2qqd: Difference between revisions

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New page: left|200px {{Structure |PDB= 2qqd |SIZE=350|CAPTION= <scene name='initialview01'>2qqd</scene>, resolution 2.00Å |SITE= <scene name='pdbsite=AC1:Ag2+Binding+Site+...
 
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[[Image:2qqd.jpg|left|200px]]


{{Structure
==N47A mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii==
|PDB= 2qqd |SIZE=350|CAPTION= <scene name='initialview01'>2qqd</scene>, resolution 2.00&Aring;
<StructureSection load='2qqd' size='340' side='right'caption='[[2qqd]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Ag2+Binding+Site+For+Residue+B+671'>AC1</scene>, <scene name='pdbsite=AC2:Ag2+Binding+Site+For+Residue+A+671'>AC2</scene>, <scene name='pdbsite=AC3:Pyr+Binding+Site+For+Residue+B+53'>AC3</scene>, <scene name='pdbsite=AC4:Pyr+Binding+Site+For+Residue+E+53'>AC4</scene>, <scene name='pdbsite=AC5:Mpd+Binding+Site+For+Residue+C+700'>AC5</scene> and <scene name='pdbsite=AC6:Mpd+Binding+Site+For+Residue+D+700'>AC6</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene> and <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>
<table><tr><td colspan='2'>[[2qqd]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QQD FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Arginine_decarboxylase Arginine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.19 4.1.1.19]  
</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&#8491;</td></tr>
|GENE= pdaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></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=2qqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qqd OCA], [https://pdbe.org/2qqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qqd RCSB], [https://www.ebi.ac.uk/pdbsum/2qqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qqd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PDAD_METJA PDAD_METJA]  
== 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/qq/2qqd_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/main_output.php?pdb_ID=2qqd ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) catalyzes the first step of the polyamine-biosynthetic pathway in plants and some archaebacteria. The pyruvoyl group of PvlArgDC is generated by an internal autoserinolysis reaction at an absolutely conserved serine residue in the proenzyme, resulting in two polypeptide chains. Based on the native structure of PvlArgDC from Methanococcus jannaschii, the conserved residues Asn47 and Glu109 were proposed to be involved in the decarboxylation and autoprocessing reactions. N47A and E109Q mutant proteins were prepared and the three-dimensional structure of each protein was determined at 2.0 A resolution. The N47A and E109Q mutant proteins showed reduced decarboxylation activity compared with the wild-type PvlArgDC. These residues may also be important for the autoprocessing reaction, which utilizes a mechanism similar to that of the decarboxylation reaction.


'''N47A mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii'''
Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii.,Soriano EV, McCloskey DE, Kinsland C, Pegg AE, Ealick SE Acta Crystallogr D Biol Crystallogr. 2008 Apr;64(Pt 4):377-82. Epub 2008, Mar 19. PMID:18391404<ref>PMID:18391404</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==Overview==
</div>
Human deoxycytidine kinase (dCK) is involved in the nucleotide-biosynthesis salvage pathway and has also been shown to phosphorylate several antitumor and antiviral prodrugs. The structures of dCK alone and the dead-end complex of dCK with substrate nucleoside and product ADP or UDP have previously been reported; however, there is currently no structure available for a substrate or product complex. Here, the structures of dCK complexes with the products dCMP, UDP and Mg2+ ion, and with dAMP, UDP and Mg2+ ion are reported. Structural comparisons show that the product complexes with UDP and a dead-end complex with substrate and UDP have similar active-site conformations.
<div class="pdbe-citations 2qqd" style="background-color:#fffaf0;"></div>
 
== References ==
==About this Structure==
<references/>
2QQD is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQD OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
Structures of human deoxycytidine kinase product complexes., Soriano EV, Clark VC, Ealick SE, Acta Crystallogr D Biol Crystallogr. 2007 Dec;63(Pt 12):1201-7. Epub 2007, Nov 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18084067 18084067]
[[Category: Arginine decarboxylase]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Protein complex]]
[[Category: Ealick SE]]
[[Category: Ealick, S E.]]
[[Category: Soriano ES]]
[[Category: Soriano, E S.]]
[[Category: AG2]]
[[Category: MPD]]
[[Category: PYR]]
[[Category: arginine decarboxylase]]
[[Category: autoprocessing]]
[[Category: decarboxylation]]
[[Category: lyase]]
[[Category: pyruvate]]
[[Category: pyruvoyl]]
[[Category: serinolysis]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:28:34 2008''

Latest revision as of 14:38, 30 August 2023

N47A mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashiiN47A mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

Structural highlights

2qqd is a 8 chain structure with sequence from Methanocaldococcus jannaschii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDAD_METJA

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

Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) catalyzes the first step of the polyamine-biosynthetic pathway in plants and some archaebacteria. The pyruvoyl group of PvlArgDC is generated by an internal autoserinolysis reaction at an absolutely conserved serine residue in the proenzyme, resulting in two polypeptide chains. Based on the native structure of PvlArgDC from Methanococcus jannaschii, the conserved residues Asn47 and Glu109 were proposed to be involved in the decarboxylation and autoprocessing reactions. N47A and E109Q mutant proteins were prepared and the three-dimensional structure of each protein was determined at 2.0 A resolution. The N47A and E109Q mutant proteins showed reduced decarboxylation activity compared with the wild-type PvlArgDC. These residues may also be important for the autoprocessing reaction, which utilizes a mechanism similar to that of the decarboxylation reaction.

Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii.,Soriano EV, McCloskey DE, Kinsland C, Pegg AE, Ealick SE Acta Crystallogr D Biol Crystallogr. 2008 Apr;64(Pt 4):377-82. Epub 2008, Mar 19. PMID:18391404[1]

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

References

  1. ↑ Soriano EV, McCloskey DE, Kinsland C, Pegg AE, Ealick SE. Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii. Acta Crystallogr D Biol Crystallogr. 2008 Apr;64(Pt 4):377-82. Epub 2008, Mar 19. PMID:18391404 doi:http://dx.doi.org/S0907444908000474

2qqd, resolution 2.00Å

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