1iu9: Difference between revisions

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New page: left|200px<br /><applet load="1iu9" size="450" color="white" frame="true" align="right" spinBox="true" caption="1iu9, resolution 2.04Å" /> '''Crystal structure of...
 
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[[Image:1iu9.jpg|left|200px]]<br /><applet load="1iu9" size="450" color="white" frame="true" align="right" spinBox="true"
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'''Crystal structure of the C-terminal domain of aspartate racemase from Pyrococcus horikoshii OT3'''<br />


==Overview==
==Crystal structure of the C-terminal domain of aspartate racemase from Pyrococcus horikoshii OT3==
The X-ray crystal structure has revealed two similar alpha/beta domains of, aspartate racemase (AspR) from Pyrococcus horikoshii OT3, and identified a, pseudo mirror-symmetric distribution of the residues around its active, site [Liu et al. (2002) J. Mol. Biol. 319, 479-489]. Structural homology, and functional similarity between the two domains suggested that this, enzyme evolved from an ancestral domain by gene duplication and gene, fusion. We have expressed solely the C-terminal domain of this AspR and, determined its three-dimensional structure by X-ray crystallography. The, high structural stability of this domain supports the existence of the, ancestral domain. In comparison with other amino acid racemases (AARs), we, suggest that gene duplication and gene fusion are conventional ways in the, evolution of pyridoxal 5'-phosphate-independent AARs.
<StructureSection load='1iu9' size='340' side='right'caption='[[1iu9]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1iu9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IU9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IU9 FirstGlance]. <br>
1IU9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Aspartate_racemase Aspartate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.13 5.1.1.13] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1IU9 OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.04&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1iu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iu9 OCA], [https://pdbe.org/1iu9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iu9 RCSB], [https://www.ebi.ac.uk/pdbsum/1iu9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iu9 ProSAT]</span></td></tr>
Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases., Liu L, Iwata K, Yohda M, Miki K, FEBS Lett. 2002 Sep 25;528(1-3):114-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12297289 12297289]
</table>
[[Category: Aspartate racemase]]
== Function ==
[[Category: Pyrococcus horikoshii]]
[https://www.uniprot.org/uniprot/RACD_PYRHO RACD_PYRHO]  
[[Category: Single protein]]
== Evolutionary Conservation ==
[[Category: Iwata, K.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Liu, L.]]
Check<jmol>
[[Category: Miki, K.]]
  <jmolCheckbox>
[[Category: Yohda, M.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iu/1iu9_consurf.spt"</scriptWhenChecked>
[[Category: CA]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: aspartate racemase]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: c-terminal domain]]
  </jmolCheckbox>
[[Category: crystal structure]]
</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=1iu9 ConSurf].
 
<div style="clear:both"></div>
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:32:57 2007''
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus horikoshii OT3]]
[[Category: Iwata K]]
[[Category: Liu L]]
[[Category: Miki K]]
[[Category: Yohda M]]

Latest revision as of 09:02, 3 April 2024

Crystal structure of the C-terminal domain of aspartate racemase from Pyrococcus horikoshii OT3Crystal structure of the C-terminal domain of aspartate racemase from Pyrococcus horikoshii OT3

Structural highlights

1iu9 is a 1 chain structure with sequence from Pyrococcus horikoshii OT3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.04Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RACD_PYRHO

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1iu9, resolution 2.04Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
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