7lkk - Revision history

OCA at 15:52, 18 October 2023

OCA — Wed, 18 Oct 2023 15:52:48 GMT

←Older revision		Revision as of 15:52, 18 October 2023
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	<StructureSection load='7lkk' size='340' side='right'caption='[[7lkk]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='7lkk' size='340' side='right'caption='[[7lkk]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7lkk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43504 Atcc 43504~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LKK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7lkk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LKK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MCF:(8R)-3-(5-S-METHYL-5-THIO-BETA-D-RIBOFURANOSYL)-3,6,7,8-TETRAHYDROIMIDAZO[4,5-D][1,3]DIAZEPIN-8-OL'>MCF</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]] 1.89Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">orf1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MCF:(8R)-3-(5-S-METHYL-5-THIO-BETA-D-RIBOFURANOSYL)-3,6,7,8-TETRAHYDROIMIDAZO[4,5-D][1,3]DIAZEPIN-8-OL'>MCF</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=7lkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lkk OCA], [https://pdbe.org/7lkk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lkk RCSB], [https://www.ebi.ac.uk/pdbsum/7lkk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lkk 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=7lkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lkk OCA], [https://pdbe.org/7lkk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lkk RCSB], [https://www.ebi.ac.uk/pdbsum/7lkk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lkk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9ZMG8_HELPJ Q9ZMG8_HELPJ]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 43504~~]]	+	[[Category: Helicobacter pylori]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Almo SC]]
-	[[Category: Bonanno~~, J B~~]]	+	[[Category: Bonanno JB]]
-	[[Category: Feng, M]]	+	[[Category: Feng M]]
-	[[Category: Harijan~~, R K~~]]	+	[[Category: Harijan RK]]
-	[[Category: Schramm~~, V L]]~~	+	[[Category: Schramm VL]]
-	~~[[Category: Aflda]]~~	+
-	~~[[Category: Aminofutalosine deaminase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-inhibitor complex]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Inhibitor complex~~]]	+

OCA at 10:11, 14 July 2021

OCA — Wed, 14 Jul 2021 10:11:21 GMT

←Older revision		Revision as of 10:11, 14 July 2021
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	==Crystal structure of Helicobacter pylori aminofutalosine deaminase (AFLDA) in complex with Methylthio-coformycin==		==Crystal structure of Helicobacter pylori aminofutalosine deaminase (AFLDA) in complex with Methylthio-coformycin==
-	<StructureSection load='7lkk' size='340' side='right'caption='[[7lkk]]' scene=''>	+	<StructureSection load='7lkk' size='340' side='right'caption='[[7lkk]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LKK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7lkk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LKK FirstGlance]. <br>
-	</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=7lkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lkk OCA], [https://pdbe.org/7lkk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lkk RCSB], [https://www.ebi.ac.uk/pdbsum/7lkk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lkk ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MCF:(8R)-3-(5-S-METHYL-5-THIO-BETA-D-RIBOFURANOSYL)-3,6,7,8-TETRAHYDROIMIDAZO[4,5-D][1,3]DIAZEPIN-8-OL'>MCF</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">orf1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</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=7lkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lkk OCA], [https://pdbe.org/7lkk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lkk RCSB], [https://www.ebi.ac.uk/pdbsum/7lkk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lkk ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Helicobacter pylori is a Gram-negative bacterium that is responsible for gastric and duodenal ulcers. H. pylori uses the unusual mqn pathway with aminofutalosine (AFL) as an intermediate for menaquinone biosynthesis. Previous reports indicate that hydrolysis of AFL by 5'-methylthioadenosine nucleosidase (HpMTAN) is the direct path for producing downstream metabolites in the mqn pathway. However, genomic analysis indicates jhp0252 is a candidate for encoding AFL deaminase (AFLDA), an activity for deaminating aminofutolasine. The product, futalosine, is not a known substrate for bacterial MTANs. Recombinant jhp0252 was expressed and characterized as an AFL deaminase (HpAFLDA). Its catalytic specificity includes AFL, 5'-methylthioadenosine, 5'-deoxyadenosine, adenosine, and S-adenosylhomocysteine. The kcat/Km value for AFL is 6.8 x 10(4) M(-1) s(-1), 26-fold greater than that for adenosine. 5'-Methylthiocoformycin (MTCF) is a slow-onset inhibitor for HpAFLDA and demonstrated inhibitory effects on H. pylori growth. Supplementation with futalosine partially restored H. pylori growth under MTCF treatment, suggesting AFL deamination is significant for cell growth. The crystal structures of apo-HpAFLDA and with MTCF at the catalytic sites show a catalytic site Zn(2+) or Fe(2+) as the water-activating group. With bound MTCF, the metal ion is 2.0 A from the sp(3) hydroxyl group of the transition state analogue. Metabolomics analysis revealed that HpAFLDA has intracellular activity and is inhibited by MTCF. The mqn pathway in H. pylori bifurcates at aminofutalosine with HpMTAN producing adenine and depurinated futalosine and HpAFLDA producing futalosine. Inhibition of cellular HpMTAN or HpAFLDA decreased the cellular content of menaquinone-6, supporting roles for both enzymes in the pathway.
		+
		+	Aminofutalosine Deaminase in the Menaquinone Pathway of Helicobacter pylori.,Feng M, Harijan RK, Harris LD, Tyler PC, Frohlich RFG, Brown M, Schramm VL Biochemistry. 2021 Jun 22;60(24):1933-1946. doi: 10.1021/acs.biochem.1c00215., Epub 2021 Jun 2. PMID:34077175<ref>PMID:34077175</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7lkk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Deaminase 3D structures\|Deaminase 3D structures]]		*[[Deaminase 3D structures\|Deaminase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43504]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Almo SC]]	+	[[Category: Almo, S C]]
-	[[Category: Bonanno JB]]	+	[[Category: Bonanno, J B]]
-	[[Category: Feng M]]	+	[[Category: Feng, M]]
-	[[Category: Harijan RK]]	+	[[Category: Harijan, R K]]
-	[[Category: Schramm VL]]	+	[[Category: Schramm, V L]]
		+	[[Category: Aflda]]
		+	[[Category: Aminofutalosine deaminase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-inhibitor complex]]
		+	[[Category: Inhibitor]]
		+	[[Category: Inhibitor complex]]

OCA at 07:32, 25 June 2021

OCA — Fri, 25 Jun 2021 07:32:37 GMT

←Older revision		Revision as of 07:32, 25 June 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7lkk is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Helicobacter pylori aminofutalosine deaminase (AFLDA) in complex with Methylthio-coformycin==
		+	<StructureSection load='7lkk' size='340' side='right'caption='[[7lkk]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LKK FirstGlance]. <br>
		+	</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=7lkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lkk OCA], [https://pdbe.org/7lkk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lkk RCSB], [https://www.ebi.ac.uk/pdbsum/7lkk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lkk ProSAT]</span></td></tr>
		+	</table>

-	~~Authors: Harijan, R.K., Feng, M., Bonanno, J.B., Almo, S.C., Schramm, V.L.~~	+	==See Also==
-		+	*[[Deaminase 3D structures\|Deaminase 3D structures]]
-	~~Description: Crystal structure of Helicobacter pylori aminofutalosine deaminase (AFLDA) in complex with Methylthio-coformycin~~	+	__TOC__
-	[[Category: ~~Unreleased~~ Structures]]	+	</StructureSection>
-	[[Category: Almo~~, S.C~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Schramm, V.L~~]]	+	[[Category: Almo SC]]
-	[[Category: ~~Bonanno, J.B~~]]	+	[[Category: Bonanno JB]]
-	[[Category: Harijan~~, R.K~~]]	+	[[Category: Feng M]]
-	[[Category: ~~Feng, M~~]]	+	[[Category: Harijan RK]]
		+	[[Category: Schramm VL]]

OCA at 08:44, 17 February 2021

OCA — Wed, 17 Feb 2021 08:44:50 GMT

←Older revision		Revision as of 08:44, 17 February 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7lkk is ON HOLD	+	The entry 7lkk is ON HOLD until Paper Publication

	Authors: Harijan, R.K., Feng, M., Bonanno, J.B., Almo, S.C., Schramm, V.L.		Authors: Harijan, R.K., Feng, M., Bonanno, J.B., Almo, S.C., Schramm, V.L.
Line 9:		Line 9:
	[[Category: Almo, S.C]]		[[Category: Almo, S.C]]
	[[Category: Schramm, V.L]]		[[Category: Schramm, V.L]]
		+	[[Category: Bonanno, J.B]]
	[[Category: Harijan, R.K]]		[[Category: Harijan, R.K]]
	[[Category: Feng, M]]		[[Category: Feng, M]]
-	[[Category: Bonanno, J.B]]

OCA: Protected "7lkk" [edit=sysop:move=sysop]

OCA — Wed, 10 Feb 2021 09:19:39 GMT

Protected "7lkk" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:19, 10 February 2021

OCA: New page: '''Unreleased structure''' The entry 7lkk is ON HOLD Authors: Harijan, R.K., Feng, M., Bonanno, J.B., Almo, S.C., Schramm, V.L. Description: Crystal structure of Helicobacter pylori am...

OCA — Wed, 10 Feb 2021 09:19:38 GMT

New page: '''Unreleased structure''' The entry 7lkk is ON HOLD Authors: Harijan, R.K., Feng, M., Bonanno, J.B., Almo, S.C., Schramm, V.L. Description: Crystal structure of Helicobacter pylori am...

New page

'''Unreleased structure'''

The entry 7lkk is ON HOLD

Authors: Harijan, R.K., Feng, M., Bonanno, J.B., Almo, S.C., Schramm, V.L.

Description: Crystal structure of Helicobacter pylori aminofutalosine deaminase (AFLDA) in complex with Methylthio-coformycin
[[Category: Unreleased Structures]]
[[Category: Almo, S.C]]
[[Category: Schramm, V.L]]
[[Category: Harijan, R.K]]
[[Category: Feng, M]]
[[Category: Bonanno, J.B]]