Pseudouridine synthase - Revision history

Michal Harel at 09:20, 5 December 2019

2019-12-05T09:20:00Z

←Older revision		Revision as of 09:20, 5 December 2019
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	</StructureSection>		</StructureSection>

-	== 3D Structures of pseudouridine synthase ==

-	~~Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}~~	+	[[Category:Topic Page]]
-	~~{{#tree:id=OrganizedByTopic\|openlevels=0\|~~	+
-		+
-	* Pseudouridine synthase	+
-		+
-	**[[~~4iqm]], [[4its]], [[4j37]], [[4nz6]] - hPUS Pus1 catalytic domain - human<br />~~	+
-	**[[4nz7]] - hPUS Pus1 catalytic domain (mutant)<br />	+
-	**[[1ze1]] – TmPUS B – ''Thermotoga maritima''<br />	+
-	**[[1vio]] - HiPUS RsuA – ''Haemophilus influenzae''<br />	+
-	**[[6gut]] – HiPUS/PILA<br />	+
-	**[[1dj0]] – EcPUS I – ''Escherichia coli''<br />	+
-	**[[1ksk]], [[1ksl]], [[1ksv]] – EcPUS RsuA <br />	+
-	**[[4lab]] - EcPUS RluB catalytic domain<br />	+
-	**[[1xpi]] - EcPUS RluC catalytic domain<br />	+
-	**[[1v9k]] - EcPUS RluC C-terminal domain (mutant) <br />	+
-	**[[2ist]] - EcPUS RluD <br />	+
-	**[[1prz]], [[1qyu]], [[1v9f]] - EcPUS RluD catalytic domain<br />	+
-	**[[2olw]] - EcPUS RluE<br />	+
-	**[[2oml]] - EcPUS RluE catalytic domain<br />	+
-	**[[2gml]] - EcPUS RluF catalytic domain<br />	+
-	**[[1vs3]] – PUS TruA – ''Thermus thermophilus''<br />	+
-	**[[1sgv]] – PUS TruB – ''Mycobacterium tuberculosis''<br />	+
-	**[[1si7]], [[1szw]], [[1sb7]] - EcPUS TruD<br />	+
-		+
-	* Pseudouridine synthase complex with RNA	+
-		+
-	**[[1k8w]] – EcPUS B + stem-loop RNA <br />	+
-	**[[1zl3]] - EcPUS B (mutant) + stem-loop RNA<br />	+
-	**[[2i82]] – EcPUS RluA + RNA<br />	+
-	**[[4lgt]] – EcPUS RluB + RNA<br />	+
-	**[[3dh3]] - EcPUS RluF + RNA<br />	+
-	**[[2nqp]], [[2nr0]], [[2nre]] – EcPUS TruA + Leu-tRNA<br />	+
-	**[[1r3e]], [[1r3f]] - EcPUS B + RNA<br />	+
-	**[[3hjw]], [[3lwo]], [[3lwp]], [[3lwq]], [[3lwr]], [[3lwv]] – PfPUS Cbf5 + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA – ''Pyrococcus furiosus''<br />	+
-	**[[3mqk]] - PfPUS Cbf5 + ribosome biogenesis protein Nop10 + small nuclear RNP Gar1-like protein + RNA<br />	+
-	**[[3hjy]] - PfPUS Cbf5 + ribosome biogenesis protein NOP10 + RNA<br />	+
-	**[[1ze2]] - TmPUS B + RNA<br />	+
-	**[[2ab4]] - TmPUS B (mutant) + RNA<br />	+
-		+
-	* Probable pseudouridine synthase	+
-		+
-	**[[2apo]] – PPUS + ribosome biogenesis protein Nop10 – ''Methanocaldococcus jannaschii''<br />	+
-	**[[2ey4]] - PfPPUS Cbf5 + ribosome biogenesis protein Nop10 + small nucleolar RNP <br />	+
-	**[[2hvy]], [[3hax]] - PfPPUS B + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA<br />	+
-	**[[2rfk]] - PfPUS B + ribosome biogenesis protein Nop10 + small nucleolar RNP + RNA<br />	+
-	**[[3hay]] - PfPPUS B + ribosome biogenesis protein Nop10 + ribosomal protein L7 + small nucleolar RNP + RNA<br />	+
-	**[[2aus]] – PPUS B + ribosome biogenesis protein Nop10 – ''Pyrococcus abyssi''<br />	+
-	**[[1z2z]] ~~– PPUS D – Methanosarcina mazei<br />~~	+
-	}}	+

Michal Harel at 09:17, 5 December 2019

2019-12-05T09:17:18Z

←Older revision		Revision as of 09:17, 5 December 2019
Line 1:		Line 1:
	<StructureSection load='1ze2' size='400' side='right' caption='tRNA pseudouridine synthase complex with RNA that contains pseudouridine monophosphate [[1ze2]]' scene='46/465439/Cv/1' pspeed='8'>		<StructureSection load='1ze2' size='400' side='right' caption='tRNA pseudouridine synthase complex with RNA that contains pseudouridine monophosphate [[1ze2]]' scene='46/465439/Cv/1' pspeed='8'>
		+	__TOC__
		+	==Function==
	[[Pseudouridine]] is an abundant modified nucleoside found in RNA molecules. It is formed post-transcriptionally in RNA molecules by isomerization of the bond between base and ribose in uridine. There are two major types of enzymes that catalyze this reaction:		[[Pseudouridine]] is an abundant modified nucleoside found in RNA molecules. It is formed post-transcriptionally in RNA molecules by isomerization of the bond between base and ribose in uridine. There are two major types of enzymes that catalyze this reaction:

Line 8:		Line 10:
	== Structural highlights ==		== Structural highlights ==
	The conversion of uridine to pseudouridine is accompanied by a conformational change of pseudouridine synthase<ref>PMID:14990747</ref>. <scene name='46/465439/Cv/4'>tRNA pseudouridine synthase binding with pseudouridine monophosphate</scene> ([[1ze2]]).		The conversion of uridine to pseudouridine is accompanied by a conformational change of pseudouridine synthase<ref>PMID:14990747</ref>. <scene name='46/465439/Cv/4'>tRNA pseudouridine synthase binding with pseudouridine monophosphate</scene> ([[1ze2]]).
		+	== 3D Structures of pseudouridine synthase ==
		+	[[Pseudouridine synthase 3D structures]]
		+
	</StructureSection>		</StructureSection>

Line 17:		Line 22:
	* Pseudouridine synthase		* Pseudouridine synthase

-	**[[~~1dj0~~]] ~~– EcPUS I – ''Escherichia coli''~~<br />	+	**[[4iqm]], [[4its]], [[4j37]], [[4nz6]] - hPUS Pus1 catalytic domain - human<br />
		+	**[[4nz7]] - hPUS Pus1 catalytic domain (mutant)<br />
	**[[1ze1]] – TmPUS B – ''Thermotoga maritima''<br />		**[[1ze1]] – TmPUS B – ''Thermotoga maritima''<br />
-	**[[1ksk]], [[1ksl]] – EcPUS RsuA <br />	+	**[[1vio]] - HiPUS RsuA – ''Haemophilus influenzae''<br />
-	**[[~~1vio~~]] - ~~PUS RsuA – ''Haemophilus influenzae''~~<br />	+	**[[6gut]] – HiPUS/PILA<br />
		+	**[[1dj0]] – EcPUS I – ''Escherichia coli''<br />
		+	**[[1ksk]], [[1ksl]], [[1ksv]] – EcPUS RsuA <br />
		+	**[[4lab]] - EcPUS RluB catalytic domain<br />
	**[[1xpi]] - EcPUS RluC catalytic domain<br />		**[[1xpi]] - EcPUS RluC catalytic domain<br />
	**[[1v9k]] - EcPUS RluC C-terminal domain (mutant) <br />		**[[1v9k]] - EcPUS RluC C-terminal domain (mutant) <br />
Line 28:		Line 37:
	**[[2oml]] - EcPUS RluE catalytic domain<br />		**[[2oml]] - EcPUS RluE catalytic domain<br />
	**[[2gml]] - EcPUS RluF catalytic domain<br />		**[[2gml]] - EcPUS RluF catalytic domain<br />
-	**[[4iqm]], [[4its]], [[4j37]], [[4nz6]] - hPUS Pus1 catalytic domain - human<br />
-	**[[4nz7]] - hPUS Pus1 catalytic domain (mutant)<br />
	**[[1vs3]] – PUS TruA – ''Thermus thermophilus''<br />		**[[1vs3]] – PUS TruA – ''Thermus thermophilus''<br />
	**[[1sgv]] – PUS TruB – ''Mycobacterium tuberculosis''<br />		**[[1sgv]] – PUS TruB – ''Mycobacterium tuberculosis''<br />
Line 39:		Line 46:
	**[[1zl3]] - EcPUS B (mutant) + stem-loop RNA<br />		**[[1zl3]] - EcPUS B (mutant) + stem-loop RNA<br />
	**[[2i82]] – EcPUS RluA + RNA<br />		**[[2i82]] – EcPUS RluA + RNA<br />
		+	**[[4lgt]] – EcPUS RluB + RNA<br />
	**[[3dh3]] - EcPUS RluF + RNA<br />		**[[3dh3]] - EcPUS RluF + RNA<br />
	**[[2nqp]], [[2nr0]], [[2nre]] – EcPUS TruA + Leu-tRNA<br />		**[[2nqp]], [[2nr0]], [[2nre]] – EcPUS TruA + Leu-tRNA<br />
		+	**[[1r3e]], [[1r3f]] - EcPUS B + RNA<br />
	**[[3hjw]], [[3lwo]], [[3lwp]], [[3lwq]], [[3lwr]], [[3lwv]] – PfPUS Cbf5 + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA – ''Pyrococcus furiosus''<br />		**[[3hjw]], [[3lwo]], [[3lwp]], [[3lwq]], [[3lwr]], [[3lwv]] – PfPUS Cbf5 + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA – ''Pyrococcus furiosus''<br />
	**[[3mqk]] - PfPUS Cbf5 + ribosome biogenesis protein Nop10 + small nuclear RNP Gar1-like protein + RNA<br />		**[[3mqk]] - PfPUS Cbf5 + ribosome biogenesis protein Nop10 + small nuclear RNP Gar1-like protein + RNA<br />
Line 46:		Line 55:
	**[[1ze2]] - TmPUS B + RNA<br />		**[[1ze2]] - TmPUS B + RNA<br />
	**[[2ab4]] - TmPUS B (mutant) + RNA<br />		**[[2ab4]] - TmPUS B (mutant) + RNA<br />
-	**[[1r3e]], [[1r3f]] - EcPUS B + RNA<br />

	* Probable pseudouridine synthase		* Probable pseudouridine synthase

Alexander Berchansky at 13:32, 20 August 2019

2019-08-20T13:32:04Z

←Older revision		Revision as of 13:32, 20 August 2019
Line 7:		Line 7:

	== Structural highlights ==		== Structural highlights ==
-	The conversion of uridine to pseudouridine is accompanied by a conformational change of pseudouridine synthase<ref>PMID:14990747</ref>. <scene name='46/465439/Cv/3'>tRNA pseudouridine synthase binding with pseudouridine monophosphate</scene> ([[1ze2]]).	+	The conversion of uridine to pseudouridine is accompanied by a conformational change of pseudouridine synthase<ref>PMID:14990747</ref>. <scene name='46/465439/Cv/4'>tRNA pseudouridine synthase binding with pseudouridine monophosphate</scene> ([[1ze2]]).
	</StructureSection>		</StructureSection>

Michal Harel at 09:46, 5 February 2019

2019-02-05T09:46:05Z

←Older revision		Revision as of 09:46, 5 February 2019
Line 10:		Line 10:
	</StructureSection>		</StructureSection>

-	== 3D Structures of ~~deaminase~~ ==	+	== 3D Structures of pseudouridine synthase ==

	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}		Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
Line 17:		Line 17:
	* Pseudouridine synthase		* Pseudouridine synthase

-	**[[1dj0]] – EcPUS I – Escherichia coli<br />	+	**[[1dj0]] – EcPUS I – ''Escherichia coli''<br />
-	**[[1ze1]] – TmPUS B – Thermotoga maritima<br />	+	**[[1ze1]] – TmPUS B – ''Thermotoga maritima''<br />
	**[[1ksk]], [[1ksl]] – EcPUS RsuA <br />		**[[1ksk]], [[1ksl]] – EcPUS RsuA <br />
-	**[[1vio]] - PUS RsuA – Haemophilus influenzae<br />	+	**[[1vio]] - PUS RsuA – ''Haemophilus influenzae''<br />
	**[[1xpi]] - EcPUS RluC catalytic domain<br />		**[[1xpi]] - EcPUS RluC catalytic domain<br />
	**[[1v9k]] - EcPUS RluC C-terminal domain (mutant) <br />		**[[1v9k]] - EcPUS RluC C-terminal domain (mutant) <br />
Line 30:		Line 30:
	**[[4iqm]], [[4its]], [[4j37]], [[4nz6]] - hPUS Pus1 catalytic domain - human<br />		**[[4iqm]], [[4its]], [[4j37]], [[4nz6]] - hPUS Pus1 catalytic domain - human<br />
	**[[4nz7]] - hPUS Pus1 catalytic domain (mutant)<br />		**[[4nz7]] - hPUS Pus1 catalytic domain (mutant)<br />
-	**[[1vs3]] – PUS TruA – Thermus thermophilus<br />	+	**[[1vs3]] – PUS TruA – ''Thermus thermophilus''<br />
-	**[[1sgv]] – PUS TruB – Mycobacterium tuberculosis<br />	+	**[[1sgv]] – PUS TruB – ''Mycobacterium tuberculosis''<br />
	**[[1si7]], [[1szw]], [[1sb7]] - EcPUS TruD<br />		**[[1si7]], [[1szw]], [[1sb7]] - EcPUS TruD<br />

Line 41:		Line 41:
	**[[3dh3]] - EcPUS RluF + RNA<br />		**[[3dh3]] - EcPUS RluF + RNA<br />
	**[[2nqp]], [[2nr0]], [[2nre]] – EcPUS TruA + Leu-tRNA<br />		**[[2nqp]], [[2nr0]], [[2nre]] – EcPUS TruA + Leu-tRNA<br />
-	**[[3hjw]], [[3lwo]], [[3lwp]], [[3lwq]], [[3lwr]], [[3lwv]] – PfPUS Cbf5 + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA – Pyrococcus furiosus<br />	+	**[[3hjw]], [[3lwo]], [[3lwp]], [[3lwq]], [[3lwr]], [[3lwv]] – PfPUS Cbf5 + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA – ''Pyrococcus furiosus''<br />
	**[[3mqk]] - PfPUS Cbf5 + ribosome biogenesis protein Nop10 + small nuclear RNP Gar1-like protein + RNA<br />		**[[3mqk]] - PfPUS Cbf5 + ribosome biogenesis protein Nop10 + small nuclear RNP Gar1-like protein + RNA<br />
	**[[3hjy]] - PfPUS Cbf5 + ribosome biogenesis protein NOP10 + RNA<br />		**[[3hjy]] - PfPUS Cbf5 + ribosome biogenesis protein NOP10 + RNA<br />
Line 50:		Line 50:
	* Probable pseudouridine synthase		* Probable pseudouridine synthase

-	**[[2apo]] – PPUS + ribosome biogenesis protein Nop10 – Methanocaldococcus jannaschii<br />	+	**[[2apo]] – PPUS + ribosome biogenesis protein Nop10 – ''Methanocaldococcus jannaschii''<br />
	**[[2ey4]] - PfPPUS Cbf5 + ribosome biogenesis protein Nop10 + small nucleolar RNP <br />		**[[2ey4]] - PfPPUS Cbf5 + ribosome biogenesis protein Nop10 + small nucleolar RNP <br />
	**[[2hvy]], [[3hax]] - PfPPUS B + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA<br />		**[[2hvy]], [[3hax]] - PfPPUS B + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA<br />
	**[[2rfk]] - PfPUS B + ribosome biogenesis protein Nop10 + small nucleolar RNP + RNA<br />		**[[2rfk]] - PfPUS B + ribosome biogenesis protein Nop10 + small nucleolar RNP + RNA<br />
	**[[3hay]] - PfPPUS B + ribosome biogenesis protein Nop10 + ribosomal protein L7 + small nucleolar RNP + RNA<br />		**[[3hay]] - PfPPUS B + ribosome biogenesis protein Nop10 + ribosomal protein L7 + small nucleolar RNP + RNA<br />
-	**[[2aus]] – PPUS B + ribosome biogenesis protein Nop10 – Pyrococcus abyssi	+	**[[2aus]] – PPUS B + ribosome biogenesis protein Nop10 – ''Pyrococcus abyssi''<br />
	**[[1z2z]] – PPUS D – Methanosarcina mazei<br />		**[[1z2z]] – PPUS D – Methanosarcina mazei<br />
	}}		}}

Michal Harel at 09:43, 5 February 2019

2019-02-05T09:43:54Z

←Older revision		Revision as of 09:43, 5 February 2019
Line 9:		Line 9:
	The conversion of uridine to pseudouridine is accompanied by a conformational change of pseudouridine synthase<ref>PMID:14990747</ref>. <scene name='46/465439/Cv/3'>tRNA pseudouridine synthase binding with pseudouridine monophosphate</scene> ([[1ze2]]).		The conversion of uridine to pseudouridine is accompanied by a conformational change of pseudouridine synthase<ref>PMID:14990747</ref>. <scene name='46/465439/Cv/3'>tRNA pseudouridine synthase binding with pseudouridine monophosphate</scene> ([[1ze2]]).
	</StructureSection>		</StructureSection>
		+
		+	== 3D Structures of deaminase ==
		+
		+	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
		+	{{#tree:id=OrganizedByTopic\|openlevels=0\|
		+
		+	* Pseudouridine synthase
		+
		+	**[[1dj0]] – EcPUS I – Escherichia coli<br />
		+	**[[1ze1]] – TmPUS B – Thermotoga maritima<br />
		+	**[[1ksk]], [[1ksl]] – EcPUS RsuA <br />
		+	**[[1vio]] - PUS RsuA – Haemophilus influenzae<br />
		+	**[[1xpi]] - EcPUS RluC catalytic domain<br />
		+	**[[1v9k]] - EcPUS RluC C-terminal domain (mutant) <br />
		+	**[[2ist]] - EcPUS RluD <br />
		+	**[[1prz]], [[1qyu]], [[1v9f]] - EcPUS RluD catalytic domain<br />
		+	**[[2olw]] - EcPUS RluE<br />
		+	**[[2oml]] - EcPUS RluE catalytic domain<br />
		+	**[[2gml]] - EcPUS RluF catalytic domain<br />
		+	**[[4iqm]], [[4its]], [[4j37]], [[4nz6]] - hPUS Pus1 catalytic domain - human<br />
		+	**[[4nz7]] - hPUS Pus1 catalytic domain (mutant)<br />
		+	**[[1vs3]] – PUS TruA – Thermus thermophilus<br />
		+	**[[1sgv]] – PUS TruB – Mycobacterium tuberculosis<br />
		+	**[[1si7]], [[1szw]], [[1sb7]] - EcPUS TruD<br />
		+
		+	* Pseudouridine synthase complex with RNA
		+
		+	**[[1k8w]] – EcPUS B + stem-loop RNA <br />
		+	**[[1zl3]] - EcPUS B (mutant) + stem-loop RNA<br />
		+	**[[2i82]] – EcPUS RluA + RNA<br />
		+	**[[3dh3]] - EcPUS RluF + RNA<br />
		+	**[[2nqp]], [[2nr0]], [[2nre]] – EcPUS TruA + Leu-tRNA<br />
		+	**[[3hjw]], [[3lwo]], [[3lwp]], [[3lwq]], [[3lwr]], [[3lwv]] – PfPUS Cbf5 + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA – Pyrococcus furiosus<br />
		+	**[[3mqk]] - PfPUS Cbf5 + ribosome biogenesis protein Nop10 + small nuclear RNP Gar1-like protein + RNA<br />
		+	**[[3hjy]] - PfPUS Cbf5 + ribosome biogenesis protein NOP10 + RNA<br />
		+	**[[1ze2]] - TmPUS B + RNA<br />
		+	**[[2ab4]] - TmPUS B (mutant) + RNA<br />
		+	**[[1r3e]], [[1r3f]] - EcPUS B + RNA<br />
		+
		+	* Probable pseudouridine synthase
		+
		+	**[[2apo]] – PPUS + ribosome biogenesis protein Nop10 – Methanocaldococcus jannaschii<br />
		+	**[[2ey4]] - PfPPUS Cbf5 + ribosome biogenesis protein Nop10 + small nucleolar RNP <br />
		+	**[[2hvy]], [[3hax]] - PfPPUS B + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA<br />
		+	**[[2rfk]] - PfPUS B + ribosome biogenesis protein Nop10 + small nucleolar RNP + RNA<br />
		+	**[[3hay]] - PfPPUS B + ribosome biogenesis protein Nop10 + ribosomal protein L7 + small nucleolar RNP + RNA<br />
		+	**[[2aus]] – PPUS B + ribosome biogenesis protein Nop10 – Pyrococcus abyssi
		+	**[[1z2z]] – PPUS D – Methanosarcina mazei<br />
		+	}}

Angel Herraez: (pseudo)uridine is a nucleoside, not nucleotide; other improvements in redaction

2018-11-16T19:13:54Z

(pseudo)uridine is a nucleoside, not nucleotide; other improvements in redaction

←Older revision		Revision as of 19:13, 16 November 2018
Line 1:		Line 1:
-	<StructureSection load='1ze2' size='400' side='right' caption='tRNA pseudouridine synthase complex with RNA ~~and~~ pseudouridine monophosphate [[1ze2]]' scene='46/465439/Cv/1' pspeed='8'>	+	<StructureSection load='1ze2' size='400' side='right' caption='tRNA pseudouridine synthase complex with RNA that contains pseudouridine monophosphate [[1ze2]]' scene='46/465439/Cv/1' pspeed='8'>
-	[[Pseudouridine]] is an abundant modified ~~nucleotide~~ found in RNA molecules. It is formed post-transcriptionally in RNA molecules by isomerization of the base of uridine. There are two major types of enzymes that catalyze this reaction:	+	[[Pseudouridine]] is an abundant modified nucleoside found in RNA molecules. It is formed post-transcriptionally in RNA molecules by isomerization of the bond between base and ribose in uridine. There are two major types of enzymes that catalyze this reaction:

-	* [[RNA-guided ~~Pseudoridine~~ synthase]] -- ~~Complexes~~ of proteins and small RNAs have been identified in archaea and eukaryotes to catalyze these reactions. The small RNA in the complex serves as a guide element to ~~specify~~ the site of modification through base-pairing with the target RNA molecule.	+	* [[RNA-guided pseudouridine synthase]] -- Some ribonucleoproteins (complexes of proteins and small RNAs) have been identified in archaea and eukaryotes to catalyze these reactions. The small RNA in the complex serves as a guide element to select the site of modification through base-pairing with the target RNA molecule.

-	* [[Guide-independent Pseudouridine synthase]] -- The alternative to using the RNA-guided mechanism for pseudouridine formation is a [[Guide-independent Pseudouridine synthase\|guide-independent mechanism]] acting through ~~stand~~-~~alone~~ enzymes to catalyze ~~formation~~.	+	* [[Guide-independent Pseudouridine synthase\|Guide-independent pseudouridine synthase]] -- The alternative to using the RNA-guided mechanism for pseudouridine formation is a [[Guide-independent Pseudouridine synthase\|guide-independent mechanism]] acting through protein-only enzymes to catalyze the isomerization.

	== Structural highlights ==		== Structural highlights ==
-	The conversion of uridine to pseudouridine ~~causes~~ conformational change of ~~PUS~~<ref>PMID:14990747</ref>. <scene name='46/465439/Cv/3'>tRNA pseudouridine synthase binding with pseudouridine monophosphate</scene> ([[1ze2]]).	+	The conversion of uridine to pseudouridine is accompanied by a conformational change of pseudouridine synthase<ref>PMID:14990747</ref>. <scene name='46/465439/Cv/3'>tRNA pseudouridine synthase binding with pseudouridine monophosphate</scene> ([[1ze2]]).
	</StructureSection>		</StructureSection>

Wayne Decatur at 17:08, 13 November 2018

2018-11-13T17:08:46Z

←Older revision		Revision as of 17:08, 13 November 2018
Line 1:		Line 1:
	<StructureSection load='1ze2' size='400' side='right' caption='tRNA pseudouridine synthase complex with RNA and pseudouridine monophosphate [[1ze2]]' scene='46/465439/Cv/1' pspeed='8'>		<StructureSection load='1ze2' size='400' side='right' caption='tRNA pseudouridine synthase complex with RNA and pseudouridine monophosphate [[1ze2]]' scene='46/465439/Cv/1' pspeed='8'>
-	== Function ==
	[[Pseudouridine]] is an abundant modified nucleotide found in RNA molecules. It is formed post-transcriptionally in RNA molecules by isomerization of the base of uridine. There are two major types of enzymes that catalyze this reaction:		[[Pseudouridine]] is an abundant modified nucleotide found in RNA molecules. It is formed post-transcriptionally in RNA molecules by isomerization of the base of uridine. There are two major types of enzymes that catalyze this reaction:

Wayne Decatur: fix link

2018-11-13T17:07:34Z

fix link

←Older revision		Revision as of 17:07, 13 November 2018
Line 3:		Line 3:
	[[Pseudouridine]] is an abundant modified nucleotide found in RNA molecules. It is formed post-transcriptionally in RNA molecules by isomerization of the base of uridine. There are two major types of enzymes that catalyze this reaction:		[[Pseudouridine]] is an abundant modified nucleotide found in RNA molecules. It is formed post-transcriptionally in RNA molecules by isomerization of the base of uridine. There are two major types of enzymes that catalyze this reaction:

-	* [[RNA-guided Pseudoridine synthase] -- ]Complexes of proteins and small RNAs have been identified in archaea and eukaryotes to catalyze these reactions. The small RNA in the complex serves as a guide element to specify the site of modification through base-pairing with the target RNA molecule.	+	* [[RNA-guided Pseudoridine synthase]] -- Complexes of proteins and small RNAs have been identified in archaea and eukaryotes to catalyze these reactions. The small RNA in the complex serves as a guide element to specify the site of modification through base-pairing with the target RNA molecule.

	* [[Guide-independent Pseudouridine synthase]] -- The alternative to using the RNA-guided mechanism for pseudouridine formation is a [[Guide-independent Pseudouridine synthase\|guide-independent mechanism]] acting through stand-alone enzymes to catalyze formation.		* [[Guide-independent Pseudouridine synthase]] -- The alternative to using the RNA-guided mechanism for pseudouridine formation is a [[Guide-independent Pseudouridine synthase\|guide-independent mechanism]] acting through stand-alone enzymes to catalyze formation.

Wayne Decatur: better specify there are two types of complexes among the pseudouridine synthases

2018-11-13T17:06:49Z

better specify there are two types of complexes among the pseudouridine synthases

←Older revision		Revision as of 17:06, 13 November 2018
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	<StructureSection load='1ze2' size='400' side='right' caption='tRNA pseudouridine synthase complex with RNA and pseudouridine monophosphate [[1ze2]]' scene='46/465439/Cv/1' pspeed='8'>		<StructureSection load='1ze2' size='400' side='right' caption='tRNA pseudouridine synthase complex with RNA and pseudouridine monophosphate [[1ze2]]' scene='46/465439/Cv/1' pspeed='8'>
	== Function ==		== Function ==
-	~~'''tRNA pseudouridine synthase''' (PUS) catalyzes the conversion of tRNA uridine to tRNA pseudouridine<ref>PMID:14566049</ref>. '''Probable tRNA pseudouridine synthase''' (PPUS)~~ is ~~a similar enzyme. PUS are active~~ in ~~the ribosomal large subunit '''Ribosomal large subunit pseudouridine synthase''' and in the ribosomal small subunit '''Ribosomal small subunit pseudouridine synthase'''.<br />~~	+	[[Pseudouridine]] is an abundant modified nucleotide found in RNA molecules. It is formed post-transcriptionally in RNA molecules by isomerization of the base of uridine. There are two major types of enzymes that catalyze this reaction:
-	~~Ribosomal large subunit pseudouridine synthases:<br />~~	+
-	*'''RluA''' is responsible for synthesis of pseudouridine from uracil in positions 746 in 23S ribosomal RNA ~~and in the anticodon loop of tRNAPhe, tRNACys and tRNALeu<ref>PMID:17188032</ref>~~.~~<br />~~	+
-	*'''RluB''' is ~~responsible for synthesis of pseudouridine from uracil~~ in ~~position 2605 in 23S ribosomal~~ RNA~~<ref>PMID:24214967</ref>.<br />~~	+
-	*'''RluC''' is responsible for synthesis of ~~pseudouridine from uracil in positions 955, 2504 and 2580 in 23S ribosomal RNA<ref>PMID:9660827</ref>.<br />~~	+
-	*'''RluD''' is responsible for synthesis of ~~pseudouridine from uracil in positions 1911, 1915 and 1917 in 23S ribosomal RNA<ref>PMID:15928344</ref>~~.~~<br />~~	+
-	*'''RluE''' is responsible for synthesis of ~~pseudouridine from uracil in position 2457 in 23S ribosomal RNA<ref>PMID~~:~~17320904</ref>.<br />~~	+
-	*'''RluF''' is responsible for synthesis of pseudouridine from uracil in position 2604 in 23S ribosomal RNA<ref>PMID:16712869</ref>.<br />	+

-	~~Ribosomal small subunit pseudouridine~~ synthase ~~'''RsuA''' is responsible for synthesis~~ of ~~pseudouridine from uracil~~ in ~~positions 516~~ in ~~16S ribosomal~~ RNA~~<ref>PMID:11953756</ref>~~.~~<br />~~	+	* [[RNA-guided Pseudoridine synthase] -- ]Complexes of proteins and small RNAs have been identified in archaea and eukaryotes to catalyze these reactions. The small RNA in the complex serves as a guide element to specify the site of modification through base-pairing with the target RNA molecule.
		+
		+	* [[Guide-independent Pseudouridine synthase]] -- The alternative to using the RNA-guided mechanism for pseudouridine formation is a [[Guide-independent Pseudouridine synthase\|guide-independent mechanism]] acting through stand-alone enzymes to catalyze formation.

	== Structural highlights ==		== Structural highlights ==
	The conversion of uridine to pseudouridine causes conformational change of PUS<ref>PMID:14990747</ref>. <scene name='46/465439/Cv/3'>tRNA pseudouridine synthase binding with pseudouridine monophosphate</scene> ([[1ze2]]).		The conversion of uridine to pseudouridine causes conformational change of PUS<ref>PMID:14990747</ref>. <scene name='46/465439/Cv/3'>tRNA pseudouridine synthase binding with pseudouridine monophosphate</scene> ([[1ze2]]).
	</StructureSection>		</StructureSection>
-	== 3D Structures of pseudouridine synthase==
-
-	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
-	{{#tree:id=OrganizedByTopic\|openlevels=0\|
-
-	*tRNA pseudouridine synthase
-
-	**[[1dj0]] – EcPUS I – ''Escherichia coli''<BR />
-	**[[4iqm]], [[4its]], [[4j37]], [[4nz6]] - hPUS Pus1 catalytic domain - human<br />
-	**[[4nz7]] - hPUS Pus1 catalytic domain (mutant)<br />
-	**[[1vs3]] – PUS TruA – ''Thermus thermophilus''<BR />
-	**[[1sgv]] – PUS TruB – ''Mycobacterium tuberculosis''<BR />
-	**[[1si7]], [[1szw]], [[1sb7]] - EcPUS TruD
-
-	*tRNA pseudouridine synthase complex with RNA
-
-	**[[1k8w]] – EcTruB + stem-loop RNA<BR />
-	**[[1zl3]] - EcTruB (mutant) + stem-loop RNA<BR />
-	**[[2nqp]], [[2nr0]], [[2nre]] – EcTruA + Leu-tRNA<BR />
-	**[[1ze2]] - TmPUS B + RNA<BR />
-	**[[2ab4]] - TmPUS B (mutant) + RNA<BR />
-	**[[1r3e]], [[1r3f]] - EcTruB + RNA<BR />
-
-	*Probable tRNA pseudouridine synthase
-
-	**[[3hjw]], [[3lwo]], [[3lwp]], [[3lwq]], [[3lwr]], [[3lwv]], [[3hax]] – PfPUS Cbf5 + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA – ''Pyrococcus furiosus''<BR />
-	**[[3hay]] – PfPUS Cbf5 + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA + small nuclear RNP protein<BR />
-	**[[2hvy]] – PfPUS Cbf5 + ribosome biogenesis protein Nop10 + ribosomal protein L7 + RNA + small nuclear RNP protein + small nuclear RNP Gar1-like protein<BR />
-	**[[3mqk]] - PfPUS Cbf5 + ribosome biogenesis protein Nop10 + small nuclear RNP Gar1-like protein + RNA<BR />
-	**[[2rfk]] - PfPUS Cbf5 (mutant) + ribosome biogenesis protein Nop10 + small nuclear RNP Gar1-like protein + RNA<BR />
-	**[[2ey4]] - PfPUS Cbf5 + ribosome biogenesis protein Nop10 + small nuclear RNP Gar1-like protein <BR />
-	**[[3hjy]] - PfPUS Cbf5 + ribosome biogenesis protein NOP10 + RNA<BR />
-	**[[2apo]] - PfPUS Cbf5 + ribosome biogenesis protein NOP10 - ''Methanocaldococcus jannaschii''<BR />
-
-	*Ribosomal large subunit pseudouridine synthase
-
-	**[[2i82]] - EcRluA catalytic domain + RNA<br />
-	**[[4lab]] - EcRluB catalytic domain <br />
-	**[[4lgt]] - EcRluB catalytic domain + RNA<br />
-	**[[1xpi]] - EcRluC catalytic domain<br />
-	**[[5vbb]] - hRluC-like<br />
-	**[[1prz]], [[1qyu]], [[1v9f]], [[1v9k]], [[2ist]] - EcRluD catalytic domain<br />
-	**[[2oml]], [[2olw]] - EcRluE catalytic domain<br />
-	**[[2gml]] - EcRluF catalytic domain<br />
-	**[[3dh3]] - EcRluF catalytic domain + RNA<br />
-
-	*Ribosomal small subunit pseudouridine synthase
-
-	**[[1vio]] - RsuA - ''Haemophilus influenzae''<br />
-	**[[1ksk]] - EcRsuA <br />
-	**[[1ksl]] - EcRsuA + uracil<br />
-	**[[1ksv]] - EcRsuA + UMP<br />
-
-
-	}}
-	== References ==
-	<references/>
-	[[Category:Topic Page]]

Michal Harel at 11:27, 12 November 2018

2018-11-12T11:27:42Z

←Older revision		Revision as of 11:27, 12 November 2018
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	The conversion of uridine to pseudouridine causes conformational change of PUS<ref>PMID:14990747</ref>. <scene name='46/465439/Cv/3'>tRNA pseudouridine synthase binding with pseudouridine monophosphate</scene> ([[1ze2]]).		The conversion of uridine to pseudouridine causes conformational change of PUS<ref>PMID:14990747</ref>. <scene name='46/465439/Cv/3'>tRNA pseudouridine synthase binding with pseudouridine monophosphate</scene> ([[1ze2]]).
	</StructureSection>		</StructureSection>
-	== 3D Structures of ~~tRNA~~ pseudouridine synthase==	+	== 3D Structures of pseudouridine synthase==

	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}		Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}