3LWO

Structure of H/ACA RNP bound to a substrate RNA containing 5BrU

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.855 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study.

Zhou, J., Lv, C., Liang, B., Chen, M., Yang, W., Li, H.

(2010) J.Mol.Biol. 401: 690-695

  • DOI: 10.1016/j.jmb.2010.06.061
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The most abundant chemical modification on RNA is isomerization of uridine (or pseudouridylation) catalyzed by pseudouridine synthases. The catalytic mechanism of this essential process remains largely speculative, partly due to lack of knowledge of ...

    The most abundant chemical modification on RNA is isomerization of uridine (or pseudouridylation) catalyzed by pseudouridine synthases. The catalytic mechanism of this essential process remains largely speculative, partly due to lack of knowledge of the pre-reactive state that is important to the identification of reactive chemical moieties. In the present study, we showed, using orthogonal space random-walk free-energy simulation, that the pre-reactive states of uridine and its reactive derivative 5-fluorouridine, bound to a ribonucleoprotein particle pseudouridine synthase, strongly prefer the syn glycosidic bond conformation, while that of the nonreactive 5-bromouridine-containing substrate is largely populated in the anti conformation state. A high-resolution crystal structure of the 5-bromouridine-containing substrate bound to the ribonucleoprotein particle pseudouridine synthase and enzyme activity assay confirmed the anti nonreactive conformation and provided the molecular basis for its confinement. The observed preference for the syn pre-reactive state by the enzyme-bound uridine may help to distinguish among currently proposed mechanisms.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pseudouridine synthase Cbf5
A
340Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: truB
EC: 5.4.99.25
Find proteins for Q7LWY0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q7LWY0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein Nop10
B
60Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: nop10
Find proteins for Q8U1R4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U1R4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7Ae
C
123Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rpl7ae
Find proteins for Q8U160 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U160
Entity ID: 4
MoleculeChainsLengthOrganism
H/ACA RNAD58N/A
Entity ID: 5
MoleculeChainsLengthOrganism
5'-R(*GP*AP*GP*CP*GP*(5BU)P*GP*CP*GP*GP*UP*UP*U)-3'E13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5BU
Query on 5BU
E
RNA LINKINGC9 H12 Br N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.855 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 184.523α = 90.00
b = 62.698β = 90.00
c = 85.335γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance