View 3D Structure Click here
D3ZDI9 View 3D Structure Click here
D3ZJ49 View 3D Structure Click here
D3ZLQ8 View 3D Structure Click here
D3ZTX7 View 3D Structure Click here
D3ZUR6 View 3D Structure Click here
D3ZVD8 View 3D Structure Click here
D3ZVQ0 View 3D Structure Click here
D4A251 View 3D Structure Click here
E5KGE0 View 3D Structure Click here
E9QG68 View 3D Structure Click here
F1LPJ7 View 3D Structure Click here
F1Q6D7 View 3D Structure Click here
F1QFS9 View 3D Structure Click here
F4IHD8 View 3D Structure Click here
F4JL64 View 3D Structure Click here
F4JL70 View 3D Structure Click here
F8W4B7 View 3D Structure Click here
I1JAZ4 View 3D Structure Click here
I1KE56 View 3D Structure Click here
I1L9D9 View 3D Structure Click here
I1LSZ2 View 3D Structure Click here
I1LZK9 View 3D Structure Click here
I1LZP8 View 3D Structure Click here
I1LZT3 View 3D Structure Click here
I1M9E2 View 3D Structure Click here
I1MCC9 View 3D Structure Click here
I1MU32 View 3D Structure Click here
I1MU69 View 3D Structure Click here
I1MWZ8 View 3D Structure Click here
I1MY83 View 3D Structure Click here
K7LRW5 View 3D Structure Click here
K7TY00 View 3D Structure Click here
M0RBY8 View 3D Structure Click here
O13747 View 3D Structure Click here
O44787 View 3D Structure Click here
O80996 View 3D Structure Click here
P38237 View 3D Structure Click here
P38748 View 3D Structure Click here
P43589 View 3D Structure Click here
P45974 View 3D Structure Click here
P50102 View 3D Structure Click here
P54201 View 3D Structure Click here
P56399 View 3D Structure Click here
P91502 View 3D Structure Click here
Q09738 View 3D Structure Click here
Q0J0M6 View 3D Structure Click here
Q0J492 View 3D Structure Click here
Q11119 View 3D Structure Click here
Q1MT86 View 3D Structure Click here
Q1MTK1 View 3D Structure Click here
Q20296 View 3D Structure Click here
Q2KJ09 View 3D Structure Click here
Q3TIX9 View 3D Structure Click here
Q4CUC6 View 3D Structure Click here
Q4DD96 View 3D Structure Click here
Q4DNU2 View 3D Structure Click here
Q4E680 View 3D Structure Click here
Q53GS9 View 3D Structure Click here
Q54QE6 View 3D Structure Click here
Q54XH4 View 3D Structure Click here
Q55AP9 View 3D Structure Click here
Q55C68 View 3D Structure Click here
Q55EJ1 View 3D Structure Click here
Q5BKP2 View 3D Structure Click here
Q5DU02 View 3D Structure Click here
Q5VRV7 View 3D Structure Click here
Q69MX3 View 3D Structure Click here
Q6H890 View 3D Structure Click here
Q6P9L4 View 3D Structure Click here
Q70CQ1 View 3D Structure Click here
Q70EK9 View 3D Structure Click here
Q70EL2 View 3D Structure Click here
Q7XTV9 View 3D Structure Click here
Q7Z569 View 3D Structure Click here
Q7ZUM8 View 3D Structure Click here
Q8C2S0 View 3D Structure Click here
Q8C6M1 View 3D Structure Click here
Q8H148 View 3D Structure Click here
Q8I1U8 View 3D Structure Click here
Q8I6Z8 View 3D Structure Click here
Q8IBN0 View 3D Structure Click here
Q8K387 View 3D Structure Click here
Q8L6Y1 View 3D Structure Click here
Q8R5K2 View 3D Structure Click here
Q8TEY7 View 3D Structure Click here
Q8W4N3 View 3D Structure Click here
Q91W36 View 3D Structure Click here
Q92995 View 3D Structure Click here
Q95QN6 View 3D Structure Click here
Q99LG0 View 3D Structure Click here
Q99MP8 View 3D Structure Click here
Q9FPT5 View 3D Structure Click here
Q9GRV2 View 3D Structure Click here
Q9H0E7 View 3D Structure Click here
Q9LEW0 View 3D Structure Click here
Q9P7S5 View 3D Structure Click here
Q9UBN7 View 3D Structure Click here
Q9UPT9 View 3D Structure Click here
Q9USR2 View 3D Structure Click here
Q9VVR1 View 3D Structure Click here
Q9VWP1 View 3D Structure Click here
Q9VZU7 View 3D Structure Click here
Q9W4C3 View 3D Structure Click here
Q9Y2K6 View 3D Structure Click here
Q9Y5T5 View 3D Structure Click here
Q9Y6I4 View 3D Structure Click here
Q9Z2V5 View 3D Structure Click here
X1WG21 View 3D Structure Click here