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26  structures 370  species 0  interactions 3934  sequences 252  architectures

Family: zf-MYND (PF01753)

Summary: MYND finger

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

MYND zinc finger Edit Wikipedia article

zf-MYND
PDB 2dj8 EBI.jpg
solution structure of zf-mynd domain of protein cbfa2ti (protein mtg8)
Identifiers
Symbol zf-MYND
Pfam PF01753
Pfam clan CL0175
InterPro IPR002893

In molecular biology the MYND-type zinc finger domain is a conserved protein domain. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants.[1][2][3] The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif.[2] Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions.[2] Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors.[4][5] Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein.[6] A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression.[7] The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface.

References[edit]

  1. ^ Feinstein PG, Kornfeld K, Hogness DS, Mann RS (June 1995). "Identification of homeotic target genes in Drosophila melanogaster including nervy, a proto-oncogene homologue". Genetics 140 (2): 573–86. PMC 1206636. PMID 7498738. 
  2. ^ a b c Gross CT, McGinnis W (April 1996). "DEAF-1, a novel protein that binds an essential region in a Deformed response element". EMBO J. 15 (8): 1961–70. PMC 450115. PMID 8617243. 
  3. ^ Owens GP, Hahn WE, Cohen JJ (August 1991). "Identification of mRNAs associated with programmed cell death in immature thymocytes". Mol. Cell. Biol. 11 (8): 4177–88. PMC 361239. PMID 2072913. 
  4. ^ Lutterbach B, Sun D, Schuetz J, Hiebert SW (June 1998). "The MYND motif is required for repression of basal transcription from the multidrug resistance 1 promoter by the t(8;21) fusion protein". Mol. Cell. Biol. 18 (6): 3604–11. PMC 108942. PMID 9584201. 
  5. ^ Lutterbach B, Westendorf JJ, Linggi B, Patten A, Moniwa M, Davie JR, Huynh KD, Bardwell VJ, Lavinsky RM, Rosenfeld MG, Glass C, Seto E, Hiebert SW (December 1998). "ETO, a target of t(8;21) in acute leukemia, interacts with the N-CoR and mSin3 corepressors". Mol. Cell. Biol. 18 (12): 7176–84. PMC 109299. PMID 9819404. 
  6. ^ Melnick AM, Westendorf JJ, Polinger A, Carlile GW, Arai S, Ball HJ, Lutterbach B, Hiebert SW, Licht JD (March 2000). "The ETO protein disrupted in t(8;21)-associated acute myeloid leukemia is a corepressor for the promyelocytic leukemia zinc finger protein". Mol. Cell. Biol. 20 (6): 2075–86. doi:10.1128/MCB.20.6.2075-2086.2000. PMC 110824. PMID 10688654. 
  7. ^ Masselink H, Bernards R (March 2000). "The adenovirus E1A binding protein BS69 is a corepressor of transcription through recruitment of N-CoR". Oncogene 19 (12): 1538–46. doi:10.1038/sj.onc.1203421. PMID 10734313. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR002893

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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Literature references

  1. Gross CT, McGinnis W; , EMBO J 1996;15:1961-1970.: DEAF-1, a novel protein that binds an essential region in a Deformed response element. PUBMED:8617243 EPMC:8617243

  2. LeBoeuf RD, Ban EM, Green MM, Stone AS, Propst SM, Blalock JE, Tauber JD; , J Biol Chem 1998;273:361-368.: Molecular cloning, sequence analysis, expression, and tissue distribution of suppressin, a novel suppressor of cell cycle entry. PUBMED:9417089 EPMC:9417089


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002893

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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [PUBMED:7498738, PUBMED:8617243, PUBMED:2072913]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif [PUBMED:8617243]. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions [PUBMED:8617243]. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [PUBMED:9584201, PUBMED:9819404]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein [PUBMED:10688654]. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression [PUBMED:10734313]. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface.

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

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

This family is a member of clan TRASH (CL0175), which has the following description:

TRASH-like domains contain well-conserved cysteine residues that are thought to be involved in metal coordination. These domains are thus expected to be involved in metal trafficking and heavy-metal resistance. It has been suggested that the members adopt a 'treble-clef' fold, with 3/4 beta strands preceding a C-terminal alpha helix [1].

The clan contains the following 11 members:

Arc_trans_TRASH ATPase-cat_bd DUF2256 DUF329 DUF581 Ribosomal_L24e YHS zf-FCS zf-HIT zf-Mss51 zf-MYND

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
(177)
Full
(3934)
Representative proteomes NCBI
(4039)
Meta
(204)
RP15
(1218)
RP35
(1661)
RP55
(2317)
RP75
(2780)
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Format an alignment

  Seed
(177)
Full
(3934)
Representative proteomes NCBI
(4039)
Meta
(204)
RP15
(1218)
RP35
(1661)
RP55
(2317)
RP75
(2780)
Alignment:
Format:
Order:
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
(177)
Full
(3934)
Representative proteomes NCBI
(4039)
Meta
(204)
RP15
(1218)
RP35
(1661)
RP55
(2317)
RP75
(2780)
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: Bateman A
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 177
Number in full: 3934
Average length of the domain: 41.10 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 7.26 %

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 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.4 20.4
Model length: 37
Family (HMM) version: 13
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 zf-MYND domain has been found. There are 26 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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