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25  structures 1008  species 0  interactions 1396  sequences 43  architectures

Family: YcaO (PF02624)

Summary: YcaO cyclodehydratase, ATP-ad Mg2+-binding

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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.

YcaO cyclodehydratase, ATP-ad Mg2+-binding Provide feedback

YcaO is an ATP- an Mg2+-binding protein involved in the peptidic biosynthesis of azoline. There three motifs involved in the binding are, in UniProtKB:P75838 71-79: Sx3ExxER, 184-203: Sx6Ex3Qx3ExxER, and 286-290: RxxxE. Three slightly different functional families are represented in this family, proteins involved in TOMM (thiazole/oxazole-modified microcin) biogenesis, non-TOMM proteins such as UniProtKB:P75838 and TfuA-associated non-TOMM proteins involved in trifolitoxin biosynthesis. UniProtKB:P75838 hydrolyses ATP to AMP and pyrophosphate [1].

Literature references

  1. Dunbar KL, Chekan JR, Cox CL, Burkhart BJ, Nair SK, Mitchell DA;, Nat Chem Biol. 2014;10:823-829.: Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis. PUBMED:25129028 EPMC:25129028


This tab holds annotation information from the InterPro database.

InterPro entry IPR003776

This domain comprises the whole of a protein in Methanocaldococcus jannaschii and Methanobacterium thermoautotrophicum, all but the N-terminal 60 residues from a protein of Mycobacterium tuberculosis, and all but the C-terminal 180 residues from a protein in Haemophilus influenzae and Escherichia coli, among proteins from published complete genomes. This domain contains a conserved ATP-binding pocket [PUBMED:25129028].

The domain can be found in Escherichia coli YcaO, which is known to be involved in beta-methylthiolation of ribosomal protein S12 [PUBMED:21169565]. YcaO-like domains have been shown to be catalytically active, and to use ATP to activate amide backbones during peptide cyclodehydrations [PUBMED:22522320]. It is likely to be involved in post-translational modification (PTM) of amino acid residues.

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, the UniProtKB sequence database, 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
(269)
Full
(1396)
Representative proteomes UniProt
(5234)
NCBI
(10675)
Meta
(81)
RP15
(195)
RP35
(702)
RP55
(1427)
RP75
(2478)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(269)
Full
(1396)
Representative proteomes UniProt
(5234)
NCBI
(10675)
Meta
(81)
RP15
(195)
RP35
(702)
RP55
(1427)
RP75
(2478)
Alignment:
Format:
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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
(269)
Full
(1396)
Representative proteomes UniProt
(5234)
NCBI
(10675)
Meta
(81)
RP15
(195)
RP35
(702)
RP55
(1427)
RP75
(2478)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: COG1944
Previous IDs: DUF181;
Type: Family
Author: Mian N, Bateman A
Number in seed: 269
Number in full: 1396
Average length of the domain: 316.10 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 57.93 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.4 25.3
Noise cut-off 22.2 24.8
Model length: 323
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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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 YcaO domain has been found. There are 25 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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