6yqd - Revision history

OCA at 13:33, 24 January 2024

OCA — Wed, 24 Jan 2024 13:33:20 GMT

←Older revision		Revision as of 13:33, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6yqd' size='340' side='right'caption='[[6yqd]], [[Resolution\|resolution]] 1.41Å' scene=''>		<StructureSection load='6yqd' size='340' side='right'caption='[[6yqd]], [[Resolution\|resolution]] 1.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yqd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4nk0 4nk0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yqd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4nk0 4nk0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 1.407Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[6yi0\|6yi0]], [[6ypr\|6ypr]], [[6ypx\|6ypx]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">HINT2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=6yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqd OCA], [https://pdbe.org/6yqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqd RCSB], [https://www.ebi.ac.uk/pdbsum/6yqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqd 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=6yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqd OCA], [https://pdbe.org/6yqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqd RCSB], [https://www.ebi.ac.uk/pdbsum/6yqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/HINT2_HUMAN HINT2_HUMAN]] Hydrolase probably involved in steroid biosynthesis. May play a role in apoptosis. Has adenosine phosphoramidase activity.<ref>PMID:16762638</ref> <ref>PMID:18653718</ref>	+	[https://www.uniprot.org/uniprot/HINT2_HUMAN HINT2_HUMAN] Hydrolase probably involved in steroid biosynthesis. May play a role in apoptosis. Has adenosine phosphoramidase activity.<ref>PMID:16762638</ref> <ref>PMID:18653718</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bujacz~~, G D~~]]	+	[[Category: Bujacz GD]]
-	[[Category: Dolot~~, R D~~]]	+	[[Category: Dolot RD]]
-	[[Category: Nawrot~~, B C~~]]	+	[[Category: Nawrot BC]]
-	[[Category: Wlodarczyk, A]]	+	[[Category: Wlodarczyk A]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nucleotide binding protein~~]]	+

OCA at 07:56, 10 November 2021

OCA — Wed, 10 Nov 2021 07:56:22 GMT

←Older revision		Revision as of 07:56, 10 November 2021
Line 1:		Line 1:

	==Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.41 A in P212121 space group==		==Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.41 A in P212121 space group==
-	<StructureSection load='6yqd' size='340' side='right'caption='[[6yqd]]' scene=''>	+	<StructureSection load='6yqd' size='340' side='right'caption='[[6yqd]], [[Resolution\|resolution]] 1.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4nk0 4nk0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YQD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yqd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4nk0 4nk0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQD FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqd OCA], [~~http~~://pdbe.org/6yqd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6yqd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6yqd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqd 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=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6yi0\|6yi0]], [[6ypr\|6ypr]], [[6ypx\|6ypx]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HINT2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqd OCA], [https://pdbe.org/6yqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqd RCSB], [https://www.ebi.ac.uk/pdbsum/6yqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/HINT2_HUMAN HINT2_HUMAN]] Hydrolase probably involved in steroid biosynthesis. May play a role in apoptosis. Has adenosine phosphoramidase activity.<ref>PMID:16762638</ref> <ref>PMID:18653718</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Human HINT2 is an important mitochondrial enzyme involved in many processes such as apoptosis and bioenergetics, but its endogenous substrates and the three-dimensional structure of the full-length protein have not been identified yet. METHODS: An HPLC assay was used to test the hydrolytic activity of HINT2 against various adenosine, guanosine, and 2'-deoxyguanosine derivatives containing phosphate bonds of different types and different leaving groups. Data on binding affinity were obtained by microscale thermophoresis (MST). Crystal structures of HINT2, in its apo form and with a dGMP ligand, were resolved to atomic resolution. RESULTS: HINT2 substrate specificity was similar to that of HINT1, but with the major exception of remarkable discrimination against substrates lacking the 2'-hydroxyl group. The biochemical results were consistent with binding affinity measurements. They showed a similar binding strength of AMP and GMP to HINT2, and much weaker binding of dGMP, in contrast to HINT1. A non-hydrolyzable analog of Ap4A (JB419) interacted with both proteins with similar Kd and Ap4A is the signaling molecule that can interact with hHINT1 and regulate the activity of some transcription factors. CONCLUSIONS: Several forms of homo- and heterodimers of different lengths of N-terminally truncated polypeptides resulting from degradation of the full-length protein were described. Ser144 in HINT2 appeared to be functionally equivalent to Ser107 in HINT1 by supporting the protonation of the leaving group in the hydrolytic mechanism of HINT2. SIGNIFICANCE: Our results should be considered in future studies on the natural function of HINT2 and its role in nucleotide prodrug processing.
		+
		+	Biochemical, crystallographic and biophysical characterization of histidine triad nucleotide-binding protein 2 with different ligands including a non-hydrolyzable analog of Ap4A.,Dolot R, Krakowiak A, Kaczmarek R, Wlodarczyk A, Pichlak M, Nawrot B Biochim Biophys Acta Gen Subj. 2021 Nov;1865(11):129968. doi:, 10.1016/j.bbagen.2021.129968. Epub 2021 Jul 27. PMID:34329705<ref>PMID:34329705</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yqd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histidine triad nucleotide-binding protein 3D structures\|Histidine triad nucleotide-binding protein 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bujacz GD]]	+	[[Category: Bujacz, G D]]
-	[[Category: Dolot RD]]	+	[[Category: Dolot, R D]]
-	[[Category: Nawrot BC]]	+	[[Category: Nawrot, B C]]
-	[[Category: Wlodarczyk A]]	+	[[Category: Wlodarczyk, A]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nucleotide binding protein]]

OCA at 06:36, 29 April 2020

OCA — Wed, 29 Apr 2020 06:36:38 GMT

←Older revision		Revision as of 06:36, 29 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6yqd is ON HOLD~~	+	==Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.41 A in P212121 space group==
-		+	<StructureSection load='6yqd' size='340' side='right'caption='[[6yqd]]' scene=''>
-	~~Authors: Dolot, R.D., Wlodarczyk, A., Bujacz, G.D., Nawrot, B.C.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4nk0 4nk0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YQD FirstGlance]. <br>
-	~~Description:~~ Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.41 A in P212121 space group	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqd OCA], [http://pdbe.org/6yqd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yqd RCSB], [http://www.ebi.ac.uk/pdbsum/6yqd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqd ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Wlodarczyk, A~~]]	+	__TOC__
-	[[Category: ~~Nawrot, B.C~~]]	+	</StructureSection>
-	[[Category: ~~Dolot, R.D~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Bujacz, G.D~~]]	+	[[Category: Bujacz GD]]
		+	[[Category: Dolot RD]]
		+	[[Category: Nawrot BC]]
		+	[[Category: Wlodarczyk A]]

OCA: Protected "6yqd" [edit=sysop:move=sysop]

OCA — Wed, 22 Apr 2020 04:33:46 GMT

Protected "6yqd" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:33, 22 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yqd is ON HOLD Authors: Dolot, R.D., Wlodarczyk, A., Bujacz, G.D., Nawrot, B.C. Description: Human histidine triad nucleotide-binding protein 2 (h...

OCA — Wed, 22 Apr 2020 04:33:45 GMT

New page: '''Unreleased structure''' The entry 6yqd is ON HOLD Authors: Dolot, R.D., Wlodarczyk, A., Bujacz, G.D., Nawrot, B.C. Description: Human histidine triad nucleotide-binding protein 2 (h...

New page

'''Unreleased structure'''

The entry 6yqd is ON HOLD

Authors: Dolot, R.D., Wlodarczyk, A., Bujacz, G.D., Nawrot, B.C.

Description: Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.41 A in P212121 space group
[[Category: Unreleased Structures]]
[[Category: Wlodarczyk, A]]
[[Category: Nawrot, B.C]]
[[Category: Dolot, R.D]]
[[Category: Bujacz, G.D]]