Summary: Zinc finger, C3HC4 type (RING finger)
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RING finger domain Edit Wikipedia article
|Zinc finger, C3HC4 type (RING finger)|
Structure of the C3HC4 domain. Zinc ions are black spheres, coordinated by cysteines residues (blue).
In molecular biology, a RING (Really Interesting New Gene) finger domain is a protein structural domain of zinc finger type which contains a C3HC4 amino acid motif which binds two zinc cations (seven cysteines and one histidine arranged non-consecutively). This protein domain contains from 40 to 60 amino acids. Many proteins containing a RING finger play a key role in the ubiquitination pathway.
Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They bind DNA, RNA, protein and/or lipid substrates. 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. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
Some Zn finger domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds.
Many RING finger domains simultaneously bind ubiquitination enzymes and their substrates and hence function as ligases. Ubiquitination in turn targets the substrate protein for degradation.
The RING finger domain has the consensus sequence C-X2-C-X[9-39]-C-X[1-3]-H-X[2-3]-C-X2-C-X[4-48]-C-X2-C. where:
- C is a conserved cysteine residue involved zinc coordination,
- H is a conserved histidine involved in zinc coordination,
- Zn is zinc atom, and
- X is any amino acid residue.
The following is a schematic representation of the structure of the RING finger domain:
x x x x x x x x x x x x x x x x x x C C C C x \ / x x \ / x x Zn x x Zn x C / \ H C / \ C x x x x x x x x x x x x x x x x x
Examples of human genes which encode proteins containing a RING finger domain include:
AMFR, BBAP, BFAR, BIRC2, BIRC3, BIRC7, BIRC8, BMI1, BRAP, BRCA1, CBL, CBLB, CBLC, CBLL1, CHFR, COMMD3, DTX1, DTX2, DTX3, DTX3L, DTX4, DZIP3, HCGV, HLTF, HOIL-1, IRF2BP2, LNX1, LNX2, LONRF1, LONRF2, LONRF3, MARCH1, MARCH10, MARCH2, MARCH3, MARCH4, MARCH5, MARCH6, MARCH7, MARCH8, MARCH9, MDM2, MEX3A, MEX3B, MEX3C, MEX3D, MGRN1, MIB1, MID1, MID2, MKRN1, MKRN2, MKRN3, MKRN4, MNAT1, MYLIP, NFX1, NFX2, PCGF1, PCGF2, PCGF3, PCGF4, PCGF5, PCGF6, PDZRN3, PDZRN4, PEX10, PHRF1, PJA1, PJA2, PML, PML-RAR, PXMP3, RAD18, RAG1, RAPSN, RBCK1, RBX1, RC3H1, RC3H2, RCHY1, RFP2, RFPL1, RFPL2, RFPL3, RFPL4B, RFWD2, RFWD3, RING1, RNF2, RNF4, RNF5, RNF6, RNF7, RNF8, RNF10, RNF11, RNF12, RNF13, RNF14, RNF19A, RNF20, RNF24, RNF25, RNF26, RNF32, RNF38, RNF39, RNF40, RNF41, RNF43, RNF44, RNF55, RNF71, RNF103, RNF111, RNF113A, RNF113B, RNF121, RNF122, RNF123, RNF125, RNF126, RNF128, RNF130, RNF133, RNF135, RNF138, RNF139, RNF141, RNF144A, RNF145, RNF146, RNF148, RNF149, RNF150, RNF151, RNF152, RNF157, RNF165, RNF166, RNF167, RNF168, RNF169, RNF170, RNF175, RNF180, RNF181, RNF182, RNF185, RNF207, RNF213, RNF215, RNFT1, SH3MD4, SH3RF1, SH3RF2, SYVN1, TIF1, TMEM118, TOPORS, TRAF2, TRAF3, TRAF4, TRAF5, TRAF6, TRAF7, TRAIP, TRIM2, TRIM3, TRIM4, TRIM5, TRIM6, TRIM7, TRIM8, TRIM9, TRIM10, TRIM11, TRIM13, TRIM15, TRIM17, TRIM21, TRIM22, TRIM23, TRIM24, TRIM25, TRIM26, TRIM27, TRIM28, TRIM31, TRIM32, TRIM33, TRIM34, TRIM35, TRIM36, TRIM38, TRIM39, TRIM40, TRIM41, TRIM42, TRIM43, TRIM45, TRIM46, TRIM47, TRIM48, TRIM49, TRIM50, TRIM52, TRIM54, TRIM55, TRIM56, TRIM58, TRIM59, TRIM60, TRIM61, TRIM62, TRIM63, TRIM65, TRIM67, TRIM68, TRIM69, TRIM71, TRIM72, TRIM73, TRIM74, TRIML1, TTC3, UHRF1, UHRF2, VPS11, VPS8, ZNF179, ZNF294, ZNF313, ZNF364, ZNF650, ZNFB7, ZNRF1, ZNRF2, ZNRF3, ZNRF4, and ZSWIM2.
- Barlow PN, Luisi B, Milner A, Elliott M, Everett R (March 1994). "Structure of the C3HC4 domain by 1H-nuclear magnetic resonance spectroscopy. A new structural class of zinc-finger". J. Mol. Biol. 237 (2): 201–11. doi:10.1006/jmbi.1994.1222. PMID 8126734.
- Borden KL, Freemont PS (1996). "The RING finger domain: a recent example of a sequence-structure family". Curr. Opin. Struct. Biol. 6 (3): 395–401. doi:10.1016/S0959-440X(96)80060-1. PMID 8804826.
- Hanson IM, Poustka A, Trowsdale J (1991). "New genes in the class II region of the human major histocompatibility complex". Genomics. 10 (2): 417–24. doi:10.1016/0888-7543(91)90327-B. PMID 1906426.
- Freemont PS, Hanson IM, Trowsdale J (1991). "A novel cysteine-rich sequence motif". Cell. 64 (3): 483–4. doi:10.1016/0092-8674(91)90229-R. PMID 1991318.
- Lovering R, Hanson IM, Borden KL, Martin S, O'Reilly NJ, Evan GI, Rahman D, Pappin DJ, Trowsdale J, Freemont PS (1993). "Identification and preliminary characterization of a protein motif related to the zinc finger". Proc. Natl. Acad. Sci. U.S.A. 90 (6): 2112–6. doi:10.1073/pnas.90.6.2112. PMC . PMID 7681583.
- Klug A (1999). "Zinc finger peptides for the regulation of gene expression". J. Mol. Biol. 293 (2): 215–8. doi:10.1006/jmbi.1999.3007. PMID 10529348.
- Hall TM (2005). "Multiple modes of RNA recognition by zinc finger proteins". Curr. Opin. Struct. Biol. 15 (3): 367–73. doi:10.1016/j.sbi.2005.04.004. PMID 15963892.
- Brown RS (2005). "Zinc finger proteins: getting a grip on RNA". Curr. Opin. Struct. Biol. 15 (1): 94–8. doi:10.1016/j.sbi.2005.01.006. PMID 15718139.
- Gamsjaeger R, Liew CK, Loughlin FE, Crossley M, Mackay JP (2007). "Sticky fingers: zinc-fingers as protein-recognition motifs". Trends Biochem. Sci. 32 (2): 63–70. doi:10.1016/j.tibs.2006.12.007. PMID 17210253.
- Matthews JM, Sunde M (2002). "Zinc fingers--folds for many occasions". IUBMB Life. 54 (6): 351–5. doi:10.1080/15216540216035. PMID 12665246.
- Laity JH, Lee BM, Wright PE (2001). "Zinc finger proteins: new insights into structural and functional diversity". Curr. Opin. Struct. Biol. 11 (1): 39–46. doi:10.1016/S0959-440X(00)00167-6. PMID 11179890.
- Lorick KL, Jensen JP, Fang S, Ong AM, Hatakeyama S, Weissman AM (1999). "RING fingers mediate ubiquitin-conjugating enzyme (E2)-dependent ubiquitination". Proc. Natl. Acad. Sci. U.S.A. 96 (20): 11364–9. doi:10.1073/pnas.96.20.11364. PMC . PMID 10500182.
- Joazeiro CA, Weissman AM (2000). "RING finger proteins: mediators of ubiquitin ligase activity". Cell. 102 (5): 549–52. doi:10.1016/S0092-8674(00)00077-5. PMID 11007473.
- Freemont PS (2000). "RING for destruction?". Curr. Biol. 10 (2): R84–7. doi:10.1016/S0960-9822(00)00287-6. PMID 10662664.
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.
Zinc finger, C3HC4 type (RING finger) Provide feedback
The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid . Many proteins containing a RING finger play a key role in the ubiquitination pathway .
Lorick KL, Jensen JP, Fang S, Ong AM, Hatakeyama S, Weissman AM; , Proc Natl Acad Sci U S A 1999;96:11364-11369.: RING fingers mediate ubiquitin-conjugating enzyme (E2)-dependent ubiquitination. PUBMED:10500182 EPMC:10500182
Internal database links
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR018957
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.
The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid [PUBMED:8804826]. Many proteins containing a RING finger play a key role in the ubiquitination pathway [PUBMED:10500182].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||metal ion binding (GO:0046872)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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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 .
The clan contains the following 43 members:Baculo_IE-1 Baculo_RING DUF1644 FANCL_C IBR Prok-RING_1 Prok-RING_2 Prok-RING_4 RINGv Rtf2 T3SS_NleG U-box UPF1_Zn_bind VATC zf-ANAPC11 zf-C3H2C3 zf-C3HC4 zf-C3HC4_2 zf-C3HC4_3 zf-C3HC4_4 zf-C3HC4_5 zf-MIZ zf-NOSIP zf-Nse zf-P11 zf-rbx1 zf-RING-like zf-RING_10 zf-RING_11 zf-RING_12 zf-RING_13 zf-RING_14 zf-RING_2 zf-RING_4 zf-RING_5 zf-RING_6 zf-RING_9 zf-RING_UBOX zf-UBP zf-UBP_var zf-UDP zinc_ribbon_16 Zn_ribbon_17
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
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|Author:||Sonnhammer ELL , Vella Briffa B|
|Number in seed:||35|
|Number in full:||10949|
|Average length of the domain:||44.80 aa|
|Average identity of full alignment:||30 %|
|Average coverage of the sequence by the domain:||7.29 %|
|HMM build commands:||
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||25|
|Download:||download the raw HMM for this family|
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This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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There are 10 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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-C3HC4 domain has been found. There are 8 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 sequence.
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