2veb

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(New page: 200px<br /><applet load="2veb" size="350" color="white" frame="true" align="right" spinBox="true" caption="2veb, resolution 1.30&Aring;" /> '''HIGH RESOLUTION STRU...)
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[[Image:2veb.jpg|left|200px]]<br /><applet load="2veb" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2veb, resolution 1.30&Aring;" />
 
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'''HIGH RESOLUTION STRUCTURE OF PROTOGLOBIN FROM METHANOSARCINA ACETIVORANS C2A'''<br />
 
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==Overview==
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==High resolution structure of protoglobin from Methanosarcina acetivorans C2A==
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The structural adaptability of the globin fold has been highlighted by the, recent discovery of the 2-on-2 haemoglobins, of neuroglobin and, cytoglobin. Protoglobin from Methanosarcina acetivorans C2A-a strictly, anaerobic methanogenic Archaea-is, to the best of our knowledge, the, latest entry adding new variability and functional complexity to the, haemoglobin (Hb) superfamily. Here, we report the 1.3 A crystal structure, of oxygenated M. acetivorans protoglobin, together with the first insight, into its ligand-binding properties. We show that, contrary to all known, globins, protoglobin-specific loops and an amino-terminal extension, completely bury the haem within the protein matrix. Access of O(2), CO and, NO to the haem is granted by the protoglobin-specific apolar tunnels, reaching the haem distal site from locations at the B/G and B/E helix, interfaces. Functionally, M. acetivorans dimeric protoglobin shows a, selectivity ratio for O(2)/CO binding to the haem that favours O(2), ligation and anticooperativity in ligand binding. Both properties are, exceptional within the Hb superfamily.
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<StructureSection load='2veb' size='340' side='right'caption='[[2veb]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2veb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_acetivorans Methanosarcina acetivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VEB 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]] 1.3&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=2veb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2veb OCA], [https://pdbe.org/2veb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2veb RCSB], [https://www.ebi.ac.uk/pdbsum/2veb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2veb ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q8TLY9_METAC Q8TLY9_METAC]
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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/ve/2veb_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=2veb 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 structural adaptability of the globin fold has been highlighted by the recent discovery of the 2-on-2 haemoglobins, of neuroglobin and cytoglobin. Protoglobin from Methanosarcina acetivorans C2A-a strictly anaerobic methanogenic Archaea-is, to the best of our knowledge, the latest entry adding new variability and functional complexity to the haemoglobin (Hb) superfamily. Here, we report the 1.3 A crystal structure of oxygenated M. acetivorans protoglobin, together with the first insight into its ligand-binding properties. We show that, contrary to all known globins, protoglobin-specific loops and an amino-terminal extension completely bury the haem within the protein matrix. Access of O(2), CO and NO to the haem is granted by the protoglobin-specific apolar tunnels reaching the haem distal site from locations at the B/G and B/E helix interfaces. Functionally, M. acetivorans dimeric protoglobin shows a selectivity ratio for O(2)/CO binding to the haem that favours O(2) ligation and anticooperativity in ligand binding. Both properties are exceptional within the Hb superfamily.
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==About this Structure==
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Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity.,Nardini M, Pesce A, Thijs L, Saito JA, Dewilde S, Alam M, Ascenzi P, Coletta M, Ciaccio C, Moens L, Bolognesi M EMBO Rep. 2008 Feb;9(2):157-63. Epub 2008 Jan 11. PMID:18188182<ref>PMID:18188182</ref>
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2VEB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_acetivorans Methanosarcina acetivorans] with <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=HEM:'>HEM</scene>, <scene name='pdbligand=OXY:'>OXY</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Hem Binding Site For Chain A'>AC1</scene>, <scene name='pdbsite=AC2:Po4 Binding Site For Chain A'>AC2</scene>, <scene name='pdbsite=AC3:Po4 Binding Site For Chain A'>AC3</scene>, <scene name='pdbsite=AC4:Gol Binding Site For Chain A'>AC4</scene> and <scene name='pdbsite=AC5:Oxy Binding Site For Chain A'>AC5</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VEB 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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Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity., Nardini M, Pesce A, Thijs L, Saito JA, Dewilde S, Alam M, Ascenzi P, Coletta M, Ciaccio C, Moens L, Bolognesi M, EMBO Rep. 2008 Jan 11;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18188182 18188182]
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</div>
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<div class="pdbe-citations 2veb" 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>
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[[Category: Large Structures]]
[[Category: Methanosarcina acetivorans]]
[[Category: Methanosarcina acetivorans]]
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[[Category: Single protein]]
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[[Category: Alam M]]
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[[Category: Alam, M.]]
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[[Category: Ascenzi P]]
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[[Category: Ascenzi, P.]]
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[[Category: Bolognesi M]]
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[[Category: Bolognesi, M.]]
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[[Category: Ciaccio C]]
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[[Category: Ciaccio, C.]]
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[[Category: Coletta M]]
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[[Category: Coletta, M.]]
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[[Category: Dewilde S]]
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[[Category: Dewilde, S.]]
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[[Category: Moens L]]
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[[Category: Moens, L.]]
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[[Category: Nardini M]]
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[[Category: Nardini, M.]]
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[[Category: Pesce A]]
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[[Category: Pesce, A.]]
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[[Category: Saito JA]]
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[[Category: Saito, J.A.]]
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[[Category: Thijs L]]
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[[Category: Thijs, L.]]
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[[Category: GOL]]
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[[Category: HEM]]
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[[Category: OXY]]
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[[Category: PO4]]
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[[Category: archaea protein]]
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[[Category: hemoprotein structure]]
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[[Category: methanogenesis]]
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[[Category: protein matrix tunnels]]
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[[Category: protoglobin]]
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[[Category: transport protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 10:56:44 2008''
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Current revision

High resolution structure of protoglobin from Methanosarcina acetivorans C2A

PDB ID 2veb

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