PDBsum entry 1v9f

Lyase

PDB id

1v9f

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Contents

			Protein chain

					250 a.a. *

			Ligands

					PO4

			Waters ×264

* Residue conservation analysis

PDB id:

1v9f

Links

Name:

Lyase

Title:

Crystal structure of catalytic domain of pseudouridine synthase rlud from escherichia coli

Structure:

Ribosomal large subunit pseudouridine synthase d. Chain: a. Synonym: pseudouridylate synthase, uracil hydrolyase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: rlud. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.70Å

R-factor:

0.201

R-free:

0.224

Authors:

K.Mizutani,Y.Machida,S.Unzai,S.-Y.Park,J.R.H.Tame

Key ref:

K.Mizutani et al. (2004). Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli. Biochemistry, 43, 4454-4463. PubMed id: 15078091 DOI: 10.1021/bi036079c

Date:

26-Jan-04

Release date:

18-May-04

PROCHECK

	Headers

	References

Protein chain

P33643 (RLUD_ECOLI) - Ribosomal large subunit pseudouridine synthase D from Escherichia coli (strain K12)

Seq: Struc:					326 a.a. 250 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.5.4.99.23 - 23S rRNA pseudouridine(1911/1915/1917) synthase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

uridine(1911/1915/1917) in 23S rRNA = pseudouridine(1911/1915/1917) in 23S rRNA

DOI no: 10.1021/bi036079c	Biochemistry 43:4454-4463 (2004)
PubMed id: 15078091

Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli.
K.Mizutani, Y.Machida, S.Unzai, S.Y.Park, J.R.Tame.

ABSTRACT

The most frequent modification of RNA, the conversion of uridine bases to pseudouridines, is found in all living organisms and often in highly conserved locations in ribosomal and transfer RNA. RluC and RluD are homologous enzymes which each convert three specific uridine bases in Escherichia coli ribosomal 23S RNA to pseudouridine: bases 955, 2504, and 2580 in the case of RluC and 1911, 1915, and 1917 in the case of RluD. Both have an N-terminal S4 RNA binding domain. While the loss of RluC has little phenotypic effect, loss of RluD results in a much reduced growth rate. We have determined the crystal structures of the catalytic domain of RluC, and full-length RluD. The S4 domain of RluD appears to be highly flexible or unfolded and is completely invisible in the electron density map. Despite the conserved topology shared by the two proteins, the surface shape and charge distribution are very different. The models suggest significant differences in substrate binding by different pseudouridine synthases.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19298824

A.Alian, A.DeGiovanni, S.L.Griner, J.S.Finer-Moore, and R.M.Stroud (2009).
Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.

J Mol Biol, 388, 785-800.

PDB code:

3dh3

17668295

A.Matte, Z.Jia, S.Sunita, J.Sivaraman, and M.Cygler (2007).
Insights into the biology of Escherichia coli through structural proteomics.

J Struct Funct Genomics, 8, 45-55.

17320904

H.Pan, J.D.Ho, R.M.Stroud, and J.Finer-Moore (2007).
The crystal structure of E. coli rRNA pseudouridine synthase RluE.

J Mol Biol, 367, 1459-1470.

PDB codes:

2olw 2oml

17872507

P.P.Vaidyanathan, M.P.Deutscher, and A.Malhotra (2007).
RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA.

RNA, 13, 1868-1876.

17188032

C.Hoang, J.Chen, C.A.Vizthum, J.M.Kandel, C.S.Hamilton, E.G.Mueller, and A.R.Ferré-D'Amaré (2006).
Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure.

Mol Cell, 24, 535-545.

PDB code:

2i82

17002302

C.S.Hamilton, T.M.Greco, C.A.Vizthum, J.M.Ginter, M.V.Johnston, and E.G.Mueller (2006).
Mechanistic investigations of the pseudouridine synthase RluA using RNA containing 5-fluorouridine.

Biochemistry, 45, 12029-12038.

16511038

A.Matte, G.V.Louie, J.Sivaraman, M.Cygler, and S.K.Burley (2005).
Structure of the pseudouridine synthase RsuA from Haemophilus influenzae.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 350-354.

PDB code:

1vio

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.