Modomics - A Database of RNA Modifications

ID Card:

Full name: H/ACA ribonucleoprotein complex subunit CBF5
Synonym: dyskerine
GI: 461698
Orf: YLR175W
COG: COG0130
UniProt: P33322
Structures: | 3UAI | 3U28 |
Alpha Fold Predicted Structure: AF-P33322-F1
Complex: H/ACA RNP
Enzyme type: pseudouridine synthase
Position of modification - modification: t:many - Y
s:many - Y
l:many - Y
n:many - Y


PDB Structures:


3UAI

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Box H/ACA ribonucleoprotein particles (RNPs) mediate pseudouridine synthesis, ribosome formation, and telomere maintenance. The structure of eukaryotic H/ACA RNPs remains poorly understood. We reconstituted functional Saccharomyces cerevisiae H/ACA RNPs with recombinant proteins Cbf5, Nop10, Gar1, and Nhp2 and a two-hairpin H/ACA RNA; determined the crystal structure of a Cbf5, Nop10, and Gar1 ternary complex at 1.9 Å resolution; and analyzed the structure-function relationship of the yeast complex. Although eukaryotic H/ACA RNAs have a conserved two-hairpin structure, isolated single-hairpin RNAs are also active in guiding pseudouridylation. Nhp2, unlike its archaeal counterpart, is largely dispensable for the activity, reflecting a functional adaptation of eukaryotic H/ACA RNPs to the variable RNA structure that Nhp2 binds. The N-terminal extension of Cbf5, a hot spot for dyskeratosis congenita mutation, forms an extra structural layer on the PUA domain. Gar1 is distinguished from the assembly factor Naf1 by containing a C-terminal extension that controls substrate turnover and the Gar1-Naf1 exchange during H/ACA RNP maturation. Our results reveal significant novel features of eukaryotic H/ACA RNPs.

Download RCSB-PDB Structures:

Pdb Files   3U28.pdb   3UAI.pdb  
Pdbx/mmCIF Files   3U28.cif   3UAI.cif  


Protein sequence:

MSKEDFVIKPEAAGASTDTSEWPLLLKNFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSGVINLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQGAGKEYVCIVRLHDALKDEKDLGRSLENLTGALFQRPPLISAVKRQLRVRTIYESNLIEFDNKRNLGVFWASCEAGTYMRTLCVHLGMLLGVGGHMQELRRVRSGALSENDNMVTLHDVMDAQWVYDNTRDESYLRSIIQPLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGVVASVKRCIMERDLYPRRWGLGPVAQKKKQMKADGKLDKYGRVNENTPEQWKKEYVPLDNAEQSTSSSQETKETEEEPKKAKEDSLIKEVETEKEEVKEDDSKKEKKEKKDKKEKKEKKEKKDKKEKKEKKEKKRKSEDGDSEEKKSKKSKK

Comments:

Pseudouridine (Ψ) is retained to stabilize the conformation of rRNAs and plays a key role in ribosomal RNA processing, being exploited in different modification positions during pre-RNAs biogenesis (Zebarjadian et al. 1999). Cbf5 is a low-affinity binding protein (Jiang et al. 1993) and the catalytic subunit of H/ACA small nuclear ribonucleoprotein (H/ACA snoRNP) complex that catalyzes the pseudouridylation of rRNA (Zebarjadian et al. 1999). A fifth protein (Shq1) is required for H/ACA RNP biogenenesis. H/ACA snoRNAs consist minimally of a helix (P1) and a hairpin (P2) flanking bulge, with a single stranded region including the conserved ACA sequence from the helix at the 3' side (Hamma et al. 2005). H/ACA and substrate RNAs form a four-helix junction that binds to Cbf5 (NAP57 in rat and dyskerin in human), Gor1, L7Ae (Nhp2 in Eukarya) and Nop10. All four proteins determine the viability in yeast. Cbf5, Nhp2, and Nop10 are required for in vivo stability of H/ACA RNAs. Cbf5 contains a repeating KKD/E sequence domain near the C-terminus that allows for microtubules binding (Jiang et al. 1993) . Catalyzes the pseudouridylation of rRNA (including 5S and 5.8S rRNA) and small RNAs (snRNAs, snoRNAs). In Eukarya, H/ACA RNPs are essential for three fundamental cellular processes: protein synthesis, mRNA splicing, and maintenance of genome integrity. For detailed information on modified positions see the (snoRNA) table.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:Y pre-rRNA   many SSU-18S Nucleus, nucleolus, cytoplasm
U:Y pre-rRNA   many LSU-L 25S Nucleus, nucleolus, cytoplasm
U:Y pre-rRNA   many LSU-35S Nucleus, nucleolus, cytoplasm
U:Y snRNA   many Nucleus, nucleolus, cytoplasm

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M S K E D F V I K P E A A G A S T D T S E W P L L L K N F D K L L V R S G H Y T P I P A G S S P L K R D L K S Y I S S G V I N L D K P S N P S S H E V V A W I K R I L R C E K T G H S G T L D P K V T G C L I V C I D R A T R L V K S Q Q G A G K E Y V C I V R L H D A L K D E K D L G R S L E N L T G A L F Q R P P L I S A V K R Q L R V R T I Y E S N L I E F D N K R N L G V F W A S C E A G T Y M R T L C V H L G M L L G V G G H M Q E L R R V R S G A L S E N D N M V T L H D V M D A Q W V Y D N T R D E S Y L R S I I Q P L E T L L V G Y K R I V V K D S A V N A V C Y G A K L M I P G L L R Y E E G I E L Y D E I V L I T T K G E A I A V A I A Q M S T V D L A S C D H G V V A S V K R C I M E R D L Y P R R W G L G P V A Q K K K Q M K A D G K L D K Y G R V N E N T P E Q W K K E Y V P L D N A E Q S T S S S Q E T K E T E E E P K K A K E D S L I K E V E T E K E E V K E D D S K K E K K E K K D K K E K K E K K E K K D K K E K K E K K E K K R K S E D G D S E E K K S K K S K K

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-P33322-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P33322-F1.cif  
DSSP Secondary Structures   P33322.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
An essential yeast protein, CBF5p, binds in vitro to centromeres and microtubules. Jiang W, Middleton K, Yoon HJ, Fouquet C, Carbon J Mol Cell Biol [details] 8336724 -
The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs. Hamma T, Reichow SL, Varani G, Ferre-D'Amare AR Nat Struct Mol Biol [details] 16286935 -
Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita. Rashid R, Liang B, Baker DL, Youssef OA, He Y, Phipps K, Terns RM, Terns MP, Li H Mol Cell [details] 16427014 -
The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Lafontaine DL, Bousquet-Antonelli C, Henry Y, Caizergues-Ferrer M, Tollervey D Genes Dev [details] 9472021 -
Point mutations in yeast CBF5 can abolish in vivo pseudouridylation of rRNA. Zebarjadian Y, King T, Fournier MJ, Clarke L, Carbon J Mol Cell Biol [details] 10523634 -
Structure of the Shq1-Cbf5-Nop10-Gar1 complex and implications for H/ACA RNP biogenesis and dyskeratosis congenita. Li S, Duan J, Li D, Ma S, Ye K EMBO J [details] 22117216 -
Cbf5p, the putative pseudouridine synthase of H/ACA-type snoRNPs, can form a complex with Gar1p and Nop10p in absence of Nhp2p and box H/ACA snoRNAs. Henras AK, Capeyrou R, Henry Y, Caizergues-Ferrer M RNA [details] 15388873 -
The box H/ACA RNP assembly factor Naf1p contains a domain homologous to Gar1p mediating its interaction with Cbf5p. Leulliot N, Godin KS, Hoareau-Aveilla C, Quevillon-Cheruel S, Varani G, Henry Y, Van Tilbeurgh H... J Mol Biol [details] 17612558 -

Links:

_SGD_
_The yeast snoRNA database_
_Wikipedia - Small nucleolar RNA_
_Wikipedia - Pseudouridylate synthase_
_PubMed_