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2  structures 548  species 1  interaction 869  sequences 3  architectures

Family: YukD (PF08817)

Summary: WXG100 protein secretion system (Wss), protein YukD

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WXG100 protein secretion system (Wss), protein YukD Provide feedback

The YukD protein family members participate in the formation of a translocon required for the secretion of WXG100 proteins (PF06013) in monoderm bacteria, with the WXG100 protein secretion system (Wss). Like the cytoplasmic protein EsaC in Staphylococcus aureus, YukD was hypothesized to play a role of a chaperone. YukD adopts a ubiquitin-like fold [1]. Usually, ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that the classical YukD lacks the capacity for covalent bond formation with other proteins [1]. In contrast to the situation in firmicutes, YukD-like proteins in actinobacteria are often fused to a transporter involved in the ESAT-6/ESX/Wss secretion pathway [6,7]. Members of the YukD family are also associated in gene neighborhoods with other enzymatic members of the ubiquitin signaling and degradation pathway such as the E1, E2 and E3 trienzyme complex that catalyze ubiquitin transfer to substrates, and the JAB family metallopeptidases that are involved in its release [7]. This suggests that a subset of the YukD family in bacteria are conjugated and released from proteins as in the eukaryotic ubiquitin-mediated signaling and degradation pathway [7].

Literature references

  1. van den Ent F, Lowe J; , FEBS Lett. 2005;579:3837-3841.: Crystal structure of the ubiquitin-like protein YukD from Bacillus subtilis. PUBMED:15978580 EPMC:15978580

  2. Burts ML, Williams WA, DeBord K, Missiakas DM; , Proc Natl Acad Sci U S A. 2005;102:1169-1174.: EsxA and EsxB are secreted by an ESAT-6-like system that is required for the pathogenesis of Staphylococcus aureus infections. PUBMED:15657139 EPMC:15657139

  3. Desvaux M, Hebraud M, Talon R, Henderson IR;, Trends Microbiol. 2009;17:338-340.: Outer membrane translocation: numerical protein secretion nomenclature in question in mycobacteria. PUBMED:19674902 EPMC:19674902

  4. Sutcliffe IC;, Antonie Van Leeuwenhoek. 2011;99:127-131.: New insights into the distribution of WXG100 protein secretion systems. PUBMED:20852931 EPMC:20852931

  5. Desvaux M, Hebraud M, Talon R, Henderson IR;, Trends Microbiol. 2009;17:139-145.: Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. PUBMED:19299134 EPMC:19299134

  6. Iyer LM, Burroughs AM, Aravind L; , Genome Biol. 2006;7:R60.: The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. PUBMED:16859499 EPMC:16859499

  7. Burroughs AM, Iyer LM, Aravind L;, Mol Biosyst. 2011;7:2261-2277.: Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system. PUBMED:21547297 EPMC:21547297


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024962

YukD adopts a ubiquitin-like fold [PUBMED:15978580]. Usually, ubiquitin covalently binds to protein and flags them for protein degradation; however conjugation assays have indicated that the classical YukD lacks the capacity for covalent bond formation with other proteins [PUBMED:15978580]. In firmicutes (Gram positive bacteria), the YukD-like proteins are standalone versions and the YukD-like family is associated in conserved gene neighbourhoods with members of the ESAT-6 export pathway (also called Type VII secretion system or ESX), suggesting a role for YukD in regulating this export system [PUBMED:16859499, PUBMED:18554323]. In actinobacteria, YukD-like proteins are often fused to a transporter involved in the ESAT-6/ESX secretion pathway [PUBMED:16859499, PUBMED:21547297]. Members of the YukD family are also associated in gene neighbourhoods with other enzymatic members of the ubiquitin signaling and degradation pathway such as the E1, E2 and E3 trienzyme complex that catalyse ubiquitin transfer to substrates, and the JAB family metallopeptidases that are involved in its release [PUBMED:21547297]. This suggests that a subset of the YukD family in bacteria are conjugated to target proteins and released from proteins as in the eukaryotic ubiquitin-mediated signaling and degradation pathway [PUBMED:21547297].

Domain organisation

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Pfam Clan

This family is a member of clan Ubiquitin (CL0072), which has the following description:

This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.

The clan contains the following 41 members:

APG12 Atg8 Blt1 Caps_synth_GfcC CIDE-N Cobl DUF1315 DUF2407 DUF4430 DWNN FERM_N Lambda_tail_I Multi_ubiq NQRA_SLBB PB1 PI3K_rbd Plug Prok_Ub RA Rad60-SLD Rad60-SLD_2 Ras_bdg_2 RBD SLBB Telomere_Sde2 TGS ThiS ThiS-like TmoB TUG-UBL1 Ub-Mut7C Ub-RnfH ubiquitin Ubiquitin_2 Ubiquitin_3 UBX Ufm1 UN_NPL4 Urm1 YchF-GTPase_C YukD

Alignments

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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
(54)
Full
(869)
Representative proteomes NCBI
(472)
Meta
(11)
RP15
(48)
RP35
(107)
RP55
(141)
RP75
(159)
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Format an alignment

  Seed
(54)
Full
(869)
Representative proteomes NCBI
(472)
Meta
(11)
RP15
(48)
RP35
(107)
RP55
(141)
RP75
(159)
Alignment:
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Sequence:
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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
(54)
Full
(869)
Representative proteomes NCBI
(472)
Meta
(11)
RP15
(48)
RP35
(107)
RP55
(141)
RP75
(159)
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.

Pfam alignments:

HMM logo

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Trees

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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_2bps
Previous IDs: none
Type: Family
Author: Mistry J, Desvaux M, Burroughs AM, Iyer LM, Aravind L
Number in seed: 54
Number in full: 869
Average length of the domain: 79.60 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 25.86 %

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 27.0 27.0
Trusted cut-off 27.1 27.0
Noise cut-off 26.7 26.9
Model length: 79
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Interactions

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YukD

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 YukD domain has been found. There are 2 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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