1s61: Difference between revisions

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New page: left|200px<br /> <applet load="1s61" size="450" color="white" frame="true" align="right" spinBox="true" caption="1s61, resolution 2.10Å" /> '''Crystal Structure o...
 
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[[Image:1s61.gif|left|200px]]<br />
<applet load="1s61" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1s61, resolution 2.10&Aring;" />
'''Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Butyl-isocyanide'''<br />


==Overview==
==Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Butyl-isocyanide==
Truncated hemoglobins (trHbs) are small hemoproteins forming a separate, cluster within the hemoglobin superfamily; their functional roles in, bacteria, plants, and unicellular eukaryotes are marginally understood., Crystallographic investigations have shown that the trHb fold (a, two-on-two alpha-helical sandwich related to the globin fold) hosts a, protein matrix tunnel system offering a potential path for ligand, diffusion to the heme distal site. The tunnel topology is conserved in, group I trHbs, although with modulation of its size/structure. Here, we, present a crystallographic investigation on trHbs from Mycobacterium, tuberculosis, Chlamydomonas eugametos, and Paramecium caudatum, showing, that treatment of trHb crystals under xenon pressure leads to binding of, xenon atoms at specific (conserved) sites along the protein matrix tunnel., The crystallographic results are in keeping with data from molecular, dynamics simulations, where a dioxygen molecule is left free to diffuse, within the protein matrix. Modulation of xenon binding over four main, sites is related to the structural properties of the tunnel system in the, three trHbs and may be connected to their functional roles. In a parallel, crystallographic investigation on M. tuberculosis trHbN, we show that, butyl isocyanide also binds within the apolar tunnel, in excellent, agreement with concepts derived from the xenon binding experiments. These, results, together with recent data on atypical CO rebinding kinetics to, group I trHbs, underline the potential role of the tunnel system in, supporting diffusion, but also accumulation in multiple copies, of low, polarity ligands/molecules within group I trHbs.
<StructureSection load='1s61' size='340' side='right'caption='[[1s61]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1s61]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S61 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NBN:N-BUTYL+ISOCYANIDE'>NBN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1s61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s61 OCA], [https://pdbe.org/1s61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s61 RCSB], [https://www.ebi.ac.uk/pdbsum/1s61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s61 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TRHBN_MYCTU TRHBN_MYCTU] Binds oxygen cooperatively with very high affinity (P(50) = 0.013 mmHg at 20 degrees Celsius) because of a fast combination (25 microM(-1).s(-1)) and a slow dissociation (0.2 s(-1)) rate.
== 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/s6/1s61_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1s61 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1S61 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with CYN, PO4, K, HEC, HEM and NBN as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA].
*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Heme-ligand tunneling in group I truncated hemoglobins., Milani M, Pesce A, Ouellet Y, Dewilde S, Friedman J, Ascenzi P, Guertin M, Bolognesi M, J Biol Chem. 2004 May 14;279(20):21520-5. Epub 2004 Mar 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15016811 15016811]
[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Single protein]]
[[Category: Ascenzi P]]
[[Category: Ascenzi, P.]]
[[Category: Bolognesi M]]
[[Category: Bolognesi, M.]]
[[Category: Dewilde S]]
[[Category: Dewilde, S.]]
[[Category: Friedman J]]
[[Category: Friedman, J.]]
[[Category: Guertin M]]
[[Category: Guertin, M.]]
[[Category: Milani M]]
[[Category: Milani, M.]]
[[Category: Ouellet Y]]
[[Category: Ouellet, Y.]]
[[Category: Pesce A]]
[[Category: Pesce, A.]]
[[Category: CYN]]
[[Category: HEC]]
[[Category: HEM]]
[[Category: K]]
[[Category: NBN]]
[[Category: PO4]]
[[Category: truncated hemoglobin]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov  8 13:17:44 2007''

Latest revision as of 11:28, 14 February 2024

Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Butyl-isocyanideCrystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Butyl-isocyanide

Structural highlights

1s61 is a 2 chain structure with sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TRHBN_MYCTU Binds oxygen cooperatively with very high affinity (P(50) = 0.013 mmHg at 20 degrees Celsius) because of a fast combination (25 microM(-1).s(-1)) and a slow dissociation (0.2 s(-1)) rate.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1s61, resolution 2.10Å

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