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1  structure 294  species 0  interactions 975  sequences 16  architectures

Family: zf-MIZ (PF02891)

Summary: MIZ/SP-RING zinc finger

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

MIZ zinc finger Edit Wikipedia article

X-ray crystal structure of MIZ1 zinc finger protein (PDB 2Q81),[1] structure created with PyMol.
zf-MIZ
Identifiers
Symbol zf-MIZ
Pfam PF02891
Pfam clan CL0229
InterPro IPR004181

In molecular biology the MIZ-type zinc finger domain is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2.[2] Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). The name MIZ is derived from Msx-interacting-zinc finger. The crystal structure of S. cerevisiae sumo e3 ligase siz1 containg this domain has been solved.

References[edit]

  1. ^ Stead, M.A., Trinh, C.H., Garnett, J.A., Carr, S.B., Baron, A.J., Edwards, T.A., Wright, S.C. (2007). "A beta-sheet interaction interface directs the tetramerisation of the Miz-1 POZ domain.". J.Mol.Biol. 373: 820–826. doi:10.1016/j.jmb.2007.08.026. 
  2. ^ Wu L, Wu H, Ma L, Sangiorgi F, Wu N, Bell JR, Lyons GE, Maxson R (July 1997). "Miz1, a novel zinc finger transcription factor that interacts with Msx2 and enhances its affinity for DNA". Mech. Dev. 65 (1-2): 3–17. doi:10.1016/S0925-4773(97)00032-4. PMID 9256341. 

This article incorporates text from the public domain Pfam and InterPro IPR004181

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.

MIZ/SP-RING zinc finger Provide feedback

This domain has SUMO (small ubiquitin-like modifier) ligase activity and is involved in DNA repair and chromosome organisation [2].

Literature references

  1. Wu L, Wu H, Ma L, Sangiorgi F, Wu N, Bell JR, Lyons GE, Maxson R; , Mech Dev 1997;65:3-17.: Miz1, a novel zinc finger transcription factor that interacts with Msx2 and enhances its affinity for DNA. PUBMED:9256341 EPMC:9256341

  2. Zhao X, Blobel G; , Proc Natl Acad Sci U S A 2005;102:4777-4782.: From The Cover: A SUMO ligase is part of a nuclear multiprotein complex that affects DNA repair and chromosomal organization. PUBMED:15738391 EPMC:15738391

  3. Cheng CH, Lo YH, Liang SS, Ti SC, Lin FM, Yeh CH, Huang HY, Wang TF; , Genes Dev. 2006;20:2067-2081.: SUMO modifications control assembly of synaptonemal complex and polycomplex in meiosis of Saccharomyces cerevisiae. PUBMED:16847351 EPMC:16847351


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004181

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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 [PUBMED:9256341]. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein).

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 RING (CL0229), which has the following description:

This clan includes the Ring zinc finger domains as well as the U-box domain that appears to have lost the zinc coordinating cysteine residues [1].

The clan contains the following 24 members:

Baculo_RING FANCL_C Prok-RING_1 Prok-RING_2 Prok-RING_4 RINGv Rtf2 U-box zf-Apc11 zf-C3HC4 zf-C3HC4_2 zf-C3HC4_3 zf-C3HC4_4 zf-MIZ zf-Nse zf-rbx1 zf-RING-like zf-RING_2 zf-RING_4 zf-RING_5 zf-RING_6 zf-RING_UBOX zf-UBP zf-UDP

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
(36)
Full
(975)
Representative proteomes NCBI
(1031)
Meta
(4)
RP15
(192)
RP35
(294)
RP55
(443)
RP75
(586)
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Format an alignment

  Seed
(36)
Full
(975)
Representative proteomes NCBI
(1031)
Meta
(4)
RP15
(192)
RP35
(294)
RP55
(443)
RP75
(586)
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
(36)
Full
(975)
Representative proteomes NCBI
(1031)
Meta
(4)
RP15
(192)
RP35
(294)
RP55
(443)
RP75
(586)
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

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Curation View help on the curation process

Seed source: Psi-blast Q9UN16
Previous IDs: none
Type: Domain
Author: Bateman A, Mistry J, Wood V
Number in seed: 36
Number in full: 975
Average length of the domain: 50.20 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 7.21 %

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 22.2 22.2
Trusted cut-off 22.3 22.3
Noise cut-off 22.1 22.1
Model length: 50
Family (HMM) version: 15
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-MIZ 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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