2yye

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP

Structural highlights

2yye is a 2 chain structure with sequence from Aquifex aeolicus VF5. The August 2008 RCSB PDB Molecule of the Month feature on Selenocysteine Synthase by David Goodsell is 10.2210/rcsb_pdb/mom_2008_8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

SELD_AQUAE Synthesizes selenophosphate from selenide and ATP (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

Selenophosphate synthetase (SPS) catalyzes the activation of selenide with adenosine 5'-triphosphate (ATP) to generate selenophosphate, the essential reactive selenium donor for the formation of selenocysteine (Sec) and 2-selenouridine residues in proteins and RNAs, respectively. Many SPS are themselves Sec-containing proteins, in which Sec replaces Cys in the catalytically essential position (Sec/Cys). We solved the crystal structures of Aquifex aeolicus SPS and its complex with adenosine 5'-(alpha,beta-methylene) triphosphate (AMPCPP). The ATP-binding site is formed at the subunit interface of the homodimer. Four Asp residues coordinate four metal ions to bind the phosphate groups of AMPCPP. In the free SPS structure, the two loop regions in the ATP-binding site are not ordered, and no enzyme-associated metal is observed. This suggests that ATP binding, metal binding, and the formation of their binding sites are interdependent. To identify the amino-acid residues that contribute to SPS activity, we prepared six mutants of SPS and examined their selenide-dependent ATP consumption. Mutational analyses revealed that Sec/Cys13 and Lys16 are essential. In SPS.AMPCPP, the N-terminal loop, including the two residues, assumes different conformations ("open" and "closed") between the two subunits. The AMPCPP gamma-phosphate group is solvent-accessible, suggesting that a putative nucleophile could attack the ATP gamma-phosphate group to generate selenophosphate and adenosine 5'-diphosphate (ADP). Selenide attached to Sec/Cys13 as -Se-Se(-)/-S-Se(-) could serve as the nucleophile in the "closed" conformation. A water molecule, fixed close to the beta-phosphate group, could function as the nucleophile in subsequent ADP hydrolysis to orthophosphate and adenosine 5'-monophosphate.

Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs.,Itoh Y, Sekine S, Matsumoto E, Akasaka R, Takemoto C, Shirouzu M, Yokoyama S J Mol Biol. 2009 Feb 6;385(5):1456-69. Epub 2008 Aug 26. PMID:18773910^[1]

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

References

↑ Itoh Y, Sekine S, Matsumoto E, Akasaka R, Takemoto C, Shirouzu M, Yokoyama S. Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs. J Mol Biol. 2009 Feb 6;385(5):1456-69. Epub 2008 Aug 26. PMID:18773910 doi:http://dx.doi.org/10.1016/j.jmb.2008.08.042

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2yye"

@@ Line 3: / Line 3: @@
 <StructureSection load='2yye' size='340' side='right'caption='[[2yye]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2yye]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquae Aquae]. The August 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YYE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2yye]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. The August 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YYE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2e0b|2e0b]], [[2zau|2zau]], [[2zod|2zod]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aq_1030 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Selenide,_water_dikinase Selenide, water dikinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.3 2.7.9.3] </span></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=2yye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yye OCA], [https://pdbe.org/2yye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yye RCSB], [https://www.ebi.ac.uk/pdbsum/2yye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yye ProSAT], [https://www.topsan.org/Proteins/RSGI/2yye TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/SELD_AQUAE SELD_AQUAE]] Synthesizes selenophosphate from selenide and ATP (By similarity).
+[https://www.uniprot.org/uniprot/SELD_AQUAE SELD_AQUAE] Synthesizes selenophosphate from selenide and ATP (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yy/2yye_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 35: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Aquae]]
+[[Category: Aquifex aeolicus VF5]]
 [[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Selenide, water dikinase]]
 [[Category: Selenocysteine Synthase]]
-[[Category: Itoh, Y]]
+[[Category: Itoh Y]]
-[[Category: Matsumoto, E]]
+[[Category: Matsumoto E]]
-[[Category: Structural genomic]]
+[[Category: Sekine S]]
-[[Category: Sekine, S]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S]]
-[[Category: Full-length selenophosphate synthetase complex with atp-analog]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Rsgi]]
-[[Category: Transferase]]

2yye

From Proteopedia

Current revision

Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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