5wvu - Revision history

OCA at 09:19, 20 March 2024

OCA — Wed, 20 Mar 2024 09:19:05 GMT

←Older revision		Revision as of 09:19, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='5wvu' size='340' side='right'caption='[[5wvu]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5wvu' size='340' side='right'caption='[[5wvu]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wvu]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thet8 Thet8~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1wgz 1wgz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WVU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WVU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wvu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1wgz 1wgz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WVU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WVU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~>, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.6Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>TTHA0270 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~300852 THET8])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Carboxypeptidase_Taq Carboxypeptidase Taq], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.19 3.4.17.19]~~ </~~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=5wvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wvu OCA], [https://pdbe.org/5wvu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wvu RCSB], [https://www.ebi.ac.uk/pdbsum/5wvu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wvu ProSAT]</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=5wvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wvu OCA], [~~http~~://pdbe.org/5wvu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wvu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wvu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wvu ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CBP1_THET8 CBP1_THET8]] Broad specificity carboxypetidase that releases amino acids sequentially from the C-terminus, including neutral, aromatic, polar and basic residues, but not Pro. Has lower activity with substrates ending with Gly or Glu.<ref>PMID:19544567</ref>	+	[https://www.uniprot.org/uniprot/CBP1_THET8 CBP1_THET8] Broad specificity carboxypetidase that releases amino acids sequentially from the C-terminus, including neutral, aromatic, polar and basic residues, but not Pro. Has lower activity with substrates ending with Gly or Glu.<ref>PMID:19544567</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Carboxypeptidase cleaves the C-terminal amino acid residue from proteins and peptides. Here, we report the functional and structural characterizations of carboxypeptidase belonging to the M32 family from the thermophilic bacterium Thermus thermophilus HB8 (TthCP). TthCP exhibits a relatively broad specificity for both hydrophilic (neutral and basic) and hydrophobic (aliphatic and aromatic) residues at the C-terminus and shows optimal activity in the temperature range of 75-80 degrees C and in the pH range of 6.8-7.2. Enzyme activity was significantly enhanced by cobalt or cadmium and was moderately inhibited by Tris at 25 degrees C. We also determined the crystal structure of TthCP at 2.6 A resolution. Two dimer types of TthCP are present in the crystal. One type consists of two subunits in different states, open and closed, with a Calpha RMSD value of 2.2 A; the other type consists of two subunits in the same open state. This structure enables us to compare the open and closed states of an M32 carboxypeptidase. The TthCP subunit can be divided into two domains, L and S, which are separated by a substrate-binding groove. The L and S domains in the open state are almost identical to those in the closed state, with Calpha RMSD values of 0.84 and 0.53 A, respectively, suggesting that the transition between the open and closed states proceeds with a large hinge-bending motion. The superimposition between the closed states of TthCP and BsuCP, another M32 family member, revealed that most putative substrate-binding residues in the grooves are oriented in the same direction.	+
-		+
-	Insight into the transition between the open and closed conformations of Thermus thermophilus carboxypeptidase.,Okai M, Yamamura A, Hayakawa K, Tsutsui S, Miyazono KI, Lee WC, Nagata K, Inoue Y, Tanokura M Biochem Biophys Res Commun. 2017 Mar 18;484(4):787-793. doi:, 10.1016/j.bbrc.2017.01.167. Epub 2017 Feb 2. PMID:28161633<ref>PMID:28161633</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5wvu" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 27:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Carboxypeptidase Taq]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet8~~]]	+	[[Category: Thermus thermophilus HB8]]
-	[[Category: Nagata, K]]	+	[[Category: Nagata K]]
-	[[Category: Okai, M]]	+	[[Category: Okai M]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Tanokura M]]
-	[[Category: Tanokura, M]]	+
-	~~[[Category: Carboxypeptidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 10:15, 26 February 2020

OCA — Wed, 26 Feb 2020 10:15:47 GMT

←Older revision		Revision as of 10:15, 26 February 2020
Line 1:		Line 1:

	==Crystal structure of carboxypeptidase from Thermus thermophilus==		==Crystal structure of carboxypeptidase from Thermus thermophilus==
-	<StructureSection load='5wvu' size='340' side='right' caption='[[5wvu]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5wvu' size='340' side='right'caption='[[5wvu]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wvu]] is a 3 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1wgz 1wgz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WVU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WVU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wvu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1wgz 1wgz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WVU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WVU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0270 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carboxypeptidase_Taq Carboxypeptidase Taq], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.19 3.4.17.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carboxypeptidase_Taq Carboxypeptidase Taq], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.19 3.4.17.19] </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=5wvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wvu OCA], [http://pdbe.org/5wvu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wvu RCSB], [http://www.ebi.ac.uk/pdbsum/5wvu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wvu ProSAT]</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=5wvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wvu OCA], [http://pdbe.org/5wvu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wvu RCSB], [http://www.ebi.ac.uk/pdbsum/5wvu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wvu ProSAT]</span></td></tr>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5wvu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5wvu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carboxypeptidase 3D structures\|Carboxypeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Carboxypeptidase Taq]]		[[Category: Carboxypeptidase Taq]]
		+	[[Category: Large Structures]]
		+	[[Category: Thet8]]
	[[Category: Nagata, K]]		[[Category: Nagata, K]]
	[[Category: Okai, M]]		[[Category: Okai, M]]

OCA at 06:53, 9 March 2017

OCA — Thu, 09 Mar 2017 06:53:45 GMT

←Older revision		Revision as of 06:53, 9 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5wvu is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of carboxypeptidase from Thermus thermophilus==
		+	<StructureSection load='5wvu' size='340' side='right' caption='[[5wvu]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5wvu]] is a 3 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1wgz 1wgz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WVU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WVU FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carboxypeptidase_Taq Carboxypeptidase Taq], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.19 3.4.17.19] </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=5wvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wvu OCA], [http://pdbe.org/5wvu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wvu RCSB], [http://www.ebi.ac.uk/pdbsum/5wvu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wvu ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CBP1_THET8 CBP1_THET8]] Broad specificity carboxypetidase that releases amino acids sequentially from the C-terminus, including neutral, aromatic, polar and basic residues, but not Pro. Has lower activity with substrates ending with Gly or Glu.<ref>PMID:19544567</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Carboxypeptidase cleaves the C-terminal amino acid residue from proteins and peptides. Here, we report the functional and structural characterizations of carboxypeptidase belonging to the M32 family from the thermophilic bacterium Thermus thermophilus HB8 (TthCP). TthCP exhibits a relatively broad specificity for both hydrophilic (neutral and basic) and hydrophobic (aliphatic and aromatic) residues at the C-terminus and shows optimal activity in the temperature range of 75-80 degrees C and in the pH range of 6.8-7.2. Enzyme activity was significantly enhanced by cobalt or cadmium and was moderately inhibited by Tris at 25 degrees C. We also determined the crystal structure of TthCP at 2.6 A resolution. Two dimer types of TthCP are present in the crystal. One type consists of two subunits in different states, open and closed, with a Calpha RMSD value of 2.2 A; the other type consists of two subunits in the same open state. This structure enables us to compare the open and closed states of an M32 carboxypeptidase. The TthCP subunit can be divided into two domains, L and S, which are separated by a substrate-binding groove. The L and S domains in the open state are almost identical to those in the closed state, with Calpha RMSD values of 0.84 and 0.53 A, respectively, suggesting that the transition between the open and closed states proceeds with a large hinge-bending motion. The superimposition between the closed states of TthCP and BsuCP, another M32 family member, revealed that most putative substrate-binding residues in the grooves are oriented in the same direction.

-	~~Authors: Okai~~, M., ~~Nagata~~, K., ~~Tanokura~~, M.~~, RIKEN Structural Genomics/Proteomics Initiative~~ (~~RSGI~~)	+	Insight into the transition between the open and closed conformations of Thermus thermophilus carboxypeptidase.,Okai M, Yamamura A, Hayakawa K, Tsutsui S, Miyazono KI, Lee WC, Nagata K, Inoue Y, Tanokura M Biochem Biophys Res Commun. 2017 Mar 18;484(4):787-793. doi:, 10.1016/j.bbrc.2017.01.167. Epub 2017 Feb 2. PMID:28161633<ref>PMID:28161633</ref>

-	~~Description: Crystal structure~~ of ~~carboxypeptidase from Thermus thermophilus~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Riken Structural Genomics/Proteomics Initiative (Rsgi)~~]]	+	<div class="pdbe-citations 5wvu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carboxypeptidase Taq]]
	[[Category: Nagata, K]]		[[Category: Nagata, K]]
-	[[Category: Tanokura, M]]
	[[Category: Okai, M]]		[[Category: Okai, M]]
		+	[[Category: Structural genomic]]
		+	[[Category: Tanokura, M]]
		+	[[Category: Carboxypeptidase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Rsgi]]

OCA at 15:14, 18 January 2017

OCA — Wed, 18 Jan 2017 15:14:56 GMT

←Older revision		Revision as of 15:14, 18 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5wvu is ON HOLD	+	The entry 5wvu is ON HOLD until Paper Publication

-	Authors: Okai, M., Nagata, K., Tanokura, M.	+	Authors: Okai, M., Nagata, K., Tanokura, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

	Description: Crystal structure of carboxypeptidase from Thermus thermophilus		Description: Crystal structure of carboxypeptidase from Thermus thermophilus
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Riken Structural Genomics/Proteomics Initiative (Rsgi)]]
	[[Category: Nagata, K]]		[[Category: Nagata, K]]
	[[Category: Tanokura, M]]		[[Category: Tanokura, M]]
	[[Category: Okai, M]]		[[Category: Okai, M]]

OCA: Protected "5wvu" [edit=sysop:move=sysop]

OCA — Wed, 04 Jan 2017 15:56:56 GMT

Protected "5wvu" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:56, 4 January 2017

OCA: New page: '''Unreleased structure''' The entry 5wvu is ON HOLD Authors: Okai, M., Nagata, K., Tanokura, M. Description: Crystal structure of carboxypeptidase from Thermus thermophilus [[Category...

OCA — Wed, 04 Jan 2017 15:56:54 GMT

New page: '''Unreleased structure''' The entry 5wvu is ON HOLD Authors: Okai, M., Nagata, K., Tanokura, M. Description: Crystal structure of carboxypeptidase from Thermus thermophilus [[Category...

New page

'''Unreleased structure'''

The entry 5wvu is ON HOLD

Authors: Okai, M., Nagata, K., Tanokura, M.

Description: Crystal structure of carboxypeptidase from Thermus thermophilus
[[Category: Unreleased Structures]]
[[Category: Nagata, K]]
[[Category: Tanokura, M]]
[[Category: Okai, M]]