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1  structure 72  species 0  interactions 1130  sequences 45  architectures

Family: FLYWCH (PF04500)

Summary: FLYWCH zinc finger domain

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This is the Wikipedia entry entitled "FLYWCH zinc finger". More...

FLYWCH zinc finger Edit Wikipedia article

FLYWCH zinc finger domain
Identifiers
Symbol FLYWCH
Pfam PF04500
Pfam clan CL0274
InterPro IPR007588

In molecular biology, the FLYWCH zinc finger is a zinc finger domain. It is found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif:

 F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH 

where X indicates any amino acid. This domain was first characterised in Drosophila modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs.[1] The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain.

FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione S-transferase (GST) domain.[2]

References

  1. ^ Dorn R, Krauss V (March 2003). "The modifier of mdg4 locus in Drosophila: functional complexity is resolved by trans splicing". Genetica 117 (2-3): 165–77. doi:10.1023/A:1022983810016. PMID 12723696. 
  2. ^ Provost E, Shearn A (August 2006). "The Suppressor of Killer of prune, a unique glutathione S-transferase". J. Bioenerg. Biomembr. 38 (3-4): 189–95. doi:10.1007/s10863-006-9034-1. PMID 16944302. 

This article incorporates text from the public domain Pfam and InterPro IPR007588

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.

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Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in [1].

Literature references

  1. Dorn R, Krauss V; , Genetica 2003;117:165-177.: The modifier of mdg4 locus in Drosophila: functional complexity is resolved by trans splicing. PUBMED:12723696 EPMC:12723696


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007588

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.

C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 [PUBMED:11361095]. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes [PUBMED:10664601]. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA [PUBMED:10940247]. C2H2 Znf's can also bind to RNA and protein targets [PUBMED:18253864].

This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif:

F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH

where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs [PUBMED:12723696]. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain.

FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain [PUBMED:16944302].

More information about these proteins can be found at Protein of the Month: Zinc Fingers [PUBMED:].

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

This family is a member of clan WRKY-GCM1 (CL0274), which has the following description:

WRKY and GCM1 are metal chelating DNA-binding domains (DBD) which share a four stranded fold [1]. We present evidence that they share a stabilising core, which suggests a possible origin from a BED finger-like intermediate that was in turn ultimately derived from a C2H2 Zn-finger domain [1].

The clan contains the following 6 members:

AFT DBD_Tnp_Mut FAR1 FLYWCH GCM WRKY

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.

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(128)
Full
(1130)
Representative proteomes NCBI
(1222)
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(0)
RP15
(187)
RP35
(296)
RP55
(645)
RP75
(775)
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Format an alignment

  Seed
(128)
Full
(1130)
Representative proteomes NCBI
(1222)
Meta
(0)
RP15
(187)
RP35
(296)
RP55
(645)
RP75
(775)
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
(128)
Full
(1130)
Representative proteomes NCBI
(1222)
Meta
(0)
RP15
(187)
RP35
(296)
RP55
(645)
RP75
(775)
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.

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.

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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.

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Seed source: Krauss V
Previous IDs: none
Type: Domain
Author: Krauss V, Dorn R
Number in seed: 128
Number in full: 1130
Average length of the domain: 60.70 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 26.35 %

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 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 62
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 FLYWCH domain has been found. There are 1 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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