Summary: RING-like domain
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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 Cys3HisCys4 amino acid motif which binds two zinc cations. 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, KIAA1542, LNX1, LNX2, LOC51136, LONRF1, LONRF2, LONRF3, MARCH1, MARCH10, MARCH2, MARCH3, MARCH4, MARCH5, MARCH6, MARCH7, MARCH8, MARCH9, 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, 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, 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, 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 46035. 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 18039. 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.
RING-like domain Provide feedback
This is a zinc finger domain that is related to the C3HC4 RING finger domain (PF00097).
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This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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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 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
We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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Curation and family details
|Author:||Mistry J, Wood V|
|Number in seed:||12|
|Number in full:||210|
|Average length of the domain:||43.10 aa|
|Average identity of full alignment:||37 %|
|Average coverage of the sequence by the domain:||14.10 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
|Download:||download the raw HMM for this family|
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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-RING-like domain has been found. There are 2 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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