1n13: Difference between revisions
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[[Image: | ==The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii== | ||
<StructureSection load='1n13' size='340' side='right' caption='[[1n13]], [[Resolution|resolution]] 1.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1n13]] is a 12 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=1N13 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N13 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=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene><br> | |||
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> | |||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1mt1|1mt1]], [[1n2m|1n2m]]</td></tr> | |||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ0316 ([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=1n13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n13 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n13 RCSB], [http://www.ebi.ac.uk/pdbsum/1n13 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/n1/1n13_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 == | |||
The three-dimensional structure of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii was determined at 1.4 A resolution. The pyruvoyl group of arginine decarboxylase is generated by an autocatalytic internal serinolysis reaction at Ser53 in the proenzyme resulting in two polypeptide chains. The structure of the nonprocessing S53A mutant was also determined. The active site of the processed enzyme unexpectedly contained the reaction product agmatine. The crystal structure confirms that arginine decarboxylase is a homotrimer. The protomer fold is a four-layer alphabetabetaalpha sandwich with topology similar to pyruvoyl-dependent histidine decarboxylase. Highly conserved residues Asn47, Ser52, Ser53, Ile54, and Glu109 are proposed to play roles in the self-processing reaction. Agmatine binding residues include the C terminus of the beta chain (Ser52) from one protomer and the Asp35 side chain and the Gly44 and Val46 carbonyl oxygen atoms from an adjacent protomer. Glu109 is proposed to play a catalytic role in the decarboxylation reaction. | |||
Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms.,Tolbert WD, Graham DE, White RH, Ealick SE Structure. 2003 Mar;11(3):285-94. PMID:12623016<ref>PMID:12623016</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
< | |||
[[Category: Arginine decarboxylase]] | [[Category: Arginine decarboxylase]] | ||
[[Category: Methanocaldococcus jannaschii]] | [[Category: Methanocaldococcus jannaschii]] | ||
Revision as of 18:10, 28 September 2014
The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashiiThe Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii
Structural highlights
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 PubMedThe three-dimensional structure of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii was determined at 1.4 A resolution. The pyruvoyl group of arginine decarboxylase is generated by an autocatalytic internal serinolysis reaction at Ser53 in the proenzyme resulting in two polypeptide chains. The structure of the nonprocessing S53A mutant was also determined. The active site of the processed enzyme unexpectedly contained the reaction product agmatine. The crystal structure confirms that arginine decarboxylase is a homotrimer. The protomer fold is a four-layer alphabetabetaalpha sandwich with topology similar to pyruvoyl-dependent histidine decarboxylase. Highly conserved residues Asn47, Ser52, Ser53, Ile54, and Glu109 are proposed to play roles in the self-processing reaction. Agmatine binding residues include the C terminus of the beta chain (Ser52) from one protomer and the Asp35 side chain and the Gly44 and Val46 carbonyl oxygen atoms from an adjacent protomer. Glu109 is proposed to play a catalytic role in the decarboxylation reaction. Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms.,Tolbert WD, Graham DE, White RH, Ealick SE Structure. 2003 Mar;11(3):285-94. PMID:12623016[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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