1VIO

Crystal structure of pseudouridylate synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the pseudouridine synthase RsuA from Haemophilus influenzae.

Matte, A.Louie, G.V.Sivaraman, J.Cygler, M.Burley, S.K.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 350-354

  • DOI: 10.1107/S1744309105005920
  • Primary Citation of Related Structures:  
    1VIO

  • PubMed Abstract: 
  • The structure of the pseudouridine synthase RsuA from Haemophilus influenza, which catalyzes the conversion of uridine to pseudouridine at a single position within 16S ribosomal RNA, has been determined at 1.59 A resolution and compared with that of ...

    The structure of the pseudouridine synthase RsuA from Haemophilus influenza, which catalyzes the conversion of uridine to pseudouridine at a single position within 16S ribosomal RNA, has been determined at 1.59 A resolution and compared with that of Escherichia coli RsuA. The H. influenza enzyme contains an N-terminal S4-like alpha3beta4 domain followed by a catalytic domain, as observed in the structure of E. coli RsuA. Whereas the individual domains of E. coli and H. influenza RsuA are structurally similar, their relative spatial disposition differs greatly between the two structures. The former displays an extended open conformation with no direct contacts between the domains, while the latter is in a closed conformation with a large interface between the two domains. Domain closure presents several basic and polar residues into a putative RNA-binding cleft. It is proposed that this relative repositioning of the S4 and catalytic domains is used to modulate the shape and size of the rRNA-binding site in RsuA and in other pseudouridine synthases possessing S4 domains.


    Related Citations: 
    • Structural analysis of a set of proteins resulting from a bacterial genomics project
      Badger, J., Sauder, J.M., Adams, J.M., Antonysamy, S., Bain, K., Bergseid, M.G., Buchanan, S.G., Buchanan, M.D., Batiyenko, Y., Christopher, J.A., Emtage, S., Eroshkina, A., Feil, I., Furlong, E.B., Gajiwala, K.S., Gao, X., He, D., Hendle, J., Huber, A., Hoda, K., Kearins, P., Kissinger, C., Laubert, B., Lewis, H.A., Lin, J., Loomis, K., Lorimer, D., Louie, G., Maletic, M., Marsh, C.D., Miller, I., Molinari, J., Muller-Dieckmann, H.J., Newman, J.M., Noland, B.W., Pagarigan, B., Park, F., Peat, T.S., Post, K.W., Radojicic, S., Ramos, A., Romero, R., Rutter, M.E., Sanderson, W.E., Schwinn, K.D., Tresser, J., Winhoven, J., Wright, T.A., Wu, L., Xu, J., Harris, T.J.
      (2005) Proteins 60: 787

    Organizational Affiliation

    Biotechnology Research Institute, Montreal, Quebec H4P 2R2, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal small subunit pseudouridine synthase AAB243Haemophilus influenzaeMutation(s): 1 
Gene Names: rsuAHI1243
EC: 4.2.1.70 (PDB Primary Data), 5.4.99.19 (UniProt)
Find proteins for P45124 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P45124 
Go to UniProtKB:  P45124
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU1
Query on BU1

Download CCD File 
A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.163α = 90
b = 76.973β = 108.75
c = 62.771γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMACrefinement
CCP4data scaling
TRUNCATEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2003-12-01 
  • Released Date: 2003-12-30 
  • Deposition Author(s): Structural GenomiX

Revision History 

  • Version 1.0: 2003-12-30
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description