1im8: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1im8.gif|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_1im8", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_1im8|  PDB=1im8  |  SCENE=  }}
'''Crystal structure of YecO from Haemophilus influenzae (HI0319), a methyltransferase with a bound S-adenosylhomocysteine'''


==Crystal structure of YecO from Haemophilus influenzae (HI0319), a methyltransferase with a bound S-adenosylhomocysteine==
<StructureSection load='1im8' size='340' side='right'caption='[[1im8]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1im8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae_Rd_KW20 Haemophilus influenzae Rd KW20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IM8 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]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SAI:S-ADENOSYL-L-HOMOSELENOCYSTEINE'>SAI</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=1im8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1im8 OCA], [https://pdbe.org/1im8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1im8 RCSB], [https://www.ebi.ac.uk/pdbsum/1im8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1im8 ProSAT]</span></td></tr>
</table>
== 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/im/1im8_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=1im8 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of YecO from Haemophilus influenzae (HI0319), a protein annotated in the sequence databases as hypothetical, and that has not been assigned a function, has been determined at 2.2-A resolution. The structure reveals a fold typical of S-adenosyl-L-methionine-dependent (AdoMet) methyltransferase enzymes. Moreover, a processed cofactor, S-adenosyl-L-homocysteine (AdoHcy), is bound to the enzyme, further confirming the biochemical function of HI0319 and its sequence family members. An active site arginine, shielded from bulk solvent, interacts with an anion, possibly a chloride ion, which in turn interacts with the sulfur atom of AdoHcy. The AdoHcy and nearby protein residues delineate a small solvent-excluded substrate binding cavity of 162 A(3) in volume. The environment surrounding the cavity indicates that the substrate molecule contains a hydrophobic moiety and an anionic group. Many of the residues that define the cavity are invariant in the HI0319 sequence family but are not conserved in other methyltransferases. Therefore, the substrate specificity of YecO enzymes is unique and differs from the substrate specificity of all other methyltransferases sequenced to date. Examination of the Enzyme Commission list of methyltransferases prompted a manual inspection of 10 possible substrates using computer graphics and suggested that the ortho-substituted benzoic acids fit best in the active site.


==Overview==
Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine.,Lim K, Zhang H, Tempczyk A, Bonander N, Toedt J, Howard A, Eisenstein E, Herzberg O Proteins. 2001 Dec 1;45(4):397-407. PMID:11746687<ref>PMID:11746687</ref>
The crystal structure of YecO from Haemophilus influenzae (HI0319), a protein annotated in the sequence databases as hypothetical, and that has not been assigned a function, has been determined at 2.2-A resolution. The structure reveals a fold typical of S-adenosyl-L-methionine-dependent (AdoMet) methyltransferase enzymes. Moreover, a processed cofactor, S-adenosyl-L-homocysteine (AdoHcy), is bound to the enzyme, further confirming the biochemical function of HI0319 and its sequence family members. An active site arginine, shielded from bulk solvent, interacts with an anion, possibly a chloride ion, which in turn interacts with the sulfur atom of AdoHcy. The AdoHcy and nearby protein residues delineate a small solvent-excluded substrate binding cavity of 162 A(3) in volume. The environment surrounding the cavity indicates that the substrate molecule contains a hydrophobic moiety and an anionic group. Many of the residues that define the cavity are invariant in the HI0319 sequence family but are not conserved in other methyltransferases. Therefore, the substrate specificity of YecO enzymes is unique and differs from the substrate specificity of all other methyltransferases sequenced to date. Examination of the Enzyme Commission list of methyltransferases prompted a manual inspection of 10 possible substrates using computer graphics and suggested that the ortho-substituted benzoic acids fit best in the active site.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1IM8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IM8 OCA].
</div>
<div class="pdbe-citations 1im8" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine., Lim K, Zhang H, Tempczyk A, Bonander N, Toedt J, Howard A, Eisenstein E, Herzberg O, Proteins. 2001 Dec 1;45(4):397-407. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11746687 11746687]
*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
[[Category: Haemophilus influenzae]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Bonander, N.]]
__TOC__
[[Category: Eisenstein, E.]]
</StructureSection>
[[Category: Herzberg, O.]]
[[Category: Haemophilus influenzae Rd KW20]]
[[Category: Howard, A.]]
[[Category: Large Structures]]
[[Category: Lim, K.]]
[[Category: Bonander N]]
[[Category: S2F, Structure 2.Function Project.]]
[[Category: Eisenstein E]]
[[Category: Tempczyk, A.]]
[[Category: Herzberg O]]
[[Category: Toedt, J.]]
[[Category: Howard A]]
[[Category: Zhang, H.]]
[[Category: Lim K]]
[[Category: Adenosylhomocysteine]]
[[Category: Tempczyk A]]
[[Category: Hypothetical protein]]
[[Category: Toedt J]]
[[Category: Methyltransferase]]
[[Category: Zhang H]]
[[Category: S2f]]
[[Category: Structural genomic]]
[[Category: Structure 2 function project]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 20:09:12 2008''
Retrieved from "https://proteopedia.org/1im8"