4kqj - Revision history

OCA at 09:07, 7 December 2022

2022-12-07T09:07:36Z

←Older revision		Revision as of 09:07, 7 December 2022
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	==Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol and NaMN==		==Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol and NaMN==
-	<StructureSection load='4kqj' size='340' side='right' caption='[[4kqj]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='4kqj' size='340' side='right'caption='[[4kqj]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kqj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Salty Salty~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KQJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kqj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KQJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCN:NICOTINATE+MONONUCLEOTIDE'>NCN</scene>, <scene name='pdbligand=PCR:P-CRESOL'>PCR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCN:NICOTINATE+MONONUCLEOTIDE'>NCN</scene>, <scene name='pdbligand=PCR:P-CRESOL'>PCR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kqf\|4kqf]], [[4kqg\|4kqg]], [[4kqh\|4kqh]], [[4kqi\|4kqi]], [[1jhu\|1jhu]], [[1jhv\|1jhv]]</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=4kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kqj OCA], [https://pdbe.org/4kqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kqj RCSB], [https://www.ebi.ac.uk/pdbsum/4kqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kqj ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobT, STM2016 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.21 2.4.2.21] </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=4kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kqj OCA], [~~http~~://pdbe.org/4kqj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kqj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kqj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kqj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/COBT_SALTY COBT_SALTY]] Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB).	+	[https://www.uniprot.org/uniprot/COBT_SALTY COBT_SALTY] Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 4kqj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4kqj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphoribosyltransferase 3D structures\|Phosphoribosyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Salty~~]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
-	[[Category: Chan~~, C H~~]]	+	[[Category: Chan CH]]
-	[[Category: Claas~~, K R~~]]	+	[[Category: Claas KR]]
-	[[Category: Escalante-Semerena~~, J C~~]]	+	[[Category: Escalante-Semerena JC]]
-	[[Category: Newmister~~, S A~~]]	+	[[Category: Newmister SA]]
-	[[Category: Rayment, I]]	+	[[Category: Rayment I]]
-	[[Category: Taylor~~, K C]]~~	+	[[Category: Taylor KC]]
-	~~[[Category: Transferase~~]]	+

OCA at 14:12, 15 November 2017

2017-11-15T14:12:59Z

←Older revision		Revision as of 14:12, 15 November 2017
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	</div>		</div>
	<div class="pdbe-citations 4kqj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4kqj" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Phosphoribosyltransferase\|Phosphoribosyltransferase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:06, 4 August 2016

2016-08-04T13:06:24Z

←Older revision		Revision as of 13:06, 4 August 2016
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		+
	==Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol and NaMN==		==Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol and NaMN==
	<StructureSection load='4kqj' size='340' side='right' caption='[[4kqj]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='4kqj' size='340' side='right' caption='[[4kqj]], [[Resolution\|resolution]] 1.95Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobT, STM2016 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobT, STM2016 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.21 2.4.2.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.21 2.4.2.21] </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=4kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kqj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kqj RCSB], [http://www.ebi.ac.uk/pdbsum/4kqj 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=4kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kqj OCA], [http://pdbe.org/4kqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kqj RCSB], [http://www.ebi.ac.uk/pdbsum/4kqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kqj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 4kqj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 14:51, 24 December 2014

2014-12-24T14:51:21Z

←Older revision		Revision as of 14:51, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4kqj\| PDB=4kqj \| SCENE= }}~~	+	==Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol and NaMN==
-	===Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol and NaMN===	+	<StructureSection load='4kqj' size='340' side='right' caption='[[4kqj]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24121107}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4kqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KQJ FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCN:NICOTINATE+MONONUCLEOTIDE'>NCN</scene>, <scene name='pdbligand=PCR:P-CRESOL'>PCR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kqf\|4kqf]], [[4kqg\|4kqg]], [[4kqh\|4kqh]], [[4kqi\|4kqi]], [[1jhu\|1jhu]], [[1jhv\|1jhv]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobT, STM2016 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.21 2.4.2.21] </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=4kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kqj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kqj RCSB], [http://www.ebi.ac.uk/pdbsum/4kqj PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/COBT_SALTY COBT_SALTY]] Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB).		[[http://www.uniprot.org/uniprot/COBT_SALTY COBT_SALTY]] Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Cobamide diversity arises from the nature of the nucleotide base. Nicotinate mononucleotide (NaMN):base phosphoribosyltransferases (CobT) synthesize alpha-linked riboside monophosphates from diverse nucleotide base substrates (e.g., benzimidazoles, purines, phenolics) that are incorporated into cobamides. METHODS: Structural investigations of two members of the CobT family of enzymes in complex with various substrate bases as well as in vivo and vitro activity analyses of enzyme variants were performed to elucidate the roles of key amino acid residues important for substrate recognition. RESULTS: Results of in vitro and in vivo studies of active-site variants of the Salmonella enterica CobT (SeCobT) enzyme suggest that a catalytic base may not be required for catalysis. This idea is supported by the analyses of crystal structures that show that two glutamate residues function primarily to maintain an active conformation of the enzyme. In light of these findings, we propose that proper positioning of the substrates in the active site triggers the attack at the C1 ribose of NaMN. CONCLUSION: Whether or not a catalytic base is needed for function is discussed within the framework of the in vitro analysis of the enzyme activity. Additionally, structure-guided site-directed mutagenesis of SeCobT broadened its substrate specificity to include phenolic bases, revealing likely evolutionary changes needed to increase cobamide diversity, and further supporting the proposed mechanism for the phosphoribosylation of phenolic substrates. GENERAL SIGNIFICANCE: Results of this study uncover key residues in the CobT enzyme that contribute to the diversity of cobamides in nature.
		+
		+	Dissecting cobamide diversity through structural and functional analyses of the base-activating CobT enzyme of Salmonella enterica.,Chan CH, Newmister SA, Talyor K, Claas KR, Rayment I, Escalante-Semerena JC Biochim Biophys Acta. 2014 Jan;1840(1):464-75. doi: 10.1016/j.bbagen.2013.09.038., Epub 2013 Oct 10. PMID:24121107<ref>PMID:24121107</ref>

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4kqj]] is~~ a ~~1 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4KQJ OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:024121107</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Phosphoribosyltransferase\|Phosphoribosyltransferase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase]]		[[Category: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase]]
-	[[Category: Chan, C H.]]	+	[[Category: Salty]]
-	[[Category: Claas, K R.]]	+	[[Category: Chan, C H]]
-	[[Category: Escalante-Semerena, J C.]]	+	[[Category: Claas, K R]]
-	[[Category: Newmister, S A.]]	+	[[Category: Escalante-Semerena, J C]]
-	[[Category: Rayment, I.]]	+	[[Category: Newmister, S A]]
-	[[Category: Taylor, K C.]]	+	[[Category: Rayment, I]]
		+	[[Category: Taylor, K C]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 13:39, 12 March 2014

2014-03-12T13:39:26Z

←Older revision		Revision as of 13:39, 12 March 2014
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-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4kqj\| PDB=4kqj \| SCENE= }}
		+	===Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol and NaMN===
		+	{{ABSTRACT_PUBMED_24121107}}

-	~~The entry 4kqj is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/COBT_SALTY COBT_SALTY]] Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB).

-	~~Authors~~: ~~Chan, C~~.H.~~, Newmister, S~~.~~A., Taylor, K.C., Claas, K.R., Rayment, I., Escalante~~-~~Semerena, J.C~~.	+	==About this Structure==
		+	[[4kqj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KQJ OCA].

-	~~Description~~:	+	==Reference==
		+	<ref group="xtra">PMID:024121107</ref><references group="xtra"/><references/>
		+	[[Category: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase]]
		+	[[Category: Chan, C H.]]
		+	[[Category: Claas, K R.]]
		+	[[Category: Escalante-Semerena, J C.]]
		+	[[Category: Newmister, S A.]]
		+	[[Category: Rayment, I.]]
		+	[[Category: Taylor, K C.]]
		+	[[Category: Transferase]]

OCA at 04:39, 12 September 2013

2013-09-12T04:39:21Z

←Older revision		Revision as of 04:39, 12 September 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4kqj is ON HOLD	+	The entry 4kqj is ON HOLD until Paper Publication

	Authors: Chan, C.H., Newmister, S.A., Taylor, K.C., Claas, K.R., Rayment, I., Escalante-Semerena, J.C.		Authors: Chan, C.H., Newmister, S.A., Taylor, K.C., Claas, K.R., Rayment, I., Escalante-Semerena, J.C.

	Description:		Description:

OCA: Protected "4kqj" [edit=sysop:move=sysop]

2013-06-19T11:54:29Z

Protected "4kqj" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:54, 19 June 2013

OCA: New page: '''Unreleased structure''' The entry 4kqj is ON HOLD Authors: Chan, C.H., Newmister, S.A., Taylor, K.C., Claas, K.R., Rayment, I., Escalante-Semerena, J.C. Description:

2013-06-19T11:54:28Z

New page: '''Unreleased structure''' The entry 4kqj is ON HOLD Authors: Chan, C.H., Newmister, S.A., Taylor, K.C., Claas, K.R., Rayment, I., Escalante-Semerena, J.C. Description:

New page

'''Unreleased structure'''

The entry 4kqj is ON HOLD

Authors: Chan, C.H., Newmister, S.A., Taylor, K.C., Claas, K.R., Rayment, I., Escalante-Semerena, J.C.

Description: