4eiz - Revision history

OCA at 07:13, 28 September 2022

OCA — Wed, 28 Sep 2022 07:13:32 GMT

←Older revision		Revision as of 07:13, 28 September 2022
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	==Structure of Nb113 bound to apoDHFR==		==Structure of Nb113 bound to apoDHFR==
-	<StructureSection load='4eiz' size='340' side='right' caption='[[4eiz]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4eiz' size='340' side='right'caption='[[4eiz]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4eiz]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Camelus_glama Camelus glama~~] and [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EIZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4EIZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4eiz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EIZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EIZ FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4eig\|4eig]], [[4ej1\|4ej1]]</td></tr>~~	+	</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=4eiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eiz OCA], [https://pdbe.org/4eiz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4eiz RCSB], [https://www.ebi.ac.uk/pdbsum/4eiz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4eiz ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA, tmrA, b0048, JW0047 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </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=4eiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eiz OCA], [~~http~~://pdbe.org/4eiz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4eiz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4eiz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4eiz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.	+	[[https://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 19:

	==See Also==		==See Also==
-	*[[Dihydrofolate reductase\|Dihydrofolate reductase]]	+	*[[Antibody 3D structures\|Antibody 3D structures]]
-	*[[3D structures of antibody\|3D structures of antibody]]	+	*[[Dihydrofolate reductase 3D structures\|Dihydrofolate reductase 3D structures]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Camelus glama~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: ~~Dihydrofolate reductase~~]]	+	[[Category: Lama glama]]
-	[[Category: ~~Ecoli~~]]	+	[[Category: Large Structures]]
-	[[Category: Oyen, D]]	+	[[Category: Oyen D]]
-	[[Category: Srinivasan, V]]	+	[[Category: Srinivasan V]]
-	~~[[Category: Nadp binding]]~~	+
-	~~[[Category: Oxidoreductase-immune system complex~~]]	+

OCA at 20:37, 4 August 2016

OCA — Thu, 04 Aug 2016 20:37:54 GMT

←Older revision		Revision as of 20:37, 4 August 2016
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		+
	==Structure of Nb113 bound to apoDHFR==		==Structure of Nb113 bound to apoDHFR==
	<StructureSection load='4eiz' size='340' side='right' caption='[[4eiz]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4eiz' size='340' side='right' caption='[[4eiz]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4eiz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~] and [http://en.wikipedia.org/wiki/~~Lama_glama Lama glama~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EIZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EIZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4eiz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EIZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EIZ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4eig\|4eig]], [[4ej1\|4ej1]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4eig\|4eig]], [[4ej1\|4ej1]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA, tmrA, b0048, JW0047 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ~~Escherichia coli K-12~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA, tmrA, b0048, JW0047 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </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=4eiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eiz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4eiz RCSB], [http://www.ebi.ac.uk/pdbsum/4eiz 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=4eiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eiz OCA], [http://pdbe.org/4eiz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4eiz RCSB], [http://www.ebi.ac.uk/pdbsum/4eiz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4eiz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4eiz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Antibody\|Antibody]]
	*[[Dihydrofolate reductase\|Dihydrofolate reductase]]		*[[Dihydrofolate reductase\|Dihydrofolate reductase]]
		+	*[[3D structures of antibody\|3D structures of antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Camelus glama]]
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
-	[[Category: ~~Escherichia coli k-12]]~~	+	[[Category: Ecoli]]
-	~~[[Category: Lama glama~~]]	+
	[[Category: Oyen, D]]		[[Category: Oyen, D]]
	[[Category: Srinivasan, V]]		[[Category: Srinivasan, V]]
	[[Category: Nadp binding]]		[[Category: Nadp binding]]
	[[Category: Oxidoreductase-immune system complex]]		[[Category: Oxidoreductase-immune system complex]]

OCA at 19:25, 24 December 2014

OCA — Wed, 24 Dec 2014 19:25:43 GMT

←Older revision		Revision as of 19:25, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4eiz~~\| ~~PDB~~=4eiz \| ~~SCENE~~= }}	+	==Structure of Nb113 bound to apoDHFR==
-	===~~Structure of Nb113 bound to apoDHFR~~===	+	<StructureSection load='4eiz' size='340' side='right' caption='[[4eiz]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23911607}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4eiz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12] and [http://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EIZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EIZ FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4eig\|4eig]], [[4ej1\|4ej1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA, tmrA, b0048, JW0047 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </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=4eiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eiz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4eiz RCSB], [http://www.ebi.ac.uk/pdbsum/4eiz PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.		[[http://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Although allosteric effector antibodies are used widely as modulators of receptors and enzymes, experimental analysis of their mechanism remains highly challenging. Here, we investigate the molecular mechanisms of allosteric and non-allosteric effector antibodies in an experimentally tractable system, consisting of single-domain antibodies (nanobodies) that target the model enzyme dihydrofolate reductase (DHFR) from Escherichia coli. A panel of thirty-five nanobodies was isolated using several strategies to increase nanobody diversity. The nanobodies exhibit a variety of effector properties, including partial inhibition, strong inhibition and stimulation of DHFR activity. Despite these diverse effector properties, chemical shift perturbation NMR epitope mapping identified only two epitope regions: epitope alpha is a new allosteric site that is over 10A from the active site, while epitope beta is located in the region of the Met20 loop. The structural basis for DHFR allosteric inhibition or activation upon nanobody binding to the alpha epitope was examined by solving the crystal structures of DHFR in complex with Nb113 (an allosteric inhibitor) and Nb179 (an allosteric activator). The structures suggest roles for conformational constraint and altered protein dynamics, but not epitope distortion, in the observed allosteric effects. The crystal structure of a beta epitope region binder (ca1698) in complex with DHFR is also reported. Although CDR3 of ca1698 occupies the substrate binding site, ca1698 displays linear mixed inhibition kinetics instead of simple competitive inhibition kinetics. Two mechanisms are proposed to account for this apparent anomaly. Evidence for structural convergence of ca1698 and Nb216 during affinity maturation is also presented.

-	~~==About this Structure==~~	+	Mechanistic analysis of allosteric and non-allosteric effects arising from nanobody binding to two epitopes of the dihyrofolate reductase of Escherichia coli.,Oyen D, Wechselberger R, Srinivasan V, Steyaert J, Barlow JN Biochim Biophys Acta. 2013 Jul 31. pii: S1570-9639(13)00282-3. doi:, 10.1016/j.bbapap.2013.07.010. PMID:23911607<ref>PMID:23911607</ref>
-	~~[[4eiz]] is a 4 chain structure with sequence~~ from ~~[http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli_k~~-~~12 Escherichia coli k~~-~~12] and [http~~:/~~/en~~.~~wikipedia~~.~~org/wiki/Lama_glama Lama glama]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4EIZ OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Antibody\|Antibody]]		*[[Antibody\|Antibody]]
	*[[Dihydrofolate reductase\|Dihydrofolate reductase]]		*[[Dihydrofolate reductase\|Dihydrofolate reductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023911607</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Lama glama]]		[[Category: Lama glama]]
-	[[Category: Oyen, D.]]	+	[[Category: Oyen, D]]
-	[[Category: Srinivasan, V.]]	+	[[Category: Srinivasan, V]]
	[[Category: Nadp binding]]		[[Category: Nadp binding]]
	[[Category: Oxidoreductase-immune system complex]]		[[Category: Oxidoreductase-immune system complex]]

OCA at 08:43, 4 September 2013

OCA — Wed, 04 Sep 2013 08:43:00 GMT

←Older revision		Revision as of 08:43, 4 September 2013
Line 10:		Line 10:

	==See Also==		==See Also==
		+	*[[Antibody\|Antibody]]
	*[[Dihydrofolate reductase\|Dihydrofolate reductase]]		*[[Dihydrofolate reductase\|Dihydrofolate reductase]]

OCA at 06:27, 14 August 2013

OCA — Wed, 14 Aug 2013 06:27:45 GMT

←Older revision		Revision as of 06:27, 14 August 2013
Line 1:		Line 1:
	{{STRUCTURE_4eiz\| PDB=4eiz \| SCENE= }}		{{STRUCTURE_4eiz\| PDB=4eiz \| SCENE= }}
	===Structure of Nb113 bound to apoDHFR===		===Structure of Nb113 bound to apoDHFR===
		+	{{ABSTRACT_PUBMED_23911607}}

	==Function==		==Function==
Line 7:		Line 8:
	==About this Structure==		==About this Structure==
	[[4eiz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12] and [http://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EIZ OCA].		[[4eiz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12] and [http://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EIZ OCA].
		+
		+	==See Also==
		+	*[[Dihydrofolate reductase\|Dihydrofolate reductase]]
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023911607</ref><references group="xtra"/><references/>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]

OCA at 11:27, 24 April 2013

OCA — Wed, 24 Apr 2013 11:27:22 GMT

←Older revision		Revision as of 11:27, 24 April 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4eiz\| PDB=4eiz \| SCENE= }}
		+	===Structure of Nb113 bound to apoDHFR===

-	~~The entry 4eiz is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.

-	~~Authors~~: Oyen, D., Srinivasan, V.	+	==About this Structure==
-		+	[[4eiz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12] and [http://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EIZ OCA].
-	~~Description~~: ~~Structure of Nb113 bound to apoDHFR~~	+	[[Category: Dihydrofolate reductase]]
		+	[[Category: Escherichia coli k-12]]
		+	[[Category: Lama glama]]
		+	[[Category: Oyen, D.]]
		+	[[Category: Srinivasan, V.]]
		+	[[Category: Nadp binding]]
		+	[[Category: Oxidoreductase-immune system complex]]

OCA at 07:12, 4 July 2012

OCA — Wed, 04 Jul 2012 07:12:32 GMT

←Older revision		Revision as of 07:12, 4 July 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Oyen, D., Srinivasan, V.		Authors: Oyen, D., Srinivasan, V.

	Description: Structure of Nb113 bound to apoDHFR		Description: Structure of Nb113 bound to apoDHFR

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

OCA — Wed, 18 Apr 2012 07:32:16 GMT

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

←Older revision

Revision as of 07:32, 18 April 2012

OCA: New page: '''Unreleased structure''' The entry 4eiz is ON HOLD Authors: Oyen, D., Srinivasan, V. Description: Structure of Nb113 bound to apoDHFR

OCA — Wed, 18 Apr 2012 07:32:15 GMT

New page: '''Unreleased structure''' The entry 4eiz is ON HOLD Authors: Oyen, D., Srinivasan, V. Description: Structure of Nb113 bound to apoDHFR

New page

'''Unreleased structure'''

The entry 4eiz is ON HOLD

Authors: Oyen, D., Srinivasan, V.

Description: Structure of Nb113 bound to apoDHFR