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29  structures 231  species 3  interactions 285  sequences 11  architectures

Family: E2_bind (PF08825)

Summary: E2 binding domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "UBE1C". More...

UBE1C Edit Wikipedia article

Ubiquitin-like modifier activating enzyme 3
Protein UBE1C PDB 1r4m.png
PDB rendering based on 1r4m.
Available structures
PDB Ortholog search: PDBe, RCSB
Identifiers
Symbols UBA3 ; NAE2; UBE1C; hUBA3
External IDs OMIM603172 MGI1341217 HomoloGene2951 GeneCards: UBA3 Gene
RNA expression pattern
PBB GE UBE1C 209115 at tn.png
More reference expression data
Orthologs
Species Human Mouse
Entrez 9039 22200
Ensembl ENSG00000144744 ENSMUSG00000030061
UniProt Q8TBC4 Q8C878
RefSeq (mRNA) NM_003968 NM_001111106
RefSeq (protein) NP_003959 NP_001104576
Location (UCSC) Chr 3:
69.1 – 69.13 Mb
Chr 6:
97.18 – 97.21 Mb
PubMed search [1] [2]
E2 binding domain
PDB 1r4n EBI.jpg
appbp1-uba3-nedd8, an e1-ubiquitin-like protein complex with atp
Identifiers
Symbol E2_bind
Pfam PF08825
InterPro IPR014929

NEDD8-activating enzyme E1 catalytic subunit is a protein that in humans is encoded by the UBA3 gene.[1][2]

The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E1 ubiquitin-activating enzyme family. The encoded enzyme associates with AppBp1, an amyloid beta precursor protein binding protein, to form a heterodimer, and then the enzyme complex activates NEDD8, a ubiquitin-like protein, which regulates cell division, signaling and embryogenesis. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.[2]

This enzyme contains an E2 binding domain, which resembles ubiquitin, and recruits the catalytic core of the E2 enzyme UBE2M (Ubc12) in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains.[3]

Interactions

UBE1C has been shown to interact with NEDD8,[4] APPBP1[5] and UBE2M.[3]

References

  1. ^ Osaka F, Kawasaki H, Aida N, Saeki M, Chiba T, Kawashima S, Tanaka K, Kato S (August 1998). "A new NEDD8-ligating system for cullin-4A". Genes Dev 12 (15): 2263–8. doi:10.1101/gad.12.15.2263. PMC 317039. PMID 9694792. 
  2. ^ a b "Entrez Gene: UBE1C ubiquitin-activating enzyme E1C (UBA3 homolog, yeast)". 
  3. ^ a b Huang DT, Paydar A, Zhuang M, Waddell MB, Holton JM, Schulman BA (February 2005). "Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1". Mol. Cell 17 (3): 341–50. doi:10.1016/j.molcel.2004.12.020. PMID 15694336. 
  4. ^ Gong, L; Yeh E T (April 1999). "Identification of the activating and conjugating enzymes of the NEDD8 conjugation pathway". J. Biol. Chem. (UNITED STATES) 274 (17): 12036–42. doi:10.1074/jbc.274.17.12036. ISSN 0021-9258. PMID 10207026. 
  5. ^ Chen, Y; McPhie D L; Hirschberg J; Neve R L (March 2000). "The amyloid precursor protein-binding protein APP-BP1 drives the cell cycle through the S-M checkpoint and causes apoptosis in neurons". J. Biol. Chem. (UNITED STATES) 275 (12): 8929–35. doi:10.1074/jbc.275.12.8929. ISSN 0021-9258. PMID 10722740. 

Further reading


This article incorporates text from the public domain Pfam and InterPro IPR014929


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

E2 binding domain Provide feedback

E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The domain resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains [1].

Literature references

  1. Huang DT, Paydar A, Zhuang M, Waddell MB, Holton JM, Schulman BA; , Mol Cell. 2005;17:341-350.: Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1. PUBMED:15694336 EPMC:15694336


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR014929

E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The protein resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains [PUBMED:15694336].

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(24)
Full
(285)
Representative proteomes NCBI
(288)
Meta
(4)
RP15
(70)
RP35
(109)
RP55
(164)
RP75
(198)
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Format an alignment

  Seed
(24)
Full
(285)
Representative proteomes NCBI
(288)
Meta
(4)
RP15
(70)
RP35
(109)
RP55
(164)
RP75
(198)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(24)
Full
(285)
Representative proteomes NCBI
(288)
Meta
(4)
RP15
(70)
RP35
(109)
RP55
(164)
RP75
(198)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: pdb_1y8x
Previous IDs: none
Type: Domain
Author: Mistry J
Number in seed: 24
Number in full: 285
Average length of the domain: 85.70 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 19.97 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.3 20.3
Trusted cut-off 20.4 21.9
Noise cut-off 20.2 19.7
Model length: 84
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

UQ_con E2_bind ThiF

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 E2_bind domain has been found. There are 29 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 seqence.

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