Modomics - A Database of RNA Modifications

ID Card:

Full name: Probable tRNA pseudouridine synthase B
Synonym: PF1785
GI: 18978157
COG: COG0130
UniProt: Q7LWY0
Structures: | 3HJW | 3HJY | 2EY4 | 2HVY | 2RFK | 3HAX | 3HAY | 3LWO | 3LWP | 3LWQ | 3LWR | 3LWV | 3MQK |
Alpha Fold Predicted Structure: AF-Q7LWY0-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:


3HJW

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

H/ACA RNA-protein complexes, comprised of four proteins and an H/ACA guide RNA, modify ribosomal and small nuclear RNAs. The H/ACA proteins are also essential components of telomerase in mammals. Cbf5 is the H/ACA protein that catalyzes isomerization of uridine to pseudouridine in target RNAs. Mutations in human Cbf5 (dyskerin) lead to dyskeratosis congenita. Here, we describe the 2.1 A crystal structure of a specific complex of three archaeal H/ACA proteins, Cbf5, Nop10, and Gar1. Cbf5 displays structural properties that are unique among known pseudouridine synthases and are consistent with its distinct function in RNA-guided pseudouridylation. We also describe the previously unknown structures of both Nop10 and Gar1 and the structural basis for their essential roles in pseudouridylation. By using information from related structures, we have modeled the entire ribonucleoprotein complex including both guide and substrate RNAs. We have also identified a dyskeratosis congenita mutation cluster site within a modeled dyskerin structure.

Download RCSB-PDB Structures:

Pdb Files   2EY4.pdb   2HVY.pdb   2RFK.pdb   3HAX.pdb   3HAY.pdb   3HJW.pdb   3HJY.pdb   3LWO.pdb   3LWP.pdb   3LWQ.pdb   3LWR.pdb   3LWV.pdb   3MQK.pdb  
Pdbx/mmCIF Files   2EY4.cif   2HVY.cif   2RFK.cif   3HAX.cif   3HAY.cif   3HJW.cif   3HJY.cif   3LWO.cif   3LWP.cif   3LWQ.cif   3LWR.cif   3LWV.cif   3MQK.cif  


Protein sequence:

MARDEVRRILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLWEKRDRS

Comments:

Archaeal Cbf5 is the catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA box snoRNP) complex. It catalyzes the pseudouridylation of rRNA, snRNA and also intron-containing pre-tRNA. It works with 3 other subunits, Gar1, Nop10 (two homologs of eukaryotic Gar1p/Nop10p), and ribosomal protein L7Ae that is unique to Archaea. However, only Nop10 seems important for tRNA modification. Archaeal L7Ae is the only core protein that is also shared by the C/D box snoRNP. Comparison of archaeal Cbf5 with bacterial tRNA Psi55 synthase (TruB) reveals structural conservation and provides insight into the guide-independent activity of archaeal Cbf5.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q7LWY0-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q7LWY0-F1.cif  
DSSP Secondary Structures   Q7LWY0.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA. Liang B, Zhou J, Kahen E, Terns RM, Terns MP, Li H Nat Struct Mol Biol [details] 19478803 -
Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase. Duan J, Li L, Lu J, Wang W, Ye K Mol Cell [details] 19481523 -
Identification of determinants in the protein partners aCBF5 and aNOP10 necessary for the tRNA:Psi55-synthase and RNA-guided RNA:Psi-synthase activities. Muller S, Fourmann JB, Loegler C, Charpentier B, Branlant C Nucleic Acids Res [details] 17704128 -
Differential roles of archaeal box H/ACA proteins in guide RNA-dependent and independent pseudouridine formation. Gurha P, Joardar A, Chaurasia P, Gupta R RNA Biol [details] 17993784 -
Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii. Blaby IK, Majumder M, Chatterjee K, Jana S, Grosjean H, de Crecy-Lagard V, Gupta R RNA [details] 21628430 -

Links:

_PubMed_
_Wikipedia - snoRNA_
_Wikipedia - pseudouridylate_synthase_