8tgb - Revision history

OCA at 09:34, 20 March 2024

OCA — Wed, 20 Mar 2024 09:34:52 GMT

←Older revision		Revision as of 09:34, 20 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q84YL2_ORYSJ Q84YL2_ORYSJ]		[https://www.uniprot.org/uniprot/Q84YL2_ORYSJ Q84YL2_ORYSJ]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	NADH cytochrome b(5) oxidoreductase (Ncb5or) is a cytosolic ferric reductase implicated in diabetes and neurological conditions. Ncb5or comprises cytochrome b(5) (b(5) ) and cytochrome b(5) reductase (b(5) R) domains separated by a CHORD-Sgt1 (CS) linker domain. Ncb5or redox activity depends on proper inter-domain interactions to mediate electron transfer from NADH or NADPH via FAD to heme. While full-length human Ncb5or has proven resistant to crystallization, we have succeeded in obtaining high-resolution atomic structures of the b(5) domain and a construct containing the CS and b(5) R domains (CS/b(5) R). Ncb5or also contains an N-terminal intrinsically disordered region of 50 residues that has no homologs in other protein families in animals but features a distinctive, conserved L(34) MDWIRL(40) motif also present in reduced lateral root formation (RLF) protein in rice and increased recombination center 21 in baker's yeast, all attaching to a b(5) domain. After unsuccessful attempts at crystallizing a human Ncb5or construct comprising the N-terminal region naturally fused to the b(5) domain, we were able to obtain a high-resolution atomic structure of a recombinant rice RLF construct corresponding to residues 25-129 of human Ncb5or (52% sequence identity; 74% similarity). The structure reveals Trp(120) (corresponding to invariant Trp(37) in Ncb5or) to be part of an 11-residue alpha-helix (S(116) QMDWLKLTRT(126) ) packing against two of the four helices in the b(5) domain that surround heme (alpha2 and alpha5). The Trp(120) side chain forms a network of interactions with the side chains of four highly conserved residues corresponding to Tyr(85) and Tyr(88) (alpha2), Cys(124) (alpha5), and Leu(47) in Ncb5or. Circular dichroism measurements of human Ncb5or fragments further support a key role of Trp(37) in nucleating the formation of the N-terminal helix, whose location in the N/b(5) module suggests a role in regulating the function of this multi-domain redox enzyme. This study revealed for the first time an ancient origin of a helical motif in the N/b(5) module as reflected by its existence in a class of cytochrome b(5) proteins from three kingdoms among eukaryotes.
-
-	The N-terminal intrinsically disordered region of Ncb5or docks with the cytochrome b(5) core to form a helical motif that is of ancient origin.,Benson DR, Deng B, Kashipathy MM, Lovell S, Battaile KP, Cooper A, Gao P, Fenton AW, Zhu H Proteins. 2023 Dec 1. doi: 10.1002/prot.26647. PMID:38041394<ref>PMID:38041394</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8tgb" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:48, 13 December 2023

OCA — Wed, 13 Dec 2023 11:48:18 GMT

←Older revision		Revision as of 11:48, 13 December 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8tgb is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of root lateral formation protein (RLF) b5-domain from Oryza sativa==
		+	<StructureSection load='8tgb' size='340' side='right'caption='[[8tgb]], [[Resolution\|resolution]] 1.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8tgb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8TGB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8TGB FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.55Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=8tgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8tgb OCA], [https://pdbe.org/8tgb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8tgb RCSB], [https://www.ebi.ac.uk/pdbsum/8tgb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8tgb ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q84YL2_ORYSJ Q84YL2_ORYSJ]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	NADH cytochrome b(5) oxidoreductase (Ncb5or) is a cytosolic ferric reductase implicated in diabetes and neurological conditions. Ncb5or comprises cytochrome b(5) (b(5) ) and cytochrome b(5) reductase (b(5) R) domains separated by a CHORD-Sgt1 (CS) linker domain. Ncb5or redox activity depends on proper inter-domain interactions to mediate electron transfer from NADH or NADPH via FAD to heme. While full-length human Ncb5or has proven resistant to crystallization, we have succeeded in obtaining high-resolution atomic structures of the b(5) domain and a construct containing the CS and b(5) R domains (CS/b(5) R). Ncb5or also contains an N-terminal intrinsically disordered region of 50 residues that has no homologs in other protein families in animals but features a distinctive, conserved L(34) MDWIRL(40) motif also present in reduced lateral root formation (RLF) protein in rice and increased recombination center 21 in baker's yeast, all attaching to a b(5) domain. After unsuccessful attempts at crystallizing a human Ncb5or construct comprising the N-terminal region naturally fused to the b(5) domain, we were able to obtain a high-resolution atomic structure of a recombinant rice RLF construct corresponding to residues 25-129 of human Ncb5or (52% sequence identity; 74% similarity). The structure reveals Trp(120) (corresponding to invariant Trp(37) in Ncb5or) to be part of an 11-residue alpha-helix (S(116) QMDWLKLTRT(126) ) packing against two of the four helices in the b(5) domain that surround heme (alpha2 and alpha5). The Trp(120) side chain forms a network of interactions with the side chains of four highly conserved residues corresponding to Tyr(85) and Tyr(88) (alpha2), Cys(124) (alpha5), and Leu(47) in Ncb5or. Circular dichroism measurements of human Ncb5or fragments further support a key role of Trp(37) in nucleating the formation of the N-terminal helix, whose location in the N/b(5) module suggests a role in regulating the function of this multi-domain redox enzyme. This study revealed for the first time an ancient origin of a helical motif in the N/b(5) module as reflected by its existence in a class of cytochrome b(5) proteins from three kingdoms among eukaryotes.

-	~~Authors: Lovell, S~~., Kashipathy, ~~M.M.~~, Battaile, K.P., ~~Benson~~, D.R.	+	The N-terminal intrinsically disordered region of Ncb5or docks with the cytochrome b(5) core to form a helical motif that is of ancient origin.,Benson DR, Deng B, Kashipathy MM, Lovell S, Battaile KP, Cooper A, Gao P, Fenton AW, Zhu H Proteins. 2023 Dec 1. doi: 10.1002/prot.26647. PMID:38041394<ref>PMID:38041394</ref>

-	~~Description: Crystal structure~~ of ~~root lateral formation protein (RLF) b5~~-~~domain from Oryza sativa~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Battaile, K.P~~]]	+	<div class="pdbe-citations 8tgb" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Lovell, S~~]]	+	== References ==
-	[[Category: Benson~~, D.R~~]]	+	<references/>
-	[[Category: Kashipathy~~, M.M~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Oryza sativa Japonica Group]]
		+	[[Category: Battaile KP]]
		+	[[Category: Benson DR]]
		+	[[Category: Kashipathy MM]]
		+	[[Category: Lovell S]]

OCA: Protected "8tgb" [edit=sysop:move=sysop]

OCA — Wed, 19 Jul 2023 05:06:12 GMT

Protected "8tgb" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:06, 19 July 2023

OCA: New page: '''Unreleased structure''' The entry 8tgb is ON HOLD until Paper Publication Authors: Lovell, S., Kashipathy, M.M., Battaile, K.P., Benson, D.R. Description: Crystal structure of root ...

OCA — Wed, 19 Jul 2023 05:06:11 GMT

New page: '''Unreleased structure''' The entry 8tgb is ON HOLD until Paper Publication Authors: Lovell, S., Kashipathy, M.M., Battaile, K.P., Benson, D.R. Description: Crystal structure of root ...

New page

'''Unreleased structure'''

The entry 8tgb is ON HOLD until Paper Publication

Authors: Lovell, S., Kashipathy, M.M., Battaile, K.P., Benson, D.R.

Description: Crystal structure of root lateral formation protein (RLF) b5-domain from Oryza sativa
[[Category: Unreleased Structures]]
[[Category: Battaile, K.P]]
[[Category: Lovell, S]]
[[Category: Benson, D.R]]
[[Category: Kashipathy, M.M]]