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2veb

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[[Image:2veb.jpg|left|200px]]
 
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{{Structure
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==High resolution structure of protoglobin from Methanosarcina acetivorans C2A==
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|PDB= 2veb |SIZE=350|CAPTION= <scene name='initialview01'>2veb</scene>, resolution 1.30&Aring;
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<StructureSection load='2veb' size='340' side='right'caption='[[2veb]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
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|SITE= <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>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
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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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|ACTIVITY=
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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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|GENE=
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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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}}
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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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'''HIGH RESOLUTION STRUCTURE OF PROTOGLOBIN FROM METHANOSARCINA ACETIVORANS C2A'''
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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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==Overview==
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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 ==
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.
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 [[Single protein]] structure of sequence from [http://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].
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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 Feb;9(2):157-63. Epub 2008 Jan 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/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 tunnel]]
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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 Thu Mar 20 18:45:41 2008''
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Current revision

High resolution structure of protoglobin from Methanosarcina acetivorans C2A

PDB ID 2veb

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