1jfl

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:28, 23 October 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1jfl.png|left|200px]]
 
-
<!--
+
==CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA==
-
The line below this paragraph, containing "STRUCTURE_1jfl", creates the "Structure Box" on the page.
+
<StructureSection load='1jfl' size='340' side='right'caption='[[1jfl]], [[Resolution|resolution]] 1.90&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'>[[1jfl]] is a 2 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=1JFL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JFL 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]] 1.9&#8491;</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=1jfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jfl OCA], [https://pdbe.org/1jfl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jfl RCSB], [https://www.ebi.ac.uk/pdbsum/1jfl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jfl ProSAT]</span></td></tr>
-
{{STRUCTURE_1jfl| PDB=1jfl | SCENE= }}
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RACD_PYRHO RACD_PYRHO]
 +
== 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/jf/1jfl_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=1jfl ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
There exists a d-enantiomer of aspartic acid in lactic acid bacteria and several hyperthermophilic archaea, which is biosynthesized from the l-enantiomer by aspartate racemase. Aspartate racemase is a representative pyridoxal 5'-phosphate (PLP)-independent amino acid racemase. The "two-base" catalytic mechanism has been proposed for this type of racemase, in which a pair of cysteine residues are utilized as the conjugated catalytic acid and base. We have determined the three-dimensional structure of aspartate racemase from the hyperthermophilic archaeum Pyrococcus horikoshii OT3 at 1.9 A resolution by X-ray crystallography and refined it to a crystallographic R factor of 19.4% (R(free) of 22.2%). This is the first structure reported for aspartate racemase, indeed for any amino acid racemase from archaea. The crystal structure revealed that this enzyme forms a stable dimeric structure with a strong three-layered inter-subunit interaction, and that its subunit consists of two structurally homologous alpha/beta domains, each containing a four-stranded parallel beta-sheet flanked by six alpha-helices. Two strictly conserved cysteine residues (Cys82 and Cys194), which have been shown biochemically to act as catalytic acid and base, are located on both sides of a cleft between the two domains. The spatial arrangement of these two cysteine residues supports the "two-base" mechanism but disproves the previous hypothesis that the active site of aspartate racemase is located at the dimeric interface. The structure revealed a unique pseudo mirror-symmetry in the spatial arrangement of the residues around the active site, which may explain the molecular recognition mechanism of the mirror-symmetric aspartate enantiomers by the non-mirror-symmetric aspartate racemase.
-
===CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA===
+
Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization.,Liu L, Iwata K, Kita A, Kawarabayasi Y, Yohda M, Miki K J Mol Biol. 2002 May 31;319(2):479-89. PMID:12051922<ref>PMID:12051922</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_12051922}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 1jfl" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 12051922 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_12051922}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
1JFL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JFL OCA].
+
[[Category: Pyrococcus horikoshii OT3]]
-
 
+
[[Category: Iwata K]]
-
==Reference==
+
[[Category: Kawarabayasi Y]]
-
Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization., Liu L, Iwata K, Kita A, Kawarabayasi Y, Yohda M, Miki K, J Mol Biol. 2002 May 31;319(2):479-89. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12051922 12051922]
+
[[Category: Kita A]]
-
[[Category: Aspartate racemase]]
+
[[Category: Liu LJ]]
-
[[Category: Pyrococcus horikoshii]]
+
[[Category: Miki K]]
-
[[Category: Single protein]]
+
[[Category: Yohda M]]
-
[[Category: Iwata, K.]]
+
-
[[Category: Kawarabayasi, Y.]]
+
-
[[Category: Kita, A.]]
+
-
[[Category: Liu, L J.]]
+
-
[[Category: Miki, K.]]
+
-
[[Category: Yohda, M.]]
+
-
[[Category: Alpha-beta structure]]
+
-
[[Category: Homo-dimer]]
+
-
[[Category: Homologous domain]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 20:10:19 2008''
+

Current revision

CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA

PDB ID 1jfl

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/1jfl"
Personal tools