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PDBsum entry 1fbn

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protein links
Ribosome PDB id
1fbn
Jmol PyMol
Contents
Protein chain
230 a.a. *
Waters ×186
* Residue conservation analysis
PDB id:
1fbn
Name: Ribosome
Title: Crystal structure of a fibrillarin homologue from methanococ jannaschii, a hyperthermophile, at 1.6 a
Structure: Mj fibrillarin homologue. Chain: a. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: psj1240.
Biol. unit: Dimer (from PQS)
Resolution:
1.60Å     R-factor:   0.229     R-free:   0.248
Authors: H.Wang,D.Boisvert,K.K.Kim,R.Kim,S.H.Kim,Berkeley Structural Center (Bsgc)
Key ref:
H.Wang et al. (2000). Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution. EMBO J, 19, 317-323. PubMed id: 10654930 DOI: 10.1093/emboj/19.3.317
Date:
25-Apr-99     Release date:   26-Apr-00    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q58108  (FLPA_METJA) -  Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Seq:
Struc:
230 a.a.
230 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     small-subunit processome   2 terms 
  Biological process     methylation   6 terms 
  Biochemical function     transferase activity     5 terms  

 

 
DOI no: 10.1093/emboj/19.3.317 EMBO J 19:317-323 (2000)
PubMed id: 10654930  
 
 
Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution.
H.Wang, D.Boisvert, K.K.Kim, R.Kim, S.H.Kim.
 
  ABSTRACT  
 
Fibrillarin is a phylogenetically conserved protein essential for efficient processing of pre-rRNA through its association with a class of small nucleolar RNAs during ribosomal biogenesis. The protein is the antigen for the autoimmune disease scleroderma. Here we report the crystal structure of the fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution. The structure consists of two domains, with a novel fold in the N-terminal region and a methyltransferase-like domain in the C-terminal region. Mapping temperature-sensitive mutations found in yeast fibrillarin Nop1 to the Methanococcus homologue structure reveals that many of the mutations cluster in the core of the methyltransferase-like domain.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 (A) A comparison of the topological representations of the C-terminal domain of Mj0697 and the consensus catalytic domain derived from other methyltransferases (Vidgren et al., 1994; Schluckebier et al., 1995; Djordjevic and Stock, 1997). Helices are shown as circles, -strands as triangles. The AdoMet-binding pocket is indicated. The location of the analogous pocket is indicated by an empty circle in the Mj0697 scheme. An extra helix present in the Methanococcus homologue that does not occur in the consensus domain is shaded darker. (B) Superposition of the C[ ]traces of the C-terminal domain in Mj0697 (black line), and of the methyltransferase catalytic domain in catechol O-methyltransferase, COMT (grey line). The diagram was prepared using INSIGHTII (Molecular Systems Inc.). (C) Structural-based sequence alignment of Mj0697 and COMT.
Figure 4.
Figure 4 Stereo diagram of the electron density map of the [1]– [1] loop (82–86) region in the Mj0697 structure. The solvent-flattened experimental electron density map was contoured at 1.5 , superimposed with the current model. This diagram was generated using the program O (Jones et al., 1991).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 317-323) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21270896 J.Lin, S.Lai, R.Jia, A.Xu, L.Zhang, J.Lu, and K.Ye (2011).
Structural basis for site-specific ribose methylation by box C/D RNA protein complexes.
  Nature, 469, 559-563.  
20572804 F.Bleichert, and S.J.Baserga (2010).
Ribonucleoprotein multimers and their functions.
  Crit Rev Biochem Mol Biol, 45, 331-350.  
20484469 Y.Soeno, Y.Taya, T.Stasyk, L.A.Huber, T.Aoba, and A.Hüttenhofer (2010).
Identification of novel ribonucleo-protein complexes from the brain-specific snoRNA MBII-52.
  RNA, 16, 1293-1300.  
19400805 E.Purta, M.O'Connor, J.M.Bujnicki, and S.Douthwaite (2009).
YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA.
  Mol Microbiol, 72, 1147-1158.  
19745151 F.Bleichert, K.T.Gagnon, B.A.Brown, E.S.Maxwell, A.E.Leschziner, V.M.Unger, and S.J.Baserga (2009).
A dimeric structure for archaeal box C/D small ribonucleoproteins.
  Science, 325, 1384-1387.  
19336398 J.W.Hardin, F.E.Reyes, and R.T.Batey (2009).
Analysis of a Critical Interaction within the Archaeal Box C/D Small Ribonucleoprotein Complex.
  J Biol Chem, 284, 15317-15324.
PDB codes: 3gqu 3gqx
19666563 K.Ye, R.Jia, J.Lin, M.Ju, J.Peng, A.Xu, and L.Zhang (2009).
Structural organization of box C/D RNA-guided RNA methyltransferase.
  Proc Natl Acad Sci U S A, 106, 13808-13813.
PDB codes: 3icx 3id5 3id6
18208838 A.B.Taylor, B.Meyer, B.Z.Leal, P.Kötter, V.Schirf, B.Demeler, P.J.Hart, K.D.Entian, and J.Wöhnert (2008).
The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.
  Nucleic Acids Res, 36, 1542-1554.
PDB codes: 3bbd 3bbe 3bbh
18417574 E.Decroly, I.Imbert, B.Coutard, M.Bouvet, B.Selisko, K.Alvarez, A.E.Gorbalenya, E.J.Snijder, and B.Canard (2008).
Coronavirus nonstructural protein 16 is a cap-0 binding enzyme possessing (nucleoside-2'O)-methyltransferase activity.
  J Virol, 82, 8071-8084.  
18457570 O.O.Zharskaya, A.S.Barsukova, and O.V.Zatsepina (2008).
Effect of roscovitine, a selective cyclin B-dependent kinase 1 inhibitor, on assembly of the nucleolus in mitosis.
  Biochemistry (Mosc), 73, 411-419.  
18539024 R.Ishitani, S.Yokoyama, and O.Nureki (2008).
Structure, dynamics, and function of RNA modification enzymes.
  Curr Opin Struct Biol, 18, 330-339.  
17318225 A.G.Matera, R.M.Terns, and M.P.Terns (2007).
Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs.
  Nat Rev Mol Cell Biol, 8, 209-220.  
17438123 C.D.Appel, and E.S.Maxwell (2007).
Structural features of the guide:target RNA duplex required for archaeal box C/D sRNA-guided nucleotide 2'-O-methylation.
  RNA, 13, 899-911.  
17473012 E.Mastrangelo, M.Bollati, M.Milani, B.Selisko, F.Peyrane, B.Canard, G.Grard, X.de Lamballerie, and M.Bolognesi (2007).
Structural bases for substrate recognition and activity in Meaban virus nucleoside-2'-O-methyltransferase.
  Protein Sci, 16, 1133-1145.
PDB code: 2oxt
17519961 F.M.Boisvert, S.van Koningsbruggen, J.Navascués, and A.I.Lamond (2007).
The multifunctional nucleolus.
  Nat Rev Mol Cell Biol, 8, 574-585.  
17284456 S.L.Reichow, T.Hamma, A.R.Ferré-D'Amaré, and G.Varani (2007).
The structure and function of small nucleolar ribonucleoproteins.
  Nucleic Acids Res, 35, 1452-1464.  
17381300 D.C.Zappulla, and T.R.Cech (2006).
RNA as a flexible scaffold for proteins: yeast telomerase and beyond.
  Cold Spring Harb Symp Quant Biol, 71, 217-224.  
16984968 J.W.Hardin, and R.T.Batey (2006).
The bipartite architecture of the sRNA in an archaeal box C/D complex is a primary determinant of specificity.
  Nucleic Acids Res, 34, 5039-5051.  
17381323 T.Kiss, E.Fayet, B.E.Jády, P.Richard, and M.Weber (2006).
Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs.
  Cold Spring Harb Symp Quant Biol, 71, 407-417.  
17019528 Y.Makimoto, H.Yano, T.Kaneta, Y.Sato, and S.Sato (2006).
Molecular cloning and gene expression of a fibrillarin homolog of tobacco BY-2 cells.
  Protoplasma, 229, 53-62.  
15870259 D.L.Baker, O.A.Youssef, M.I.Chastkofsky, D.A.Dy, R.M.Terns, and M.P.Terns (2005).
RNA-guided RNA modification: functional organization of the archaeal H/ACA RNP.
  Genes Dev, 19, 1238-1248.  
15843864 S.Sato, H.Yano, Y.Makimoto, T.Kaneta, and Y.Sato (2005).
Nucleolonema as a fundamental substructure of the nucleolus.
  J Plant Res, 118, 71-81.  
15014443 A.Irimia, D.Madern, G.Zaccaï, and F.M.Vellieux (2004).
Methanoarchaeal sulfolactate dehydrogenase: prototype of a new family of NADH-dependent enzymes.
  EMBO J, 23, 1234-1244.
PDB code: 2x06
15286083 M.Aittaleb, T.Visone, M.O.Fenley, and H.Li (2004).
Structural and thermodynamic evidence for a stabilizing role of Nop5p in S-adenosyl-L-methionine binding to fibrillarin.
  J Biol Chem, 279, 41822-41829.  
14583623 M.Yanagida, T.Hayano, Y.Yamauchi, T.Shinkawa, T.Natsume, T.Isobe, and N.Takahashi (2004).
Human fibrillarin forms a sub-complex with splicing factor 2-associated p32, protein arginine methyltransferases, and tubulins alpha 3 and beta 1 that is independent of its association with preribosomal ribonucleoprotein complexes.
  J Biol Chem, 279, 1607-1614.  
15130473 T.Moore, Y.Zhang, M.O.Fenley, and H.Li (2004).
Molecular basis of box C/D RNA-protein interactions; cocrystal structure of archaeal L7Ae and a box C/D RNA.
  Structure, 12, 807-818.
PDB code: 1rlg
12694609 A.D.Omer, S.Ziesche, W.A.Decatur, M.J.Fournier, and P.P.Dennis (2003).
RNA-modifying machines in archaea.
  Mol Microbiol, 48, 617-629.  
12660717 A.Fatica, and D.Tollervey (2003).
Insights into the structure and function of a guide RNP.
  Nat Struct Biol, 10, 237-239.  
12547423 C.Zhang, and S.H.Kim (2003).
Overview of structural genomics: from structure to function.
  Curr Opin Chem Biol, 7, 28-32.  
14581554 D.Yoo, S.K.Wootton, G.Li, C.Song, and R.R.Rowland (2003).
Colocalization and interaction of the porcine arterivirus nucleocapsid protein with the small nucleolar RNA-associated protein fibrillarin.
  J Virol, 77, 12173-12183.  
12881427 E.J.Tran, X.Zhang, and E.S.Maxwell (2003).
Efficient RNA 2'-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C'/D' RNPs.
  EMBO J, 22, 3930-3940.  
12523999 J.W.Brown, M.Echeverria, and L.H.Qu (2003).
Plant snoRNAs: functional evolution and new modes of gene expression.
  Trends Plant Sci, 8, 42-49.  
14612397 K.Newton, E.Petfalski, D.Tollervey, and J.F.Cáceres (2003).
Fibrillarin is essential for early development and required for accumulation of an intron-encoded small nucleolar RNA in the mouse.
  Mol Cell Biol, 23, 8519-8527.  
12598892 M.Aittaleb, R.Rashid, Q.Chen, J.R.Palmer, C.J.Daniels, and H.Li (2003).
Structure and function of archaeal box C/D sRNP core proteins.
  Nat Struct Biol, 10, 256-263.
PDB code: 1nt2
14602911 M.L.Bortolin, J.P.Bachellerie, and B.Clouet-d'Orval (2003).
In vitro RNP assembly and methylation guide activity of an unusual box C/D RNA, cis-acting archaeal pre-tRNA(Trp).
  Nucleic Acids Res, 31, 6524-6535.  
14656444 P.G.Foster, C.R.Nunes, P.Greene, D.Moustakas, and R.M.Stroud (2003).
The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate.
  Structure, 11, 1609-1620.
PDB codes: 1sqf 1sqg
12887897 T.Hirose, M.D.Shu, and J.A.Steitz (2003).
Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells.
  Mol Cell, 12, 113-123.  
12560482 T.S.Rozhdestvensky, T.H.Tang, I.V.Tchirkova, J.Brosius, J.P.Bachellerie, and A.Hüttenhofer (2003).
Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea.
  Nucleic Acids Res, 31, 869-877.  
12431975 W.A.Decatur, and M.J.Fournier (2003).
RNA-guided nucleotide modification of ribosomal and other RNAs.
  J Biol Chem, 278, 695-698.  
11959980 A.D.Omer, S.Ziesche, H.Ebhardt, and P.P.Dennis (2002).
In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex.
  Proc Natl Acad Sci U S A, 99, 5289-5294.  
11918670 H.Hori, T.Suzuki, K.Sugawara, Y.Inoue, T.Shibata, S.Kuramitsu, S.Yokoyama, T.Oshima, and K.Watanabe (2002).
Identification and characterization of tRNA (Gm18) methyltransferase from Thermus thermophilus HB8: domain structure and conserved amino acid sequence motifs.
  Genes Cells, 7, 259-272.  
12181314 J.Hager, B.L.Staker, H.Bugl, and U.Jakob (2002).
Active site in RrmJ, a heat shock-induced methyltransferase.
  J Biol Chem, 277, 41978-41986.  
11809845 J.M.Waggener, and P.J.DiMario (2002).
Two splice variants of Nopp140 in Drosophila melanogaster.
  Mol Biol Cell, 13, 362-381.  
12401494 L.B.Szewczak, S.J.DeGregorio, S.A.Strobel, and J.A.Steitz (2002).
Exclusive interaction of the 15.5 kD protein with the terminal box C/D motif of a methylation guide snoRNP.
  Chem Biol, 9, 1095-1107.  
12032088 M.P.Egloff, D.Benarroch, B.Selisko, J.L.Romette, and B.Canard (2002).
An RNA cap (nucleoside-2'-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization.
  EMBO J, 21, 2757-2768.
PDB codes: 1l9k 2p1d
12417735 N.J.Watkins, A.Dickmanns, and R.Lührmann (2002).
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, 8342-8352.  
12379800 S.C.Ogg, and A.I.Lamond (2002).
Cajal bodies and coilin--moving towards function.
  J Cell Biol, 159, 17-21.  
12215523 S.Galardi, A.Fatica, A.Bachi, A.Scaloni, C.Presutti, and I.Bozzoni (2002).
Purified box C/D snoRNPs are able to reproduce site-specific 2'-O-methylation of target RNA in vitro.
  Mol Cell Biol, 22, 6663-6668.  
12381732 S.Granneman, G.J.Pruijn, W.Horstman, W.J.van Venrooij, R.Luhrmann, and N.J.Watkins (2002).
The hU3-55K protein requires 15.5K binding to the box B/C motif as well as flanking RNA elements for its association with the U3 small nucleolar RNA in Vitro.
  J Biol Chem, 277, 48490-48500.  
12007400 T.Kiss (2002).
Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions.
  Cell, 109, 145-148.  
11839271 W.A.Speckmann, Z.H.Li, T.M.Lowe, S.R.Eddy, R.M.Terns, and M.P.Terns (2002).
Archaeal guide RNAs function in rRNA modification in the eukaryotic nucleus.
  Curr Biol, 12, 199-203.  
12067654 W.Filipowicz, and V.Pogacić (2002).
Biogenesis of small nucleolar ribonucleoproteins.
  Curr Opin Cell Biol, 14, 319-327.  
12032087 X.Darzacq, B.E.Jády, C.Verheggen, A.M.Kiss, E.Bertrand, and T.Kiss (2002).
Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs.
  EMBO J, 21, 2746-2756.  
11157760 B.E.Jády, and T.Kiss (2001).
A small nucleolar guide RNA functions both in 2'-O-ribose methylation and pseudouridylation of the U5 spliceosomal RNA.
  EMBO J, 20, 541-551.  
11509571 K.W.Jones, K.Gorzynski, C.M.Hales, U.Fischer, F.Badbanchi, R.M.Terns, and M.P.Terns (2001).
Direct interaction of the spinal muscular atrophy disease protein SMN with the small nucleolar RNA-associated protein fibrillarin.
  J Biol Chem, 276, 38645-38651.  
11359559 P.P.Dennis, A.Omer, and T.Lowe (2001).
A guided tour: small RNA function in Archaea.
  Mol Microbiol, 40, 509-519.  
12762059 S.A.Gerbi, A.V.Borovjagin, M.Ezrokhi, and T.S.Lange (2001).
Ribosome biogenesis: role of small nucleolar RNA in maturation of eukaryotic rRNA.
  Cold Spring Harb Symp Quant Biol, 66, 575-590.  
11406387 S.A.Teichmann, A.G.Murzin, and C.Chothia (2001).
Determination of protein function, evolution and interactions by structural genomics.
  Curr Opin Struct Biol, 11, 354-363.  
11604509 T.H.King, W.A.Decatur, E.Bertrand, E.S.Maxwell, and M.J.Fournier (2001).
A well-connected and conserved nucleoplasmic helicase is required for production of box C/D and H/ACA snoRNAs and localization of snoRNP proteins.
  Mol Cell Biol, 21, 7731-7746.  
11447102 T.Kiss (2001).
Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs.
  EMBO J, 20, 3617-3622.  
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
  Nucleic Acids Res, 29, 3784-3795.  
10982841 A.Colley, J.D.Beggs, D.Tollervey, and D.L.Lafontaine (2000).
Dhr1p, a putative DEAH-box RNA helicase, is associated with the box C+D snoRNP U3.
  Mol Cell Biol, 20, 7238-7246.  
11163207 I.Vidovic, S.Nottrott, K.Hartmuth, R.Lührmann, and R.Ficner (2000).
Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment.
  Mol Cell, 6, 1331-1342.
PDB code: 1e7k
11106375 J.Cavaillé, K.Buiting, M.Kiefmann, M.Lalande, C.I.Brannan, B.Horsthemke, J.P.Bachellerie, J.Brosius, and A.Hüttenhofer (2000).
Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization.
  Proc Natl Acad Sci U S A, 97, 14311-14316.  
10827942 J.D.Lewis, and D.Tollervey (2000).
Like attracts like: getting RNA processing together in the nucleus.
  Science, 288, 1385-1389.  
11080641 M.M.Skinner, J.M.Puvathingal, R.L.Walter, and A.M.Friedman (2000).
Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair.
  Structure, 8, 1189-1201.
PDB code: 1dl5
11081632 N.J.Watkins, V.Ségault, B.Charpentier, S.Nottrott, P.Fabrizio, A.Bachi, M.Wilm, M.Rosbash, C.Branlant, and R.Lührmann (2000).
A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceosomal U4 snRNP.
  Cell, 103, 457-466.  
11071934 W.A.Speckmann, R.M.Terns, and M.P.Terns (2000).
The box C/D motif directs snoRNA 5'-cap hypermethylation.
  Nucleic Acids Res, 28, 4467-4473.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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