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1z7b

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(New page: 200px<br /><applet load="1z7b" size="450" color="white" frame="true" align="right" spinBox="true" caption="1z7b, resolution 2.31&Aring;" /> '''Crystal structure of...)
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[[Image:1z7b.gif|left|200px]]<br /><applet load="1z7b" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1z7b, resolution 2.31&Aring;" />
 
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'''Crystal structure of E.coli ArnA dehydrogenase (decarboxylase) domain, R619E mutant'''<br />
 
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==Overview==
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==Crystal structure of E.coli ArnA dehydrogenase (decarboxylase) domain, R619E mutant==
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The modification of lipid A with 4-amino-4-deoxy-L-arabinose (Ara4N), allows gram-negative bacteria to resist the antimicrobial activity of, cationic antimicrobial peptides and antibiotics such as polymyxin. ArnA is, the first enzyme specific to the lipid A-Ara4N pathway. It contains two, functionally and physically separable domains: a dehydrogenase domain, (ArnA_DH) catalyzing the NAD+-dependent oxidative decarboxylation of, UDP-Glucuronic acid (UDP-GlcA), and a transformylase domain that, formylates UDP-Ara4N. Here, we describe the crystal structure of the, full-length bifunctional ArnA with UDP-GlcA and ATP bound to the, dehydrogenase domain. Binding of UDP-GlcA triggers a 17 A conformational, change in ArnA_DH that opens the NAD+ binding site while trapping, UDP-GlcA. We propose an ordered mechanism of substrate binding and product, release. Mutation of residues R619 and S433 demonstrates their importance, in catalysis and suggests that R619 functions as a general acid in, catalysis. The proposed mechanism for ArnA_DH has important implications, for the design of selective inhibitors.
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<StructureSection load='1z7b' size='340' side='right'caption='[[1z7b]], [[Resolution|resolution]] 2.31&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1z7b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z7B FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.31&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z7b OCA], [https://pdbe.org/1z7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z7b RCSB], [https://www.ebi.ac.uk/pdbsum/1z7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z7b ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ARNA_ECOLI ARNA_ECOLI] Bifunctional enzyme that catalyzes the oxidative decarboxylation of UDP-glucuronic acid (UDP-GlcUA) to UDP-4-keto-arabinose (UDP-Ara4O) and the addition of a formyl group to UDP-4-amino-4-deoxy-L-arabinose (UDP-L-Ara4N) to form UDP-L-4-formamido-arabinose (UDP-L-Ara4FN). The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides.<ref>PMID:11706007</ref> <ref>PMID:15695810</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/1z7b_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1z7b ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The modification of lipid A with 4-amino-4-deoxy-L-arabinose (Ara4N) allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. ArnA is the first enzyme specific to the lipid A-Ara4N pathway. It contains two functionally and physically separable domains: a dehydrogenase domain (ArnA_DH) catalyzing the NAD+-dependent oxidative decarboxylation of UDP-Glucuronic acid (UDP-GlcA), and a transformylase domain that formylates UDP-Ara4N. Here, we describe the crystal structure of the full-length bifunctional ArnA with UDP-GlcA and ATP bound to the dehydrogenase domain. Binding of UDP-GlcA triggers a 17 A conformational change in ArnA_DH that opens the NAD+ binding site while trapping UDP-GlcA. We propose an ordered mechanism of substrate binding and product release. Mutation of residues R619 and S433 demonstrates their importance in catalysis and suggests that R619 functions as a general acid in catalysis. The proposed mechanism for ArnA_DH has important implications for the design of selective inhibitors.
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==About this Structure==
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Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance.,Gatzeva-Topalova PZ, May AP, Sousa MC Structure. 2005 Jun;13(6):929-42. PMID:15939024<ref>PMID:15939024</ref>
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1Z7B is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Z7B OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance., Gatzeva-Topalova PZ, May AP, Sousa MC, Structure. 2005 Jun;13(6):929-42. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15939024 15939024]
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</div>
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<div class="pdbe-citations 1z7b" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Gatzeva-Topalova, P.Z.]]
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[[Category: Gatzeva-Topalova PZ]]
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[[Category: May, A.P.]]
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[[Category: May AP]]
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[[Category: Sousa, M.C.]]
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[[Category: Sousa MC]]
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[[Category: SO4]]
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[[Category: rossmann fold]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:16:42 2007''
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Current revision

Crystal structure of E.coli ArnA dehydrogenase (decarboxylase) domain, R619E mutant

PDB ID 1z7b

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