3LWO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

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:  
    3LWO, 3LWP

  • 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 pre-reactive state that is important to the identification of reactive chemical moieties ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pseudouridine synthase Cbf5A340Pyrococcus furiosusMutation(s): 0 
Gene Names: truBPF1785
EC: 5.4.99 (PDB Primary Data), 5.4.99.25 (UniProt)
UniProt
Find proteins for Q7LWY0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q7LWY0 
Go to UniProtKB:  Q7LWY0
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UniProt GroupQ7LWY0
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein Nop10B60Pyrococcus furiosusMutation(s): 0 
Gene Names: PF1141
UniProt
Find proteins for Q8U1R4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U1R4 
Go to UniProtKB:  Q8U1R4
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UniProt GroupQ8U1R4
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeC123Pyrococcus furiosusMutation(s): 0 
Gene Names: PF1367rpl7ae
UniProt
Find proteins for Q8U160 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U160 
Go to UniProtKB:  Q8U160
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UniProt GroupQ8U160
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Entity ID: 4
MoleculeChainsLengthOrganismImage
H/ACA RNAD 58N/A
Protein Feature View
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Entity ID: 5
MoleculeChainsLengthOrganismImage
5'-R(*GP*AP*GP*CP*GP*(5BU)P*GP*CP*GP*GP*UP*UP*U)-3'E 13N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.523α = 90
b = 62.698β = 90
c = 85.335γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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