3gzd: Difference between revisions

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[[Image:3gzd.png|left|200px]]


<!--
==Human selenocysteine lyase, P1 crystal form==
The line below this paragraph, containing "STRUCTURE_3gzd", creates the "Structure Box" on the page.
<StructureSection load='3gzd' size='340' side='right'caption='[[3gzd]], [[Resolution|resolution]] 1.80&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'>[[3gzd]] is a 4 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=3GZD 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]] 1.8&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PLR:(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL+DIHYDROGEN+PHOSPHATE'>PLR</scene></td></tr>
{{STRUCTURE_3gzd|  PDB=3gzd  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzd OCA], [https://pdbe.org/3gzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gzd RCSB], [https://www.ebi.ac.uk/pdbsum/3gzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gzd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SCLY_HUMAN SCLY_HUMAN] Catalyzes the decomposition of L-selenocysteine to L-alanine and elemental selenium (By similarity).
== 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/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=3gzd 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.


===Human selenocysteine lyase, P1 crystal form===
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>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3gzd" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_22295093}}, adds the Publication Abstract to the page
*[[Selenocysteine lyase|Selenocysteine lyase]]
(as it appears on PubMed at http://www.pubmed.gov), where 22295093 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_22295093}}
__TOC__
 
</StructureSection>
==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: Large Structures]]
[[Category: Arrowsmith, C H.]]
[[Category: Arrowsmith CH]]
[[Category: Berg, S Van Den.]]
[[Category: Berglund H]]
[[Category: Berglund, H.]]
[[Category: Bountra C]]
[[Category: Bountra, C.]]
[[Category: Collins R]]
[[Category: Collins, R.]]
[[Category: Edwards AM]]
[[Category: Edwards, A M.]]
[[Category: Flodin S]]
[[Category: Flodin, S.]]
[[Category: Flores A]]
[[Category: Flores, A.]]
[[Category: Graslund S]]
[[Category: Graslund, S.]]
[[Category: Hammarstrom M]]
[[Category: Hammarstrom, M.]]
[[Category: Hogbom M]]
[[Category: Hogbom, M.]]
[[Category: Johansson A]]
[[Category: Johansson, A.]]
[[Category: Johansson I]]
[[Category: Johansson, I.]]
[[Category: Karlberg T]]
[[Category: Karlberg, T.]]
[[Category: Kotenyova T]]
[[Category: Kotenyova, T.]]
[[Category: Moche M]]
[[Category: Moche, M.]]
[[Category: Nordlund P]]
[[Category: Nordlund, P.]]
[[Category: Nyman T]]
[[Category: Nyman, T.]]
[[Category: Persson C]]
[[Category: Persson, C.]]
[[Category: Sagemark J]]
[[Category: SGC, Structural Genomics Consortium.]]
[[Category: Schuler H]]
[[Category: Sagemark, J.]]
[[Category: Schutz P]]
[[Category: Schuler, H.]]
[[Category: Siponen MI]]
[[Category: Schutz, P.]]
[[Category: Thorsell AG]]
[[Category: Siponen, M I.]]
[[Category: Tresaugues L]]
[[Category: Thorsell, A G.]]
[[Category: Van Den Berg S]]
[[Category: Tresaugues, L.]]
[[Category: Weigelt J]]
[[Category: Weigelt, J.]]
[[Category: Welin M]]
[[Category: Welin, M.]]
[[Category: Wisniewska M]]
[[Category: Wisniewska, M.]]
[[Category: Human]]
[[Category: Lyase]]
[[Category: Plp]]
[[Category: Pyridoxal-5'-phosphate]]
[[Category: Scly]]
[[Category: Selenocysteine]]
[[Category: Sgc]]
[[Category: Structural genomic]]
[[Category: Structural genomics consortium]]

Latest revision as of 04:52, 21 November 2024

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.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SCLY_HUMAN Catalyzes the decomposition of L-selenocysteine to L-alanine and elemental selenium (By similarity).

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.

See Also

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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