2a3l: Difference between revisions

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[[Image:2a3l.gif|left|200px]]


{{Structure
==X-Ray Structure of Adenosine 5'-Monophosphate Deaminase from Arabidopsis Thaliana in Complex with Coformycin 5'-Phosphate==
|PDB= 2a3l |SIZE=350|CAPTION= <scene name='initialview01'>2a3l</scene>, resolution 3.34&Aring;
<StructureSection load='2a3l' size='340' side='right'caption='[[2a3l]], [[Resolution|resolution]] 3.34&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene> and <scene name='pdbligand=CF5:COFORMYCIN 5&#39;-PHOSPHATE'>CF5</scene>
<table><tr><td colspan='2'>[[2a3l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A3L FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.34&#8491;</td></tr>
|GENE= At2g38280 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CF5:COFORMYCIN+5-PHOSPHATE'>CF5</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2a3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a3l OCA], [https://pdbe.org/2a3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a3l RCSB], [https://www.ebi.ac.uk/pdbsum/2a3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a3l ProSAT], [https://www.topsan.org/Proteins/CESG/2a3l TOPSAN]</span></td></tr>
 
</table>
'''X-Ray Structure of Adenosine 5'-Monophosphate Deaminase from Arabidopsis Thaliana in Complex with Coformycin 5'-Phosphate'''
== Function ==
 
[https://www.uniprot.org/uniprot/AMPD_ARATH AMPD_ARATH] AMP deaminase plays a critical role in energy metabolism. Essential for the transition from zygote to embryo.<ref>PMID:15918887</ref>
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
Embryonic factor 1 (FAC1) is one of the earliest expressed plant genes and encodes an AMP deaminase (AMPD), which is also an identified herbicide target. This report identifies an N-terminal transmembrane domain in Arabidopsis FAC1, explores subcellular fractionation, and presents a 3.3-A globular catalytic domain x-ray crystal structure with a bound herbicide-based transition state inhibitor that provides the first glimpse of a complete AMPD active site. FAC1 contains an (alpha/beta)(8)-barrel characterized by loops in place of strands 5 and 6 that places it in a small subset of the amidohydrolase superfamily with imperfect folds. Unlike tetrameric animal orthologs, FAC1 is a dimer and each subunit contains an exposed Walker A motif that may be involved in the dramatic combined K(m) (25-80-fold lower) and V(max) (5-6-fold higher) activation by ATP. Normal mode analysis predicts a hinge motion that flattens basic surfaces on each monomer that flank the dimer interface, which suggests a reversible association between the FAC1 globular catalytic domain and intracellular membranes, with N-terminal transmembrane and disordered linker regions serving as the anchor and attachment to the globular catalytic domain, respectively.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a3/2a3l_consurf.spt"</scriptWhenChecked>
2A3L is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A3L OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
Membrane association, mechanism of action, and structure of Arabidopsis embryonic factor 1 (FAC1)., Han BW, Bingman CA, Mahnke DK, Bannen RM, Bednarek SY, Sabina RL, Phillips GN Jr, J Biol Chem. 2006 May 26;281(21):14939-47. Epub 2006 Mar 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16543243 16543243]
</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=2a3l ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Allard, S T.M.]]
[[Category: Allard STM]]
[[Category: Bingman, C A.]]
[[Category: Bingman CA]]
[[Category: Bitto, E.]]
[[Category: Bitto E]]
[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
[[Category: Han BW]]
[[Category: Han, B W.]]
[[Category: Phillips Jr GN]]
[[Category: Jr., G N.Phillips.]]
[[Category: Wesenberg GE]]
[[Category: Wesenberg, G E.]]
[[Category: CF5]]
[[Category: PO4]]
[[Category: ZN]]
[[Category: adenosine 5'-monophosphate deaminase]]
[[Category: at2g38280]]
[[Category: atampd]]
[[Category: center for eukaryotic structural genomic]]
[[Category: cesg]]
[[Category: coformycin 5'-phosphate]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: structural genomic]]
 
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Retrieved from "https://proteopedia.org/2a3l"