3gzd: Difference between revisions

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[[Image:3gzd.png|left|200px]]
==Human selenocysteine lyase, P1 crystal form==
<StructureSection load='3gzd' size='340' side='right' caption='[[3gzd]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3gzd]] is a 4 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=3GZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GZD FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PLR:(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL+DIHYDROGEN+PHOSPHATE'>PLR</scene><br>
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gzc|3gzc]]</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SCL, SCLY ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Selenocysteine_lyase Selenocysteine lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.16 4.4.1.16] </span></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=3gzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gzd RCSB], [http://www.ebi.ac.uk/pdbsum/3gzd 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/gz/3gzd_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 ==
Selenium and sulfur are two closely related basic elements utilized in nature for a vast array of biochemical reactions. While toxic at higher concentrations, selenium is an essential trace element incorporated into selenoproteins as selenocysteine (Sec), the selenium analogue of cysteine (Cys). Sec lyases (SCLs) and Cys desulfurases (CDs) catalyze the removal of selenium or sulfur from Sec or Cys and generally act on both substrates. In contrast, human SCL (hSCL) is specific for Sec although the only difference between Sec and Cys is the identity of a single atom. The chemical basis of this selenium-over-sulfur discrimination is not understood. Here we describe the X-ray crystal structure of hSCL and identify Asp146 as the key residue that provides the Sec specificity. A D146K variant resulted in loss of Sec specificity and appearance of CD activity. A dynamic active site segment also provides the structural prerequisites for direct product delivery of selenide produced by Sec cleavage, thus avoiding release of reactive selenide species into the cell. We thus here define a molecular determinant for enzymatic specificity discrimination between a single selenium versus sulfur atom, elements with very similar chemical properties. Our findings thus provide molecular insights into a key level of control in human selenium and selenoprotein turnover and metabolism.


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Biochemical discrimination between selenium and sulfur 1: a single residue provides selenium specificity to human selenocysteine lyase.,Collins R, Johansson AL, Karlberg T, Markova N, van den Berg S, Olesen K, Hammarstrom M, Flores A, Schuler H, Schiavone LH, Brzezinski P, Arner ES, Hogbom M PLoS One. 2012;7(1):e30581. Epub 2012 Jan 25. PMID:22295093<ref>PMID:22295093</ref>
The line below this paragraph, containing "STRUCTURE_3gzd", 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.
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{{STRUCTURE_3gzd|  PDB=3gzd  |  SCENE=  }}


===Human selenocysteine lyase, P1 crystal form===
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
 
</div>
 
== References ==
<!--
<references/>
The line below this paragraph, {{ABSTRACT_PUBMED_22295093}}, adds the Publication Abstract to the page
__TOC__
(as it appears on PubMed at http://www.pubmed.gov), where 22295093 is the PubMed ID number.
</StructureSection>
-->
{{ABSTRACT_PUBMED_22295093}}
 
==About this Structure==
[[3gzd]] is a 4 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=3GZD OCA].
 
==Reference==
<ref group="xtra">PMID:022295093</ref><references group="xtra"/>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Selenocysteine lyase]]
[[Category: Selenocysteine lyase]]

Revision as of 12:50, 21 May 2014

Human selenocysteine lyase, P1 crystal formHuman selenocysteine lyase, P1 crystal form

Structural highlights

3gzd is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
NonStd Res:
Related:3gzc
Gene:SCL, SCLY (Homo sapiens)
Activity:Selenocysteine lyase, with EC number 4.4.1.16
Resources:FirstGlance, OCA, RCSB, PDBsum

Evolutionary Conservation

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

Publication Abstract from PubMed

Selenium and sulfur are two closely related basic elements utilized in nature for a vast array of biochemical reactions. While toxic at higher concentrations, selenium is an essential trace element incorporated into selenoproteins as selenocysteine (Sec), the selenium analogue of cysteine (Cys). Sec lyases (SCLs) and Cys desulfurases (CDs) catalyze the removal of selenium or sulfur from Sec or Cys and generally act on both substrates. In contrast, human SCL (hSCL) is specific for Sec although the only difference between Sec and Cys is the identity of a single atom. The chemical basis of this selenium-over-sulfur discrimination is not understood. Here we describe the X-ray crystal structure of hSCL and identify Asp146 as the key residue that provides the Sec specificity. A D146K variant resulted in loss of Sec specificity and appearance of CD activity. A dynamic active site segment also provides the structural prerequisites for direct product delivery of selenide produced by Sec cleavage, thus avoiding release of reactive selenide species into the cell. We thus here define a molecular determinant for enzymatic specificity discrimination between a single selenium versus sulfur atom, elements with very similar chemical properties. Our findings thus provide molecular insights into a key level of control in human selenium and selenoprotein turnover and metabolism.

Biochemical discrimination between selenium and sulfur 1: a single residue provides selenium specificity to human selenocysteine lyase.,Collins R, Johansson AL, Karlberg T, Markova N, van den Berg S, Olesen K, Hammarstrom M, Flores A, Schuler H, Schiavone LH, Brzezinski P, Arner ES, Hogbom M PLoS One. 2012;7(1):e30581. Epub 2012 Jan 25. PMID:22295093[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Collins R, Johansson AL, Karlberg T, Markova N, van den Berg S, Olesen K, Hammarstrom M, Flores A, Schuler H, Schiavone LH, Brzezinski P, Arner ES, Hogbom M. Biochemical discrimination between selenium and sulfur 1: a single residue provides selenium specificity to human selenocysteine lyase. PLoS One. 2012;7(1):e30581. Epub 2012 Jan 25. PMID:22295093 doi:10.1371/journal.pone.0030581

3gzd, resolution 1.80Å

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