3tdb - Revision history

OCA at 10:07, 1 March 2024

2024-03-01T10:07:37Z

←Older revision		Revision as of 10:07, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3tdb' size='340' side='right'caption='[[3tdb]], [[Resolution\|resolution]] 2.27Å' scene=''>		<StructureSection load='3tdb' size='340' side='right'caption='[[3tdb]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tdb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TDB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tdb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TDB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3TB:N-[(1E,2R)-1-[(2R)-2-{[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]CARBAMOYL}CYCLOPENTYLIDENE]-3-(PHOSPHONOOXY)PROPAN-2-YL]-L-PHENYLALANINAMIDE'>3TB</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.267Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1f8a\|1f8a]], [[1pin\|1pin]], [[2q5a\|2q5a]], [[2itk\|2itk]], [[3tcz\|3tcz]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3TB:N-[(1E,2R)-1-[(2R)-2-{[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]CARBAMOYL}CYCLOPENTYLIDENE]-3-(PHOSPHONOOXY)PROPAN-2-YL]-L-PHENYLALANINAMIDE'>3TB</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PIN1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tdb OCA], [https://pdbe.org/3tdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tdb RCSB], [https://www.ebi.ac.uk/pdbsum/3tdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tdb ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tdb OCA], [https://pdbe.org/3tdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tdb RCSB], [https://www.ebi.ac.uk/pdbsum/3tdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tdb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PIN1_HUMAN PIN1_HUMAN]] Essential PPIase that regulates mitosis presumably by interacting with NIMA and attenuating its mitosis-promoting activity. Displays a preference for an acidic residue N-terminal to the isomerized proline bond. Catalyzes pSer/Thr-Pro cis/trans isomerizations. Down-regulates kinase activity of BTK. Can transactivate multiple oncogenes and induce centrosome amplification, chromosome instability and cell transformation. Required for the efficient dephosphorylation and recycling of RAF1 after mitogen activation.<ref>PMID:15664191</ref> <ref>PMID:16644721</ref> <ref>PMID:21497122</ref>	+	[https://www.uniprot.org/uniprot/PIN1_HUMAN PIN1_HUMAN] Essential PPIase that regulates mitosis presumably by interacting with NIMA and attenuating its mitosis-promoting activity. Displays a preference for an acidic residue N-terminal to the isomerized proline bond. Catalyzes pSer/Thr-Pro cis/trans isomerizations. Down-regulates kinase activity of BTK. Can transactivate multiple oncogenes and induce centrosome amplification, chromosome instability and cell transformation. Required for the efficient dephosphorylation and recycling of RAF1 after mitogen activation.<ref>PMID:15664191</ref> <ref>PMID:16644721</ref> <ref>PMID:21497122</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The C-terminal domain (CTD) of eukaryotic RNA polymerase II is an essential regulator for RNA polymerase II-mediated transcription. It is composed of multiple repeats of a consensus sequence Tyr(1)Ser(2)Pro(3)Thr(4)Ser(5)Pro(6)Ser(7). CTD regulation of transcription is mediated by both phosphorylation of the serines and prolyl isomerization of the two prolines. Interestingly, the phosphorylation sites are typically close to prolines, and thus the conformation of the adjacent proline could impact the specificity of the corresponding kinases and phosphatases. Experimental evidence of cross-talk between these two regulatory mechanisms has been elusive. Pin1 is a highly conserved phosphorylation-specific peptidyl-prolyl isomerase (PPIase) that recognizes the phospho-Ser/Thr (pSer/Thr)-Pro motif with CTD as one of its primary substrates in vivo. In the present study, we provide structural snapshots and kinetic evidence that support the concept of cross-talk between prolyl isomerization and phosphorylation. We determined the structures of Pin1 bound with two substrate isosteres that mimic peptides containing pSer/Thr-Pro motifs in cis or trans conformations. The results unequivocally demonstrate the utility of both cis- and trans-locked alkene isosteres as close geometric mimics of peptides bound to a protein target. Building on this result, we identified a specific case in which Pin1 differentially affects the rate of dephosphorylation catalyzed by two phosphatases (Scp1 and Ssu72) that target the same serine residue in the CTD heptad repeat but have different preferences for the isomerization state of the adjacent proline residue. These data exemplify for the first time how modulation of proline isomerization can kinetically impact signal transduction in transcription regulation.	+
-		+
-	Structural and Kinetic Analysis of Prolyl-isomerization/Phosphorylation Cross-Talk in the CTD Code.,Zhang M, Wang XJ, Chen X, Bowman ME, Luo Y, Noel JP, Ellington AD, Etzkorn FA, Zhang Y ACS Chem Biol. 2012 Jun 18. PMID:22670809<ref>PMID:22670809</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3tdb" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 28:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Peptidylprolyl isomerase]]~~	+	[[Category: Zhang M]]
-	[[Category: Zhang, M]]	+	[[Category: Zhang Y]]
-	[[Category: Zhang, Y]]	+
-	~~[[Category: Isomerase-inhibitor complex]]~~	+
-	~~[[Category: Peptidyl-prolyl isomerase]]~~	+
-	~~[[Category: Ppiase domain]]~~	+
-	~~[[Category: Ww domain~~]]	+

OCA at 16:52, 6 July 2022

2022-07-06T16:52:59Z

←Older revision		Revision as of 16:52, 6 July 2022
Line 1:		Line 1:

	==Human Pin1 bound to trans peptidomimetic inhibitor==		==Human Pin1 bound to trans peptidomimetic inhibitor==
-	<StructureSection load='3tdb' size='340' side='right' caption='[[3tdb]], [[Resolution\|resolution]] 2.27Å' scene=''>	+	<StructureSection load='3tdb' size='340' side='right'caption='[[3tdb]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tdb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TDB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TDB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tdb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TDB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3TB:N-[(1E,2R)-1-[(2R)-2-{[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]CARBAMOYL}CYCLOPENTYLIDENE]-3-(PHOSPHONOOXY)PROPAN-2-YL]-L-PHENYLALANINAMIDE'>3TB</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3TB:N-[(1E,2R)-1-[(2R)-2-{[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]CARBAMOYL}CYCLOPENTYLIDENE]-3-(PHOSPHONOOXY)PROPAN-2-YL]-L-PHENYLALANINAMIDE'>3TB</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f8a\|1f8a]], [[1pin\|1pin]], [[2q5a\|2q5a]], [[2itk\|2itk]], [[3tcz\|3tcz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1f8a\|1f8a]], [[1pin\|1pin]], [[2q5a\|2q5a]], [[2itk\|2itk]], [[3tcz\|3tcz]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PIN1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PIN1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tdb OCA], [~~http~~://pdbe.org/3tdb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3tdb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3tdb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3tdb ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tdb OCA], [https://pdbe.org/3tdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tdb RCSB], [https://www.ebi.ac.uk/pdbsum/3tdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tdb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PIN1_HUMAN PIN1_HUMAN]] Essential PPIase that regulates mitosis presumably by interacting with NIMA and attenuating its mitosis-promoting activity. Displays a preference for an acidic residue N-terminal to the isomerized proline bond. Catalyzes pSer/Thr-Pro cis/trans isomerizations. Down-regulates kinase activity of BTK. Can transactivate multiple oncogenes and induce centrosome amplification, chromosome instability and cell transformation. Required for the efficient dephosphorylation and recycling of RAF1 after mitogen activation.<ref>PMID:15664191</ref> <ref>PMID:16644721</ref> <ref>PMID:21497122</ref>	+	[[https://www.uniprot.org/uniprot/PIN1_HUMAN PIN1_HUMAN]] Essential PPIase that regulates mitosis presumably by interacting with NIMA and attenuating its mitosis-promoting activity. Displays a preference for an acidic residue N-terminal to the isomerized proline bond. Catalyzes pSer/Thr-Pro cis/trans isomerizations. Down-regulates kinase activity of BTK. Can transactivate multiple oncogenes and induce centrosome amplification, chromosome instability and cell transformation. Required for the efficient dephosphorylation and recycling of RAF1 after mitogen activation.<ref>PMID:15664191</ref> <ref>PMID:16644721</ref> <ref>PMID:21497122</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[Peptidyl-prolyl cis-trans isomerase\|Peptidyl-prolyl cis-trans isomerase]]	+	*[[Peptidyl-prolyl cis-trans isomerase 3D structures\|Peptidyl-prolyl cis-trans isomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Peptidylprolyl isomerase]]		[[Category: Peptidylprolyl isomerase]]
	[[Category: Zhang, M]]		[[Category: Zhang, M]]

OCA at 07:42, 4 August 2016

2016-08-04T07:42:33Z

←Older revision		Revision as of 07:42, 4 August 2016
Line 1:		Line 1:
		+
	==Human Pin1 bound to trans peptidomimetic inhibitor==		==Human Pin1 bound to trans peptidomimetic inhibitor==
	<StructureSection load='3tdb' size='340' side='right' caption='[[3tdb]], [[Resolution\|resolution]] 2.27Å' scene=''>		<StructureSection load='3tdb' size='340' side='right' caption='[[3tdb]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tdb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TDB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tdb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TDB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3TB:N-[(1E,2R)-1-[(2R)-2-{[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]CARBAMOYL}CYCLOPENTYLIDENE]-3-(PHOSPHONOOXY)PROPAN-2-YL]-L-PHENYLALANINAMIDE'>3TB</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3TB:N-[(1E,2R)-1-[(2R)-2-{[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]CARBAMOYL}CYCLOPENTYLIDENE]-3-(PHOSPHONOOXY)PROPAN-2-YL]-L-PHENYLALANINAMIDE'>3TB</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f8a\|1f8a]], [[1pin\|1pin]], [[2q5a\|2q5a]], [[2itk\|2itk]], [[3tcz\|3tcz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f8a\|1f8a]], [[1pin\|1pin]], [[2q5a\|2q5a]], [[2itk\|2itk]], [[3tcz\|3tcz]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PIN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PIN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tdb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tdb RCSB], [http://www.ebi.ac.uk/pdbsum/3tdb PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tdb OCA], [http://pdbe.org/3tdb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tdb RCSB], [http://www.ebi.ac.uk/pdbsum/3tdb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tdb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3tdb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Peptidyl-prolyl cis-trans isomerase\|Peptidyl-prolyl cis-trans isomerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Peptidylprolyl isomerase]]		[[Category: Peptidylprolyl isomerase]]
	[[Category: Zhang, M]]		[[Category: Zhang, M]]

OCA at 07:00, 25 December 2014

2014-12-25T07:00:58Z

←Older revision		Revision as of 07:00, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3tdb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TDB FirstGlance]. <br>		<table><tr><td colspan='2'>[[3tdb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TDB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3TB:N-[(1E,2R)-1-[(2R)-2-{[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]CARBAMOYL}CYCLOPENTYLIDENE]-3-(PHOSPHONOOXY)PROPAN-2-YL]-L-PHENYLALANINAMIDE'>3TB</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3TB:N-[(1E,2R)-1-[(2R)-2-{[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]CARBAMOYL}CYCLOPENTYLIDENE]-3-(PHOSPHONOOXY)PROPAN-2-YL]-L-PHENYLALANINAMIDE'>3TB</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f8a\|1f8a]], [[1pin\|1pin]], [[2q5a\|2q5a]], [[2itk\|2itk]], [[3tcz\|3tcz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f8a\|1f8a]], [[1pin\|1pin]], [[2q5a\|2q5a]], [[2itk\|2itk]], [[3tcz\|3tcz]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PIN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PIN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tdb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tdb RCSB], [http://www.ebi.ac.uk/pdbsum/3tdb PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tdb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tdb RCSB], [http://www.ebi.ac.uk/pdbsum/3tdb PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PIN1_HUMAN PIN1_HUMAN]] Essential PPIase that regulates mitosis presumably by interacting with NIMA and attenuating its mitosis-promoting activity. Displays a preference for an acidic residue N-terminal to the isomerized proline bond. Catalyzes pSer/Thr-Pro cis/trans isomerizations. Down-regulates kinase activity of BTK. Can transactivate multiple oncogenes and induce centrosome amplification, chromosome instability and cell transformation. Required for the efficient dephosphorylation and recycling of RAF1 after mitogen activation.<ref>PMID:15664191</ref> <ref>PMID:16644721</ref> <ref>PMID:21497122</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 25:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Peptidylprolyl isomerase]]		[[Category: Peptidylprolyl isomerase]]
-	[[Category: Zhang, M.]]	+	[[Category: Zhang, M]]
-	[[Category: Zhang, Y.]]	+	[[Category: Zhang, Y]]
	[[Category: Isomerase-inhibitor complex]]		[[Category: Isomerase-inhibitor complex]]
	[[Category: Peptidyl-prolyl isomerase]]		[[Category: Peptidyl-prolyl isomerase]]
	[[Category: Ppiase domain]]		[[Category: Ppiase domain]]
	[[Category: Ww domain]]		[[Category: Ww domain]]

OCA at 06:52, 25 June 2014

2014-06-25T06:52:22Z

←Older revision		Revision as of 06:52, 25 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3tdb.~~png~~\|~~left~~\|~~200px~~]]	+	==Human Pin1 bound to trans peptidomimetic inhibitor==
		+	<StructureSection load='3tdb' size='340' side='right' caption='[[3tdb]], [[Resolution\|resolution]] 2.27Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3tdb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TDB FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3TB:N-[(1E,2R)-1-[(2R)-2-{[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]CARBAMOYL}CYCLOPENTYLIDENE]-3-(PHOSPHONOOXY)PROPAN-2-YL]-L-PHENYLALANINAMIDE'>3TB</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f8a\|1f8a]], [[1pin\|1pin]], [[2q5a\|2q5a]], [[2itk\|2itk]], [[3tcz\|3tcz]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PIN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tdb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tdb RCSB], [http://www.ebi.ac.uk/pdbsum/3tdb PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The C-terminal domain (CTD) of eukaryotic RNA polymerase II is an essential regulator for RNA polymerase II-mediated transcription. It is composed of multiple repeats of a consensus sequence Tyr(1)Ser(2)Pro(3)Thr(4)Ser(5)Pro(6)Ser(7). CTD regulation of transcription is mediated by both phosphorylation of the serines and prolyl isomerization of the two prolines. Interestingly, the phosphorylation sites are typically close to prolines, and thus the conformation of the adjacent proline could impact the specificity of the corresponding kinases and phosphatases. Experimental evidence of cross-talk between these two regulatory mechanisms has been elusive. Pin1 is a highly conserved phosphorylation-specific peptidyl-prolyl isomerase (PPIase) that recognizes the phospho-Ser/Thr (pSer/Thr)-Pro motif with CTD as one of its primary substrates in vivo. In the present study, we provide structural snapshots and kinetic evidence that support the concept of cross-talk between prolyl isomerization and phosphorylation. We determined the structures of Pin1 bound with two substrate isosteres that mimic peptides containing pSer/Thr-Pro motifs in cis or trans conformations. The results unequivocally demonstrate the utility of both cis- and trans-locked alkene isosteres as close geometric mimics of peptides bound to a protein target. Building on this result, we identified a specific case in which Pin1 differentially affects the rate of dephosphorylation catalyzed by two phosphatases (Scp1 and Ssu72) that target the same serine residue in the CTD heptad repeat but have different preferences for the isomerization state of the adjacent proline residue. These data exemplify for the first time how modulation of proline isomerization can kinetically impact signal transduction in transcription regulation.

-	~~{{STRUCTURE_3tdb\| PDB=3tdb \| SCENE= }}~~	+	Structural and Kinetic Analysis of Prolyl-isomerization/Phosphorylation Cross-Talk in the CTD Code.,Zhang M, Wang XJ, Chen X, Bowman ME, Luo Y, Noel JP, Ellington AD, Etzkorn FA, Zhang Y ACS Chem Biol. 2012 Jun 18. PMID:22670809<ref>PMID:22670809</ref>

-	~~===Human Pin1 bound to trans peptidomimetic inhibitor===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22670809}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3tdb]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3TDB OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022670809<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Peptidylprolyl isomerase]]		[[Category: Peptidylprolyl isomerase]]

OCA at 05:48, 5 September 2012

2012-09-05T05:48:17Z

←Older revision		Revision as of 05:48, 5 September 2012
Line 1:		Line 1:
-	[[Image:3tdb.~~jpg~~\|left\|200px]]	+	[[Image:3tdb.png\|left\|200px]]

	{{STRUCTURE_3tdb\| PDB=3tdb \| SCENE= }}		{{STRUCTURE_3tdb\| PDB=3tdb \| SCENE= }}

OCA at 05:47, 27 June 2012

2012-06-27T05:47:44Z

←Older revision		Revision as of 05:47, 27 June 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3tdb.jpg\|left\|200px]]

-	~~The entry~~ 3tdb ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_3tdb\| PDB=3tdb \| SCENE= }}

-	~~Authors: Zhang, M., Zhang, Y.~~	+	===Human Pin1 bound to trans peptidomimetic inhibitor===

-	~~Description~~: ~~Human Pin1 bound to trans peptidomimetic~~ inhibitor	+	{{ABSTRACT_PUBMED_22670809}}
		+
		+	==About this Structure==
		+	[[3tdb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TDB OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022670809</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Peptidylprolyl isomerase]]
		+	[[Category: Zhang, M.]]
		+	[[Category: Zhang, Y.]]
		+	[[Category: Isomerase-inhibitor complex]]
		+	[[Category: Peptidyl-prolyl isomerase]]
		+	[[Category: Ppiase domain]]
		+	[[Category: Ww domain]]

OCA at 06:08, 5 October 2011

2011-10-05T06:08:20Z

←Older revision		Revision as of 06:08, 5 October 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3tdb is ON HOLD	+	The entry 3tdb is ON HOLD until Paper Publication

	Authors: Zhang, M., Zhang, Y.		Authors: Zhang, M., Zhang, Y.

	Description: Human Pin1 bound to trans peptidomimetic inhibitor		Description: Human Pin1 bound to trans peptidomimetic inhibitor

OCA at 06:23, 31 August 2011

2011-08-31T06:23:22Z

←Older revision		Revision as of 06:23, 31 August 2011
Line 3:		Line 3:
	The entry 3tdb is ON HOLD		The entry 3tdb is ON HOLD

-	Authors: ~~ZHANG~~, ~~MENGMENG~~, ~~ZHANG~~, ~~YAN~~	+	Authors: Zhang, M., Zhang, Y.

	Description: Human Pin1 bound to trans peptidomimetic inhibitor		Description: Human Pin1 bound to trans peptidomimetic inhibitor

OCA: Protected "3tdb" [edit=sysop:move=sysop]

2011-08-17T05:58:04Z

Protected "3tdb" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:58, 17 August 2011