This is the Wikipedia entry entitled "Fibrillarin". More...
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Fibrillarin Edit Wikipedia article
PDB rendering based on 2ipx.
|Symbols||; FIB; FLRN; RNU3IP1|
|RNA expression pattern|
pyrococcus horikoshii fibrillarin pre-rrna processing protein
This gene product is a component of a nucleolar small nuclear ribonucleoprotein (snRNP) particle thought to participate in the first step in processing pre-ribosomal (r)RNA. It is associated with the U3, U8, and U13 small nuclear RNAs and is located in the dense fibrillar component (DFC) of the nucleolus. The encoded protein contains an N-terminal repetitive domain that is rich in glycine and arginine residues, like fibrillarins in other species. Its central region resembles an RNA-binding domain and contains an RNP consensus sequence. Antisera from approximately 8% of humans with the autoimmune disease scleroderma recognize fibrillarin.
Fibrillarin is a component of several ribonucleoproteins including a nucleolar small nuclear ribonucleoprotein (SnRNP) and one of the two classes of small nucleolar ribonucleoproteins (snoRNPs). SnRNAs function in RNA splicing while snoRNPs function in ribosomal RNA processing.
Fibrillarin is associated with U3, U8 and U13 small nuclear RNAs in mammals and is similar to the yeast NOP1 protein. Fibrillarin has a well conserved sequence of around 320 amino acids, and contains 3 domains, an N-terminal Gly/Arg-rich region; a central domain resembling other RNA-binding proteins and containing an RNP-2-like consensus sequence; and a C-terminal alpha-helical domain. An evolutionarily related pre-rRNA processing protein, which lacks the Gly/Arg-rich domain, has been found in various archaebacteria.
A study by Schultz et al. indicated that the K-turn binding 15.5-kDa protein (called Snu13 in yeast) interacts with spliceosome proteins hPRP31, hPRP3, hPRP4, CYPH and the small nucleolar ribonucleoproteins NOP56, NOP58, and fibrillarin. The 15.5-kDa protein has sequence similarity to other RNA-binding proteins such as ribosomal proteins S12, L7a, and L30 and the snoRNP protein NHP2. The U4/U6 snRNP contains 15.5-kDa protein. The 15.5-kDa protein also exists in a ribonucleoprotein complex that binds the U3 box B/C motif. The 15.5-kDa protein also exists as one of the four core proteins of the C/D small nucleolar ribonucleoprotein that mediates methylation of pre-ribosomal RNAs.
- Aris JP, Blobel G (March 1991). "cDNA cloning and sequencing of human fibrillarin, a conserved nucleolar protein recognized by autoimmune antisera". Proc. Natl. Acad. Sci. U.S.A. 88 (3): 931–5. doi:10.1073/pnas.88.3.931. PMC 50928. PMID 1846968.
- Jansen RP, Hurt EC, Kern H, Lehtonen H, Carmo-Fonseca M, Lapeyre B, Tollervey D (June 1991). "Evolutionary conservation of the human nucleolar protein fibrillarin and its functional expression in yeast". J Cell Biol 113 (4): 715–29. doi:10.1083/jcb.113.4.715. PMC 2288999. PMID 2026646.
- "Entrez Gene: FBL fibrillarin".
- Protein-Protein and Protein-RNA Contacts both Contribute to the 15.5K-Mediated Assembly of the U4/U6 snRNP and the Box C/D snoRNPs by Annemarie Schultz, Stephanie Nottrott, Nicholas James Watkins and Reinhard Lührmann in Molecular and Cellular Biology (2006) Volume 26, pages 5146–5154.
- The structure and function of small nucleolar ribonucleoproteins by Steve L. Reichow, Tomoko Hamma, Adrian R. Ferré-D'Amaré and Gabriele Varani in Nucleic Acids Research (2007) Volume 35, pages 1452–1464.
- Nicol, S M; Causevic M; Prescott A R; Fuller-Pace F V (June 2000). "The nuclear DEAD box RNA helicase p68 interacts with the nucleolar protein fibrillarin and colocalizes specifically in nascent nucleoli during telophase". Exp. Cell Res. (UNITED STATES) 257 (2): 272–80. doi:10.1006/excr.2000.4886. ISSN 0014-4827. PMID 10837141.
- Pellizzoni, L; Baccon J; Charroux B; Dreyfuss G (July 2001). "The survival of motor neurons (SMN) protein interacts with the snoRNP proteins fibrillarin and GAR1". Curr. Biol. (England) 11 (14): 1079–88. doi:10.1016/S0960-9822(01)00316-5. ISSN 0960-9822. PMID 11509230.
- Baserga SJ, Yang XD, Steitz JA (1991). "An intact Box C sequence in the U3 snRNA is required for binding of fibrillarin, the protein common to the major family of nucleolar snRNPs". EMBO J. 10 (9): 2645–51. PMC 452965. PMID 1714385.
- Okano Y, Steen VD, Medsger TA (1992). "Autoantibody to U3 nucleolar ribonucleoprotein (fibrillarin) in patients with systemic sclerosis". Arthritis Rheum. 35 (1): 95–100. doi:10.1002/art.1780350114. PMID 1731817.
- Lischwe MA, Ochs RL, Reddy R et al. (1985). "Purification and partial characterization of a nucleolar scleroderma antigen (Mr = 34,000; pI, 8.5) rich in NG,NG-dimethylarginine". J. Biol. Chem. 260 (26): 14304–10. PMID 2414294.
- Méhes G, Pajor L (1995). "Nucleolin and fibrillarin expression in stimulated lymphocytes and differentiating HL-60 cells. A flow cytometric assay". Cell Prolif. 28 (6): 329–36. doi:10.1111/j.1365-2184.1995.tb00074.x. PMID 7626687.
- Liu Q, Dreyfuss G (1996). "A novel nuclear structure containing the survival of motor neurons protein". EMBO J. 15 (14): 3555–65. PMC 451956. PMID 8670859.
- Magoulas C, Zatsepina OV, Jordan PW et al. (1998). "The SURF-6 protein is a component of the nucleolar matrix and has a high binding capacity for nucleic acids in vitro". Eur. J. Cell Biol. 75 (2): 174–83. doi:10.1016/s0171-9335(98)80059-9. PMID 9548374.
- Ai LS, Lin CH, Hsieh M, Li C (1999). "Arginine methylation of a glycine and arginine rich peptide derived from sequences of human FMRP and fibrillarin". Proc. Natl. Sci. Counc. Repub. China B 23 (4): 175–80. PMID 10518318.
- Pintard L, Kressler D, Lapeyre B (2000). "Spb1p Is a Yeast Nucleolar Protein Associated with Nop1p and Nop58p That Is Able To Bind S-Adenosyl-l-Methionine In Vitro". Mol. Cell. Biol. 20 (4): 1370–81. doi:10.1128/MCB.20.4.1370-1381.2000. PMC 85287. PMID 10648622.
- Nicol SM, Causevic M, Prescott AR, Fuller-Pace FV (2000). "The nuclear DEAD box RNA helicase p68 interacts with the nucleolar protein fibrillarin and colocalizes specifically in nascent nucleoli during telophase". Exp. Cell Res. 257 (2): 272–80. doi:10.1006/excr.2000.4886. PMID 10837141.
- Pellizzoni L, Baccon J, Charroux B, Dreyfuss G (2001). "The survival of motor neurons (SMN) protein interacts with the snoRNP proteins fibrillarin and GAR1". Curr. Biol. 11 (14): 1079–88. doi:10.1016/S0960-9822(01)00316-5. PMID 11509230.
- Zhou X, Tan FK, Xiong M et al. (2001). "Systemic sclerosis (scleroderma): specific autoantigen genes are selectively overexpressed in scleroderma fibroblasts". Journal of Immunology 167 (12): 7126–33. doi:10.4049/jimmunol.167.12.7126. PMID 11739535.
- Andersen JS, Lyon CE, Fox AH et al. (2002). "Directed proteomic analysis of the human nucleolus". Curr. Biol. 12 (1): 1–11. doi:10.1016/S0960-9822(01)00650-9. PMID 11790298.
- Cimato TR, Tang J, Xu Y et al. (2002). "Nerve growth factor-mediated increases in protein methylation occur predominantly at type I arginine methylation sites and involve protein arginine methyltransferase 1". J. Neurosci. Res. 67 (4): 435–42. doi:10.1002/jnr.10123. PMID 11835310.
- Fujiyama S, Yanagida M, Hayano T et al. (2002). "Isolation and proteomic characterization of human Parvulin-associating preribosomal ribonucleoprotein complexes". J. Biol. Chem. 277 (26): 23773–80. doi:10.1074/jbc.M201181200. PMID 11960984.
- Whitehead SE, Jones KW, Zhang X et al. (2003). "Determinants of the interaction of the spinal muscular atrophy disease protein SMN with the dimethylarginine-modified box H/ACA small nucleolar ribonucleoprotein GAR1". J. Biol. Chem. 277 (50): 48087–93. doi:10.1074/jbc.M204551200. PMID 12244096.
- Herrera-Esparza R, Kruse L, von Essen M et al. (2003). "U3 snoRNP associates with fibrillarin a component of the scleroderma clumpy nucleolar domain". Arch. Dermatol. Res. 294 (7): 310–7. doi:10.1007/s00403-002-0338-7. PMID 12373336.
- Chen M, Rockel T, Steinweger G et al. (2003). "Subcellular Recruitment of Fibrillarin to Nucleoplasmic Proteasomes: Implications for Processing of a Nucleolar Autoantigen". Mol. Biol. Cell 13 (10): 3576–87. doi:10.1091/mbc.02-05-0083. PMC 129967. PMID 12388758.
- Watkins NJ, Dickmanns A, Lührmann R (2003). "Conserved Stem II of the Box C/D Motif Is Essential for Nucleolar Localization and Is Required, Along with the 15.5K Protein, for the Hierarchical Assembly of the Box C/D snoRNP". Mol. Cell. Biol. 22 (23): 8342–52. doi:10.1128/MCB.22.23.8342-8352.2002. PMC 134055. PMID 12417735.
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Fibrillarin Provide feedback
No Pfam abstract.
Internal database links
|Similarity to PfamA using HHSearch:||FtsJ PCMT Methyltransf_11 Methyltransf_12 Methyltransf_18 Methyltransf_24 Methyltransf_25 Methyltransf_26 Methyltransf_31|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000692Fibrillarin is a component of a nucleolar small nuclear ribonucleoprotein (SnRNP), functioning in vivo in ribosomal RNA processing [PUBMED:2026646, PUBMED:8493104]. It is associated with U3, U8 and U13 small nuclear RNAs in mammals [PUBMED:2026646] and is similar to the yeast NOP1 protein [PUBMED:2686980]. Fibrillarin has a well conserved sequence of around 320 amino acids, and contains 3 domains, an N-terminal Gly/Arg-rich region; a central domain resembling other RNA-binding proteins and containing an RNP-2-like consensus sequence; and a C-terminal alpha-helical domain. An evolutionarily related pre-rRNA processing protein, which lacks the Gly/Arg-rich domain, has been found in various archaebacteria.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||RNA binding (GO:0003723)|
|methyltransferase activity (GO:0008168)|
|Biological process||rRNA processing (GO:0006364)|
|tRNA processing (GO:0008033)|
- the number of sequences which exhibit this architecture
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A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme. The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction. Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site . In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.
The clan contains the following 180 members:2-Hacid_dh_C 3Beta_HSD 3HCDH_N adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa Bac_GDH Bin3 CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 DAO DapB_N DFP DNA_circ_N DNA_methylase DOT1 DREV dTMP_synthase DUF1442 DUF1776 DUF2431 DUF268 DUF3321 DUF43 DUF633 DUF938 DXP_redisom_C DXP_reductoisom Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ G-7-MTase G6PD_N GCD14 GDI GFO_IDH_MocA GIDA GidB GLF Glyco_hydro_4 GMC_oxred_N Gp_dh_N GRAS GRDA HI0933_like HIM1 IlvN K_oxygenase KR LCM Ldh_1_N Lycopene_cycl Malic_M Mannitol_dh Met_10 Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_26 Methyltransf_27 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C Mqo MT-A70 MTS Mur_ligase N2227 N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_11 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS Nol1_Nop2_Fmu Nol1_Nop2_Fmu_2 NSP13 OCD_Mu_crystall PARP_regulatory PCMT PDH Polysacc_synt_2 Pox_MCEL Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Saccharop_dh SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth Strep_67kDa_ant TehB THF_DHG_CYH_C Thi4 ThiF TPMT TrkA_N TRM TRM13 tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 V_cholerae_RfbT XdhC_C YjeF_N
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Author:||Finn RD, Bateman A|
|Number in seed:||42|
|Number in full:||616|
|Average length of the domain:||215.80 aa|
|Average identity of full alignment:||57 %|
|Average coverage of the sequence by the domain:||78.68 %|
|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:||12|
|Download:||download the raw HMM for this family|
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There are 2 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 Fibrillarin domain has been found. There are 19 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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