2qqd: Difference between revisions

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[[Image:2qqd.png|left|200px]]
==N47A mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii==
<StructureSection load='2qqd' size='340' side='right' caption='[[2qqd]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2qqd]] is a 8 chain structure with sequence 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QQD FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><br>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2qqc|2qqc]]</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pdaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=2qqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qqd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qqd RCSB], [http://www.ebi.ac.uk/pdbsum/2qqd 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/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/chain_selection.php?pdb_ID=2ata 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.


{{STRUCTURE_2qqd|  PDB=2qqd  |  SCENE=  }}
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>


===N47A mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_18391404}}
== References ==
 
<references/>
==About this Structure==
__TOC__
[[2qqd]] is a 8 chain structure with sequence 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].
</StructureSection>
[[Category: Arginine decarboxylase]]
[[Category: Arginine decarboxylase]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]

Revision as of 21:35, 30 September 2014

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.
Ligands:, ,
Related:2qqc
Gene:pdaD (Methanocaldococcus jannaschii)
Activity:Arginine decarboxylase, with EC number 4.1.1.19
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

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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