1ig0: Difference between revisions

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~~[[Image:1ig0.gif|left|200px]]~~

{{Structure

==Crystal Structure of yeast Thiamin Pyrophosphokinase==

~~|PDB~~= 1ig0 |~~SIZE~~=~~350|CAPTION~~= <~~scene name~~='~~initialview01~~'>1ig0</~~scene~~>, ~~resolution~~ 1.80&~~Aring~~;

|~~SITE~~=

== Structural highlights ==

~~|LIGAND~~= <scene name='pdbligand=VIB:3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM'>VIB</scene>

<table><tr><td colspan='2'>[[1ig0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IG0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IG0 FirstGlance]. <br>

~~|ACTIVITY=~~ <~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Thiamine_diphosphokinase Thiamine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno~~=~~2.7.6.2 2.7.6.2]~~ <~~/span~~>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr>

~~|GENE= THI80 ([http~~://~~www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])~~

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VIB:3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM'>VIB</scene></td></tr>

~~|DOMAIN=~~

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ig0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ig0 OCA], [https://pdbe.org/1ig0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ig0 RCSB], [https://www.ebi.ac.uk/pdbsum/1ig0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ig0 ProSAT]</span></td></tr>

~~|RELATEDENTRY=~~

</table>

~~|RESOURCES~~=<span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ig0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ig0 OCA], [~~http~~://www.ebi.ac.uk/pdbsum/1ig0 PDBsum], [~~http~~://~~www~~.~~rcsb~~.org/~~pdb~~/~~explore.do~~?~~structureId~~=1ig0 ~~RCSB~~]</span>

== Function ==

}}

[https://www.uniprot.org/uniprot/THI80_YEAST THI80_YEAST] Essential protein, it is the only enzyme in yeast capable of synthesizing thiamine pyrophosphate (TPP).

== Evolutionary Conservation ==

~~'''Crystal Structure of yeast Thiamin Pyrophosphokinase'''~~

[[Image:Consurf_key_small.gif|200px|right]]

Check<jmol>

==~~Overview~~==

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ig/1ig0_consurf.spt"</scriptWhenChecked>

~~BACKGROUND~~: ~~Thiamin pyrophosphokinase (TPK) catalyzes~~ the ~~transfer~~ of ~~a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin~~ pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. TPK has no sequence homologs in the PDB and functions by an unknown mechanism. The TPK structure has been determined as a significant step toward elucidating its catalytic action. RESULTS: The crystal structure of Saccharomyces cerevisiae TPK complexed with thiamin has been determined at 1.8 A resolution. TPK is a homodimer, and each subunit consists of two domains. One domain resembles a Rossman fold with four alpha helices on each side of a 6 strand parallel beta sheet. The other domain has one 4 strand and one 6 strand antiparallel beta sheet, which form a flattened sandwich structure containing a jelly-roll topology. The active site is located in a cleft at the dimer interface and is formed from residues from domains of both subunits. The TPK dimer contains two compound active sites at the subunit interface. CONCLUSIONS: The structure of TPK with one substrate bound identifies the location of the thiamin binding site and probable catalytic residues. The structure also suggests a likely binding site for ATP. These findings are further supported by TPK sequence homologies. Although possessing no significant sequence homology with other pyrophospokinases, thiamin pyrophosphokinase may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.

<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>

<text>to colour the structure by Evolutionary Conservation</text>

==~~About this Structure~~==

</jmolCheckbox>

~~1IG0 is a~~ [[~~Single protein~~]] structure ~~of sequence from~~ [http://en.~~wikipedia~~.~~org~~/~~wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. ~~Full crystallographic information is~~ available from [http://~~oca~~.~~weizmann~~.ac.il/~~oca-bin~~/~~ocashort~~?id=~~1IG0 OCA~~].

</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=1ig0 ConSurf].

~~==Reference==~~

__TOC__

~~The crystal structure of yeast thiamin pyrophosphokinase., Baker LJ, Dorocke JA, Harris RA, Timm DE, Structure. 2001 Jun;9(6):539-46. PMID:~~[~~http~~:~~//www.ncbi.nlm.nih.gov/pubmed/11435118 11435118~~]

</StructureSection>

[[Category: Large Structures]]

[[Category: Saccharomyces cerevisiae]]

~~[[Category: Single protein]]~~

[[Category: Baker L-J]]

~~[[Category: Thiamine diphosphokinase]]~~

[[Category: Dorocke JA]]

[[Category: Baker, L J.]]

[[Category: Harris RA]]

[[Category: Dorocke~~, J A.~~]]

[[Category: Timm DE]]

[[Category: Harris~~, R A.~~]]

[[Category: Timm~~, D E.]]~~

~~[[Category: alpha-beta-alpha]]~~

~~[[Category: beta sandwich]]~~

~~[[Category: compound active site~~]]

~~[[Category: protein-substrate complex]]~~

~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:19:17 2008''~~

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@@ Line 1: / Line 1: @@
-[[Image:1ig0.gif|left|200px]]
- {{Structure
+==Crystal Structure of yeast Thiamin Pyrophosphokinase==
-|PDB= 1ig0 |SIZE=350|CAPTION= <scene name='initialview01'>1ig0</scene>, resolution 1.80&Aring;
+<StructureSection load='1ig0' size='340' side='right'caption='[[1ig0]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=VIB:3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM'>VIB</scene>
+<table><tr><td colspan='2'>[[1ig0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IG0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IG0 FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Thiamine_diphosphokinase Thiamine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.2 2.7.6.2] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-|GENE= THI80 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VIB:3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM'>VIB</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ig0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ig0 OCA], [https://pdbe.org/1ig0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ig0 RCSB], [https://www.ebi.ac.uk/pdbsum/1ig0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ig0 ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ig0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ig0 OCA], [http://www.ebi.ac.uk/pdbsum/1ig0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ig0 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/THI80_YEAST THI80_YEAST] Essential protein, it is the only enzyme in yeast capable of synthesizing thiamine pyrophosphate (TPP).
+== Evolutionary Conservation ==
-'''Crystal Structure of yeast Thiamin Pyrophosphokinase'''
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
-==Overview==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ig/1ig0_consurf.spt"</scriptWhenChecked>
-BACKGROUND: Thiamin pyrophosphokinase (TPK) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. TPK has no sequence homologs in the PDB and functions by an unknown mechanism. The TPK structure has been determined as a significant step toward elucidating its catalytic action. RESULTS: The crystal structure of Saccharomyces cerevisiae TPK complexed with thiamin has been determined at 1.8 A resolution. TPK is a homodimer, and each subunit consists of two domains. One domain resembles a Rossman fold with four alpha helices on each side of a 6 strand parallel beta sheet. The other domain has one 4 strand and one 6 strand antiparallel beta sheet, which form a flattened sandwich structure containing a jelly-roll topology. The active site is located in a cleft at the dimer interface and is formed from residues from domains of both subunits. The TPK dimer contains two compound active sites at the subunit interface. CONCLUSIONS: The structure of TPK with one substrate bound identifies the location of the thiamin binding site and probable catalytic residues. The structure also suggests a likely binding site for ATP. These findings are further supported by TPK sequence homologies. Although possessing no significant sequence homology with other pyrophospokinases, thiamin pyrophosphokinase may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==About this Structure==
+  </jmolCheckbox>
-IG0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IG0 OCA].
+</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=1ig0 ConSurf].
+<div style="clear:both"></div>
-==Reference==
+__TOC__
-The crystal structure of yeast thiamin pyrophosphokinase., Baker LJ, Dorocke JA, Harris RA, Timm DE, Structure. 2001 Jun;9(6):539-46. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11435118 11435118]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Baker L-J]]
-[[Category: Thiamine diphosphokinase]]
+[[Category: Dorocke JA]]
-[[Category: Baker, L J.]]
+[[Category: Harris RA]]
-[[Category: Dorocke, J A.]]
+[[Category: Timm DE]]
-[[Category: Harris, R A.]]
-[[Category: Timm, D E.]]
-[[Category: alpha-beta-alpha]]
-[[Category: beta sandwich]]
-[[Category: compound active site]]
-[[Category: protein-substrate complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:19:17 2008''