1ub3

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:51, 6 November 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ub3.jpg|left|200px]]
 
-
<!--
+
==Crystal Structure of Tetrameric Structure of Aldolase from thermus thermophilus HB8==
-
The line below this paragraph, containing "STRUCTURE_1ub3", creates the "Structure Box" on the page.
+
<StructureSection load='1ub3' size='340' side='right'caption='[[1ub3]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1ub3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UB3 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPD:1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE'>HPD</scene></td></tr>
-
{{STRUCTURE_1ub3| PDB=1ub3 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ub3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ub3 OCA], [https://pdbe.org/1ub3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ub3 RCSB], [https://www.ebi.ac.uk/pdbsum/1ub3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ub3 ProSAT], [https://www.topsan.org/Proteins/RSGI/1ub3 TOPSAN]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DEOC_THET8 DEOC_THET8] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate (By similarity).[HAMAP-Rule:MF_00114]
 +
== 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/ub/1ub3_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=1ub3 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
2-Deoxyribose-5-phosphate aldolase catalyzes a reversible aldol condensation of two aldehydes via formation of a covalent Schiff-base intermediate at the active lysine residue. The crystal structure of 2-deoxyribose-5-phosphate aldolase from Thermus thermophilus HB8 has been determined with and without the substrate at atomic resolution. This enzyme, which has a unique homotetramer structure, has been compared with the previously reported crystal structures of two orthologues from Escherichia coli and Aeropyrum pernix. In contrast to the similar alpha/beta-barrel fold of the monomers, substantial quaternary structural differences are observed between these three enzymes. Further comparison of the subunit-subunit interface areas of these aldolases showed a clear positive correlation between the interface area and the living temperature of the source organism. From these results, it is concluded that the oligomeric state of 2-deoxyribose-5-phosphate aldolase is important for the thermostability and not for the catalytic function.
-
'''Crystal Structure of Tetrameric Structure of Aldolase from thermus thermophilus HB8'''
+
Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability.,Lokanath NK, Shiromizu I, Ohshima N, Nodake Y, Sugahara M, Yokoyama S, Kuramitsu S, Miyano M, Kunishima N Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1816-23. Epub 2004, Sep 23. PMID:15388928<ref>PMID:15388928</ref>
-
 
+
-
 
+
-
==Overview==
+
-
2-Deoxyribose-5-phosphate aldolase catalyzes a reversible aldol condensation of two aldehydes via formation of a covalent Schiff-base intermediate at the active lysine residue. The crystal structure of 2-deoxyribose-5-phosphate aldolase from Thermus thermophilus HB8 has been determined with and without the substrate at atomic resolution. This enzyme, which has a unique homotetramer structure, has been compared with the previously reported crystal structures of two orthologues from Escherichia coli and Aeropyrum pernix. In contrast to the similar alpha/beta-barrel fold of the monomers, substantial quaternary structural differences are observed between these three enzymes. Further comparison of the subunit-subunit interface areas of these aldolases showed a clear positive correlation between the interface area and the living temperature of the source organism. From these results, it is concluded that the oligomeric state of 2-deoxyribose-5-phosphate aldolase is important for the thermostability and not for the catalytic function.
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
1UB3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UB3 OCA].
+
</div>
 +
<div class="pdbe-citations 1ub3" style="background-color:#fffaf0;"></div>
-
==Reference==
+
==See Also==
-
Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability., Lokanath NK, Shiromizu I, Ohshima N, Nodake Y, Sugahara M, Yokoyama S, Kuramitsu S, Miyano M, Kunishima N, Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1816-23. Epub 2004, Sep 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15388928 15388928]
+
*[[Aldolase 3D structures|Aldolase 3D structures]]
-
[[Category: Deoxyribose-phosphate aldolase]]
+
== References ==
-
[[Category: Single protein]]
+
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
-
[[Category: Kunishima, N.]]
+
[[Category: Kunishima N]]
-
[[Category: Kuramitsu, S.]]
+
[[Category: Kuramitsu S]]
-
[[Category: Lokanath, N K.]]
+
[[Category: Lokanath NK]]
-
[[Category: Miyano, M.]]
+
[[Category: Miyano M]]
-
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+
[[Category: Yokoyama S]]
-
[[Category: Yokoyama, S.]]
+
-
[[Category: Carbinolamine]]
+
-
[[Category: Deoxyribose phosphate]]
+
-
[[Category: Riken structural genomics/proteomics initiative]]
+
-
[[Category: Rsgi]]
+
-
[[Category: Schiff base]]
+
-
[[Category: Structural genomic]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 10:59:15 2008''
+

Current revision

Crystal Structure of Tetrameric Structure of Aldolase from thermus thermophilus HB8

PDB ID 1ub3

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ub3"
Personal tools