2a2d - Revision history

OCA at 07:17, 23 August 2023

2023-08-23T07:17:47Z

← Older revision		Revision as of 07:17, 23 August 2023
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	==X-ray structure of human n-acetyl galactosamine kinase complexed with Mn-AMPPNP and n-acetyl glactosamine==		==X-ray structure of human n-acetyl galactosamine kinase complexed with Mn-AMPPNP and n-acetyl glactosamine==
	<StructureSection load='2a2d' size='340' side='right'caption='[[2a2d]]' scene=''>		<StructureSection load='2a2d' size='340' side='right'caption='[[2a2d]], [[Resolution\|resolution]] 2.20Å' 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=2A2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2a2d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A2D 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=2a2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a2d OCA], [https://pdbe.org/2a2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a2d RCSB], [https://www.ebi.ac.uk/pdbsum/2a2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a2d ProSAT]</span></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]] 2.2Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=2a2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a2d OCA], [https://pdbe.org/2a2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a2d RCSB], [https://www.ebi.ac.uk/pdbsum/2a2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a2d ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/GALK2_HUMAN GALK2_HUMAN] Acts on GalNAc. Also acts as a galactokinase when galactose is present at high concentrations. May be involved in a salvage pathway for the reutilization of free GalNAc derived from the degradation of complex carbohydrates.<ref>PMID:8798585</ref> <ref>PMID:16006554</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2a2d ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2a2d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Galactokinase plays a key role in normal galactose metabolism by catalyzing the conversion of alpha-d-galactose to galactose 1-phosphate. Within recent years, the three-dimensional structures of human galactokinase and two bacterial forms of the enzyme have been determined. Originally, the gene encoding galactokinase in humans was mapped to chromosome 17. An additional gene, encoding a protein with sequence similarity to galactokinase, was subsequently mapped to chromosome 15. Recent reports have shown that this second gene (GALK2) encodes an enzyme with greater activity against GalNAc than galactose. This enzyme, GalNAc kinase, has been implicated in a salvage pathway for the reutilization of free GalNAc derived from the degradation of complex carbohydrates. Here we report the first structural analysis of a GalNAc kinase. The structure of the human enzyme was solved in the presence of MnAMPPNP and GalNAc or MgATP and GalNAc (which resulted in bound products in the active site). The enzyme displays a distinctly bilobal appearance with its active site wedged between the two domains. The N-terminal region is dominated by a seven-stranded mixed beta-sheet, whereas the C-terminal motif contains two layers of anti-parallel beta-sheet. The overall topology displayed by GalNAc kinase places it into the GHMP superfamily of enzymes, which generally function as small molecule kinases. From this investigation, the geometry of the GalNAc kinase active site before and after catalysis has been revealed, and the determinants of substrate specificity have been defined on a molecular level.

			The molecular architecture of human N-acetylgalactosamine kinase.,Thoden JB, Holden HM J Biol Chem. 2005 Sep 23;280(38):32784-91. Epub 2005 Jul 8. PMID:16006554<ref>PMID:16006554</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 2a2d" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Holden HM]]		[[Category: Holden HM]]
	[[Category: Thoden JB]]		[[Category: Thoden JB]]

OCA at 11:30, 3 February 2021

2021-02-03T11:30:37Z

← Older revision		Revision as of 11:30, 3 February 2021
Line 1:		Line 1:

	==X-ray structure of human n-acetyl galactosamine kinase complexed with Mn-AMPPNP and n-acetyl glactosamine==		==X-ray structure of human n-acetyl galactosamine kinase complexed with Mn-AMPPNP and n-acetyl glactosamine==
	<StructureSection load='2a2d' size='340' side='right' caption='[[2a2d]]~~, [[Resolution\|resolution]] 2.20Å~~' scene=''>		<StructureSection load='2a2d' size='340' side='right'caption='[[2a2d]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[2a2d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2A2D FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A2D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=2a2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a2d OCA], [https://pdbe.org/2a2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a2d RCSB], [https://www.ebi.ac.uk/pdbsum/2a2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a2d ProSAT]</span></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a2c\|2a2c]]</td></tr>~~
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GALK2, GK2 ([http://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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2a2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a2d OCA], [~~http~~://pdbe.org/2a2d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2a2d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2a2d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2a2d ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[[http://www.uniprot.org/uniprot/GALK2_HUMAN GALK2_HUMAN]] Acts on GalNAc. Also acts as a galactokinase when galactose is present at high concentrations. May be involved in a salvage pathway for the reutilization of free GalNAc derived from the degradation of complex carbohydrates.<ref>PMID:8798585</ref> <ref>PMID:16006554</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 16:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2a2d ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2a2d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Galactokinase plays a key role in normal galactose metabolism by catalyzing the conversion of alpha-d-galactose to galactose 1-phosphate. Within recent years, the three-dimensional structures of human galactokinase and two bacterial forms of the enzyme have been determined. Originally, the gene encoding galactokinase in humans was mapped to chromosome 17. An additional gene, encoding a protein with sequence similarity to galactokinase, was subsequently mapped to chromosome 15. Recent reports have shown that this second gene (GALK2) encodes an enzyme with greater activity against GalNAc than galactose. This enzyme, GalNAc kinase, has been implicated in a salvage pathway for the reutilization of free GalNAc derived from the degradation of complex carbohydrates. Here we report the first structural analysis of a GalNAc kinase. The structure of the human enzyme was solved in the presence of MnAMPPNP and GalNAc or MgATP and GalNAc (which resulted in bound products in the active site). The enzyme displays a distinctly bilobal appearance with its active site wedged between the two domains. The N-terminal region is dominated by a seven-stranded mixed beta-sheet, whereas the C-terminal motif contains two layers of anti-parallel beta-sheet. The overall topology displayed by GalNAc kinase places it into the GHMP superfamily of enzymes, which generally function as small molecule kinases. From this investigation, the geometry of the GalNAc kinase active site before and after catalysis has been revealed, and the determinants of substrate specificity have been defined on a molecular level.

	~~The molecular architecture of human N-acetylgalactosamine kinase.,Thoden JB, Holden HM J Biol Chem. 2005 Sep 23;280(38):32784-91. Epub 2005 Jul 8. PMID:16006554<ref>PMID:16006554</ref>~~

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2a2d" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Large Structures]]
	[[Category: Holden~~, H M~~]]		[[Category: Holden HM]]
	[[Category: Thoden~~, J B]]~~		[[Category: Thoden JB]]
	~~[[Category: Galactokinase]]~~
	~~[[Category: Kinase]]~~
	~~[[Category: Transferase~~]]

OCA at 06:54, 9 May 2018

2018-05-09T06:54:26Z

← Older revision		Revision as of 06:54, 9 May 2018
Line 1:		Line 1:

	==X-ray structure of human n-acetyl galactosamine kinase complexed with Mn-AMPPNP and n-acetyl glactosamine==		==X-ray structure of human n-acetyl galactosamine kinase complexed with Mn-AMPPNP and n-acetyl glactosamine==
	<StructureSection load='2a2d' size='340' side='right' caption='[[2a2d]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2a2d' size='340' side='right' caption='[[2a2d]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a2c\|2a2c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a2c\|2a2c]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GALK2, GK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GALK2, GK2 ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a2d OCA], [http://pdbe.org/2a2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a2d RCSB], [http://www.ebi.ac.uk/pdbsum/2a2d 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=2a2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a2d OCA], [http://pdbe.org/2a2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a2d RCSB], [http://www.ebi.ac.uk/pdbsum/2a2d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2a2d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a2/2a2d_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a2/2a2d_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2a2d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:32, 12 September 2015

2015-09-12T00:32:06Z

← Older revision		Revision as of 00:32, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='2a2d' size='340' side='right' caption='[[2a2d]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2a2d' size='340' side='right' caption='[[2a2d]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2a2d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2a2d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A2D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a2c\|2a2c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a2c\|2a2c]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GALK2, GK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GALK2, GK2 ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a2d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a2d RCSB], [http://www.ebi.ac.uk/pdbsum/2a2d 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=2a2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a2d OCA], [http://pdbe.org/2a2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a2d RCSB], [http://www.ebi.ac.uk/pdbsum/2a2d PDBsum]</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 2a2d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]
	[[Category: Thoden, J B]]		[[Category: Thoden, J B]]

OCA at 21:27, 25 December 2014

2014-12-25T21:27:59Z

← Older revision		Revision as of 21:27, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2a2d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2a2d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A2D FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a2c\|2a2c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a2c\|2a2c]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GALK2, GK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GALK2, GK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a2d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a2d RCSB], [http://www.ebi.ac.uk/pdbsum/2a2d 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=2a2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a2d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a2d RCSB], [http://www.ebi.ac.uk/pdbsum/2a2d PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/GALK2_HUMAN GALK2_HUMAN]] Acts on GalNAc. Also acts as a galactokinase when galactose is present at high concentrations. May be involved in a salvage pathway for the reutilization of free GalNAc derived from the degradation of complex carbohydrates.<ref>PMID:8798585</ref> <ref>PMID:16006554</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Holden, H M.]]		[[Category: Holden, H M]]
	[[Category: Thoden, J B.]]		[[Category: Thoden, J B]]
	[[Category: Galactokinase]]		[[Category: Galactokinase]]
	[[Category: Kinase]]		[[Category: Kinase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 00:51, 30 September 2014

2014-09-30T00:51:10Z

← Older revision		Revision as of 00:51, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2a2d~~.~~png~~\|~~left~~\|~~200px~~]]		==X-ray structure of human n-acetyl galactosamine kinase complexed with Mn-AMPPNP and n-acetyl glactosamine==
			<StructureSection load='2a2d' size='340' side='right' caption='[[2a2d]], [[Resolution\|resolution]] 2.20Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2a2d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A2D FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a2c\|2a2c]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GALK2, GK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a2d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a2d RCSB], [http://www.ebi.ac.uk/pdbsum/2a2d PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a2/2a2d_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Galactokinase plays a key role in normal galactose metabolism by catalyzing the conversion of alpha-d-galactose to galactose 1-phosphate. Within recent years, the three-dimensional structures of human galactokinase and two bacterial forms of the enzyme have been determined. Originally, the gene encoding galactokinase in humans was mapped to chromosome 17. An additional gene, encoding a protein with sequence similarity to galactokinase, was subsequently mapped to chromosome 15. Recent reports have shown that this second gene (GALK2) encodes an enzyme with greater activity against GalNAc than galactose. This enzyme, GalNAc kinase, has been implicated in a salvage pathway for the reutilization of free GalNAc derived from the degradation of complex carbohydrates. Here we report the first structural analysis of a GalNAc kinase. The structure of the human enzyme was solved in the presence of MnAMPPNP and GalNAc or MgATP and GalNAc (which resulted in bound products in the active site). The enzyme displays a distinctly bilobal appearance with its active site wedged between the two domains. The N-terminal region is dominated by a seven-stranded mixed beta-sheet, whereas the C-terminal motif contains two layers of anti-parallel beta-sheet. The overall topology displayed by GalNAc kinase places it into the GHMP superfamily of enzymes, which generally function as small molecule kinases. From this investigation, the geometry of the GalNAc kinase active site before and after catalysis has been revealed, and the determinants of substrate specificity have been defined on a molecular level.

	~~{{STRUCTURE_2a2d\| PDB=2a2d \| SCENE= }}~~		The molecular architecture of human N-acetylgalactosamine kinase.,Thoden JB, Holden HM J Biol Chem. 2005 Sep 23;280(38):32784-91. Epub 2005 Jul 8. PMID:16006554<ref>PMID:16006554</ref>

	~~===X-ray structure~~ of ~~human n-acetyl galactosamine kinase complexed with Mn-AMPPNP and n-acetyl glactosamine===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16006554}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2a2d]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016006554<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Holden, H M.]]		[[Category: Holden, H M.]]

OCA: Protected "2a2d" [edit=sysop:move=sysop]

2013-01-06T10:10:38Z

Protected "2a2d" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:10, 6 January 2013
(No difference)

OCA at 10:10, 6 January 2013

2013-01-06T10:10:36Z

← Older revision		Revision as of 10:10, 6 January 2013
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	~~{{Seed}}~~
	[[Image:2a2d.png\|left\|200px]]		[[Image:2a2d.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2a2d", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2a2d\| PDB=2a2d \| SCENE= }}		{{STRUCTURE_2a2d\| PDB=2a2d \| SCENE= }}

	===X-ray structure of human n-acetyl galactosamine kinase complexed with Mn-AMPPNP and n-acetyl glactosamine===		===X-ray structure of human n-acetyl galactosamine kinase complexed with Mn-AMPPNP and n-acetyl glactosamine===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16006554}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16006554 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16006554}}		{{ABSTRACT_PUBMED_16006554}}

	==About this Structure==		==About this Structure==
	~~2A2D~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA].		[[2a2d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16006554~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016006554</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Holden, H M.]]		[[Category: Holden, H M.]]
Line 29:		Line 17:
	[[Category: Galactokinase]]		[[Category: Galactokinase]]
	[[Category: Kinase]]		[[Category: Kinase]]
			[[Category: Transferase]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 08:10:00 2009''~~

OCA at 06:10, 18 February 2009

2009-02-18T06:10:01Z

← Older revision		Revision as of 06:10, 18 February 2009
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	==About this Structure==		==About this Structure==
	2A2D is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA].		2A2D is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A2D OCA].

	==Reference==		==Reference==
	~~The molecular architecture of human N-acetylgalactosamine kinase., Thoden JB, Holden HM, J Biol Chem. 2005 Sep 23;280(38):32784-91. Epub 2005 Jul 8.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16006554 16006554]~~		<ref group="xtra">PMID:16006554</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	~~[[Category: Single protein]]~~
	[[Category: Holden, H M.]]		[[Category: Holden, H M.]]
	[[Category: Thoden, J B.]]		[[Category: Thoden, J B.]]
Line 31:		Line 30:
	[[Category: Kinase]]		[[Category: Kinase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 14~~:35:~~25 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:10:00 2009''

OCA at 11:35, 29 July 2008

2008-07-29T11:35:34Z

← Older revision		Revision as of 11:35, 29 July 2008
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	[[Image:2a2d.~~gif~~\|left\|200px]]		{{Seed}}
			[[Image:2a2d.png\|left\|200px]]

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	{{STRUCTURE_2a2d\| PDB=2a2d \| SCENE= }}		{{STRUCTURE_2a2d\| PDB=2a2d \| SCENE= }}

	~~'''~~X-ray structure of human n-acetyl galactosamine kinase complexed with Mn-AMPPNP and n-acetyl glactosamine~~'''~~		===X-ray structure of human n-acetyl galactosamine kinase complexed with Mn-AMPPNP and n-acetyl glactosamine===


	~~==Overview==~~		<!--
	~~Galactokinase plays a key role in normal galactose metabolism by catalyzing the conversion of alpha~~-d-~~galactose to galactose 1-phosphate. Within recent years~~, ~~the three-dimensional structures of human galactokinase and two bacterial forms of the enzyme have been determined. Originally~~, the ~~gene encoding galactokinase in humans was mapped~~ to ~~chromosome 17~~. ~~An additional gene, encoding a protein with sequence similarity to galactokinase, was subsequently mapped to chromosome 15~~. ~~Recent reports have shown that this second gene (GALK2~~) ~~encodes an enzyme with greater activity against GalNAc than galactose. This enzyme~~, ~~GalNAc kinase, has been implicated in a salvage pathway for the reutilization of free GalNAc derived from~~ the ~~degradation of complex carbohydrates~~. Here we report the first structural analysis of a GalNAc kinase. The structure of the human enzyme was solved in the presence of MnAMPPNP and GalNAc or MgATP and GalNAc (which resulted in bound products in the active site). The enzyme displays a distinctly bilobal appearance with its active site wedged between the two domains. The N-terminal region is dominated by a seven-~~stranded mixed beta~~-sheet, whereas the C-terminal motif contains two layers of anti-parallel beta-sheet. The overall topology displayed by GalNAc kinase places it into the GHMP superfamily of enzymes, which generally function as small molecule kinases. From this investigation, the geometry of the GalNAc kinase active site before and after catalysis has been revealed, and the determinants of substrate specificity have been defined on a molecular level.		The line below this paragraph, {{ABSTRACT_PUBMED_16006554}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 16006554 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_16006554}}

	==About this Structure==		==About this Structure==
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	[[Category: Galactokinase]]		[[Category: Galactokinase]]
	[[Category: Kinase]]		[[Category: Kinase]]
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