This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2gkm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:28, 14 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2gkm.gif|left|200px]]<br /><applet load="2gkm" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2gkm, resolution 1.731&Aring;" />
 
-
'''Crystal structure of Mycobacterium tuberculosis trHbN TyrB10Phe mutant'''<br />
 
-
==Overview==
+
==Crystal structure of Mycobacterium tuberculosis trHbN TyrB10Phe mutant==
-
The crystallographic structure of oxygenated trHbN from Mycobacterium, tuberculosis showed an extended heme distal site hydrogen-bonding network, that includes Y(B10), Q(E11), and the bound O(2) (Milani, M., et al., (2001) EMBO J. 20, 3902-3909). In the present work, we analyze the effects, that substitutions at the B10 and E11 positions exert on the heme and its, coordinated ligands, using steady-state resonance Raman spectroscopy, absorption spectroscopy and X-ray crystallography. Our results show that, (1) residues Y(B10) and Q(E11) control the binding and the ionization, state of the heme-bound water molecules in ferric trHbN and are important, in keeping the sixth coordination position vacant in deoxy trHbN; (2), residue Q(E11) plays a role in maintaining the integrity of the proximal, Fe-His bond in deoxy trHbN; (3) in wild-type oxy-trHbN, the size and, hydrogen-bonding capability of residue E11 is important to sustain proper, interaction between Y(B10) and the heme-bound O(2); (4) CO-trHbN is in a, conformational equilibrium, where either the Y(B10) or the Q(E11) residue, interacts with the heme-bound CO; and (5) Y(B10) and Q(E11) residues, control the conformation (and likely the dynamics) of the protein matrix, tunnel gating residue F(E15). These findings suggest that the functional, processes of ligand binding and diffusion are controlled in trHbN through, the dynamic interaction of residues Y(B10), Q(E11), F(E15), and the heme, ligand.
+
<StructureSection load='2gkm' size='340' side='right'caption='[[2gkm]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[2gkm]] 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=2GKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GKM FirstGlance]. <br>
-
2GKM 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 <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=CYN:'>CYN</scene> and <scene name='pdbligand=HEM:'>HEM</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GKM OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.731&#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=NA:SODIUM+ION'>NA</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gkm OCA], [https://pdbe.org/2gkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gkm RCSB], [https://www.ebi.ac.uk/pdbsum/2gkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gkm ProSAT]</span></td></tr>
-
Ligand interactions in the distal heme pocket of Mycobacterium tuberculosis truncated hemoglobin N: roles of TyrB10 and GlnE11 residues., Ouellet Y, Milani M, Couture M, Bolognesi M, Guertin M, Biochemistry. 2006 Jul 25;45(29):8770-81. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16846220 16846220]
+
</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/gk/2gkm_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=2gkm ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
-
[[Category: Single protein]]
+
[[Category: Bolognesi M]]
-
[[Category: Bolognesi, M.]]
+
[[Category: Milani M]]
-
[[Category: Milani, M.]]
+
-
[[Category: CYN]]
+
-
[[Category: HEM]]
+
-
[[Category: NA]]
+
-
[[Category: truncated hemoglobin; mutant]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 17:28:20 2008''
+

Current revision

Crystal structure of Mycobacterium tuberculosis trHbN TyrB10Phe mutant

PDB ID 2gkm

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2gkm"
Personal tools