2veb: Difference between revisions

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{{Seed}}
[[Image:2veb.png|left|200px]]


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==High resolution structure of protoglobin from Methanosarcina acetivorans C2A==
The line below this paragraph, containing "STRUCTURE_2veb", creates the "Structure Box" on the page.
<StructureSection load='2veb' size='340' side='right'caption='[[2veb]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
{{STRUCTURE_2veb|  PDB=2veb  |  SCENE=  }}
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q8TLY9_METAC Q8TLY9_METAC]
== 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/ve/2veb_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=2veb ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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.


===HIGH RESOLUTION STRUCTURE OF PROTOGLOBIN FROM METHANOSARCINA ACETIVORANS C2A===
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>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_18188182}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2veb" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 18188182 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18188182}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
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].
 
==Reference==
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]
[[Category: Methanosarcina acetivorans]]
[[Category: Methanosarcina acetivorans]]
[[Category: Single protein]]
[[Category: Alam M]]
[[Category: Alam, M.]]
[[Category: Ascenzi P]]
[[Category: Ascenzi, P.]]
[[Category: Bolognesi M]]
[[Category: Bolognesi, M.]]
[[Category: Ciaccio C]]
[[Category: Ciaccio, C.]]
[[Category: Coletta M]]
[[Category: Coletta, M.]]
[[Category: Dewilde S]]
[[Category: Dewilde, S.]]
[[Category: Moens L]]
[[Category: Moens, L.]]
[[Category: Nardini M]]
[[Category: Nardini, M.]]
[[Category: Pesce A]]
[[Category: Pesce, A.]]
[[Category: Saito JA]]
[[Category: Saito, J A.]]
[[Category: Thijs L]]
[[Category: Thijs, L.]]
[[Category: Archaea protein]]
[[Category: Hemoprotein structure]]
[[Category: Methanogenesis]]
[[Category: Protein matrix tunnel]]
[[Category: Protoglobin]]
[[Category: Transport protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 19:06:45 2008''
Retrieved from "https://proteopedia.org/2veb"