J Biol Chem. 2004 Jun 4;279(23):24585-91. Epub 2004 Mar 17.

Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft.

Chaudhuri BN, Chan S, Perry LJ, Yeates TO.

Source

UCLA-Department of Energy Institute for Genomics and Proteomics, Los Angeles, California 90095, USA.

Abstract

The three-dimensional structure of the RNA-modifying enzyme, psi55 tRNA pseudouridine synthase from Mycobacterium tuberculosis, is reported. The 1.9-A resolution crystal structure reveals the enzyme, free of substrate, in two distinct conformations. The structure depicts an interesting mode of protein flexibility involving a hinged bending in the central beta-sheet of the catalytic module. Key parts of the active site cleft are also found to be disordered in the substrate-free form of the enzyme. The hinge bending appears to act as a clamp to position the substrate. Our structural data furthers the previously proposed mechanism of tRNA recognition. The present crystal structure emphasizes the significant role that protein dynamics must play in tRNA recognition, base flipping, and modification.

PMID:: 15028724; [PubMed - indexed for MEDLINE]

Free full text

LinkOut - more resources

Full Text Sources

Other Literature Sources

COS Scholar Universe

Supplemental Content

Save items

Related citations in PubMed

Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli. [J Mol Biol. 2004]
Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli.
Sivaraman J, Iannuzzi P, Cygler M, Matte A. J Mol Biol. 2004 Jan 2; 335(1):87-101.
Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit. [Proc Natl Acad Sci U S A. 2003]
Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.
Pan H, Agarwalla S, Moustakas DT, Finer-Moore J, Stroud RM. Proc Natl Acad Sci U S A. 2003 Oct 28; 100(22):12648-53. Epub 2003 Oct 17.
Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme. [Cell. 2001]
Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
Hoang C, Ferré-D'Amaré AR. Cell. 2001 Dec 28; 107(7):929-39.
Review The roles of the essential Asp-48 and highly conserved His-43 elucidated by the pH dependence of the pseudouridine synthase TruB. [Arch Biochem Biophys. 2005]
Review The roles of the essential Asp-48 and highly conserved His-43 elucidated by the pH dependence of the pseudouridine synthase TruB.
Hamilton CS, Spedaliere CJ, Ginter JM, Johnston MV, Mueller EG. Arch Biochem Biophys. 2005 Jan 1; 433(1):322-34.
Review Dissecting the catalytic mechanism of a plant beta-D-glucan glucohydrolase through structural biology using inhibitors and substrate analogues. [Carbohydr Res. 2007]
Review Dissecting the catalytic mechanism of a plant beta-D-glucan glucohydrolase through structural biology using inhibitors and substrate analogues.
Hrmova M, Fincher GB. Carbohydr Res. 2007 Sep 3; 342(12-13):1613-23. Epub 2007 May 18.

See reviews... See all...

Cited by 9 PubMed Central articles

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. 2009]
Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.
Alian A, DeGiovanni A, Griner SL, Finer-Moore JS, Stroud RM. J Mol Biol. 2009 May 15; 388(4):785-800. Epub 2009 Mar 17.
Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA. [RNA. 2008]
Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA.
Gurha P, Gupta R. RNA. 2008 Dec; 14(12):2521-7. Epub 2008 Oct 24.
Partial activity is seen with many substitutions of highly conserved active site residues in human Pseudouridine synthase 1. [RNA. 2008]
Partial activity is seen with many substitutions of highly conserved active site residues in human Pseudouridine synthase 1.
Sibert BS, Fischel-Ghodsian N, Patton JR. RNA. 2008 Sep; 14(9):1895-906. Epub 2008 Jul 22.

See all...

Structures reported by this article

Structure Of Trna Psi55 Pseudouridine Synthase (Trub)ÿ

PDB: 1SGV

Source: Mycobacterium tuberculosis H37Rv

Method: X-Ray Diffraction

Resolution: 1.9 Å

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Gene
Gene records that cite the current articles. Citations in Gene are added manually by NCBI or imported from outside public resources.
Nucleotide (Weighted)
Nucleotide records associated with the current articles through the Gene database. These are the related sequences on the Gene record that are added manually by NCBI.
Protein (RefSeq)
NCBI protein Reference Sequences (RefSeqs) that are cited in the current articles, included in the corresponding Gene Reference into Function, or that include the PubMed articles as references.
Protein (Weighted)
Protein records associated with the current articles through related Gene database records. These are the related sequences on the Gene record that are added manually by NCBI.
Protein Clusters
Clusters of related proteins from the Protein Clusters database that cite the current articles. Sources of references in Protein Clusters include the associated Gene and Conserved Domain records as well as NCBI added citations.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Taxonomy via GenBank
Taxonomy records associated with the current articles through taxonomic information on related molecular database records (Nucleotide, Protein, Gene, SNP, Structure).
Domains
Conserved Domain Database (CDD) records that cite the current articles. Citations are from the CDD source database records (PFAM, SMART).
Protein
Protein translation features of primary database (GenBank) nucleotide records reported in the current articles as well as Reference Sequences (RefSeqs) that include the articles as references.
Structure
Three-dimensional structure records in the NCBI Structure database for data reported in the current articles.
GEO Profiles
Gene Expression Omnibus (GEO) Profiles of molecular abundance data. The current articles are references on the Gene record associated with the GEO profile.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from My...
Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft.
J Biol Chem. 2004 Jun 4 ;279(23):24585-91. Epub 2004 Mar 17 .

PubMed
Idebenone delays the onset of cardiac functional alteration without correction o...
Idebenone delays the onset of cardiac functional alteration without correction of Fe-S enzymes deficit in a mouse model for Friedreich ataxia.
Hum Mol Genet. 2004 May 15 ;13(10):1017-24. Epub 2004 Mar 17 .

PubMed
Protein 14-3-3zeta binds to protein phosphatase PP1gamma2 in bovine epididymal s...
Protein 14-3-3zeta binds to protein phosphatase PP1gamma2 in bovine epididymal spermatozoa.
Biol Reprod. 2004 Jul ;71(1):177-84. Epub 2004 Mar 17 .

PubMed
Long-term intracavernous therapy responders can potentially switch to sildenafil...
Long-term intracavernous therapy responders can potentially switch to sildenafil citrate after radical prostatectomy.
Urology. 2004 Mar ;63(3):532-7; discussion 538.

PubMed
Routine pouchograms are not necessary after continent urinary diversion.
Routine pouchograms are not necessary after continent urinary diversion.
Urology. 2004 Mar ;63(3):435-7.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to:

Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft.

Source

Abstract

Publication Types, MeSH Terms, Substances, Secondary Source ID, Grant Support

Publication Types

MeSH Terms

Substances

Secondary Source ID

Grant Support

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Save items

Related citations in PubMed

Cited by 9 PubMed Central articles

Structures reported by this article

Related information

Recent activity

Simple NCBI Directory

Getting Started

Resources

Popular

Featured

NCBI Information