1prz
From Proteopedia
(New page: 200px<br /><applet load="1prz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1prz, resolution 1.80Å" /> '''Crystal structure of...) |
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| - | [[Image:1prz.jpg|left|200px]]<br /><applet load="1prz" size=" | + | [[Image:1prz.jpg|left|200px]]<br /><applet load="1prz" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1prz, resolution 1.80Å" /> | caption="1prz, resolution 1.80Å" /> | ||
'''Crystal structure of pseudouridine synthase RluD catalytic module'''<br /> | '''Crystal structure of pseudouridine synthase RluD catalytic module'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Pseudouridine (5-beta-D-ribofuranosyluracil, Psi) is the most commonly | + | Pseudouridine (5-beta-D-ribofuranosyluracil, Psi) is the most commonly found modified base in RNA. Conversion of uridine to Psi is performed enzymatically in both prokaryotes and eukaryotes by pseudouridine synthases (EC 4.2.1.70). The Escherichia coli Psi-synthase RluD modifies uridine to Psi at positions 1911, 1915 and 1917 within 23S rRNA. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis. Here, we report the crystal structure of the catalytic module of RluD (residues 68-326; DeltaRluD) refined at 1.8A to a final R-factor of 21.8% (R(free)=24.3%). DeltaRluD is a monomeric enzyme having an overall mixed alpha/beta fold. The DeltaRluD molecule consists of two subdomains, a catalytic subdomain and C-terminal subdomain with the RNA-binding cleft formed by loops extending from the catalytic sub-domain. The catalytic sub-domain of DeltaRluD has a similar fold as in TruA, TruB and RsuA, with the location of the RNA-binding cleft, active-site and conserved, catalytic Asp residue superposing in all four structures. Superposition of the crystal structure of TruB bound to a T-stem loop with RluD reveals that similar RNA-protein interactions for the flipped-out uridine base would exist in both structures, implying that base-flipping is necessary for catalysis. This observation also implies that the specificity determinants for site-specific RNA-binding and recognition likely reside in parts of RluD beyond the active site. |
==About this Structure== | ==About this Structure== | ||
| - | 1PRZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] Full crystallographic information is available from [http:// | + | 1PRZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PRZ OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Pseudouridylate synthase]] | [[Category: Pseudouridylate synthase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: BSGI, Montreal-Kingston | + | [[Category: BSGI, Montreal-Kingston Bacterial Structural Genomics Initiative.]] |
[[Category: Cygler, M.]] | [[Category: Cygler, M.]] | ||
[[Category: Iannuzzi, P.]] | [[Category: Iannuzzi, P.]] | ||
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[[Category: structural genomics]] | [[Category: structural genomics]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:31:57 2008'' |
Revision as of 12:32, 21 February 2008
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Crystal structure of pseudouridine synthase RluD catalytic module
Overview
Pseudouridine (5-beta-D-ribofuranosyluracil, Psi) is the most commonly found modified base in RNA. Conversion of uridine to Psi is performed enzymatically in both prokaryotes and eukaryotes by pseudouridine synthases (EC 4.2.1.70). The Escherichia coli Psi-synthase RluD modifies uridine to Psi at positions 1911, 1915 and 1917 within 23S rRNA. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis. Here, we report the crystal structure of the catalytic module of RluD (residues 68-326; DeltaRluD) refined at 1.8A to a final R-factor of 21.8% (R(free)=24.3%). DeltaRluD is a monomeric enzyme having an overall mixed alpha/beta fold. The DeltaRluD molecule consists of two subdomains, a catalytic subdomain and C-terminal subdomain with the RNA-binding cleft formed by loops extending from the catalytic sub-domain. The catalytic sub-domain of DeltaRluD has a similar fold as in TruA, TruB and RsuA, with the location of the RNA-binding cleft, active-site and conserved, catalytic Asp residue superposing in all four structures. Superposition of the crystal structure of TruB bound to a T-stem loop with RluD reveals that similar RNA-protein interactions for the flipped-out uridine base would exist in both structures, implying that base-flipping is necessary for catalysis. This observation also implies that the specificity determinants for site-specific RNA-binding and recognition likely reside in parts of RluD beyond the active site.
About this Structure
1PRZ is a Single protein structure of sequence from Escherichia coli. Active as Pseudouridylate synthase, with EC number 4.2.1.70 Full crystallographic information is available from OCA.
Reference
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. PMID:14659742
Page seeded by OCA on Thu Feb 21 14:31:57 2008
Categories: Escherichia coli | Pseudouridylate synthase | Single protein | BSGI, Montreal-Kingston Bacterial Structural Genomics Initiative. | Cygler, M. | Iannuzzi, P. | Matte, A. | Sivaraman, J. | Bsgi | Crystal structure | Montreal-kingston bacterial structural genomics initiative | Pseudouridine synthase | Rlud | Structural genomics
