1nmp: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1nmp.jpg|left|200px]]<br /><applet load="1nmp" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1nmp, resolution 2.20&Aring;" />
'''Structural genomics, ybgI protein, unknown function'''<br />


==Overview==
==Structural genomics, ybgI protein, unknown function==
BACKGROUND: The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function. RESULTS: The structure of the ybgI protein is a toroid composed of six polypeptide chains forming a trimer of dimers. Each polypeptide chain binds two metal ions on the inside of the toroid. CONCLUSION: The toroidal structure is comparable to that of some proteins that are involved in DNA metabolism. The di-nuclear metal site could imply that the specific function of this protein is as a hydrolase-oxidase enzyme.
<StructureSection load='1nmp' size='340' side='right'caption='[[1nmp]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1nmp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NMP FirstGlance]. <br>
1NMP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli,_and_escherichia_coli_o157:h7 Escherichia coli, and escherichia coli o157:h7] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMP 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]] 2.2&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1nmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmp OCA], [https://pdbe.org/1nmp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nmp RCSB], [https://www.ebi.ac.uk/pdbsum/1nmp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nmp ProSAT]</span></td></tr>
Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site., Ladner JE, Obmolova G, Teplyakov A, Howard AJ, Khil PP, Camerini-Otero RD, Gilliland GL, BMC Struct Biol. 2003 Sep 30;3:7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14519207 14519207]
</table>
[[Category: Escherichia coli, and escherichia coli o157:h7]]
== Function ==
[[Category: Single protein]]
[https://www.uniprot.org/uniprot/GCH1L_ECOLI GCH1L_ECOLI] Provides significant protection from radiation damage and may be involved in the degradation of radiation-damaged nucleotides.<ref>PMID:25049088</ref>
[[Category: Camerini-Otero, R D.]]
== Evolutionary Conservation ==
[[Category: Gilliland, G L.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Khil, P P.]]
Check<jmol>
[[Category: Ladner, J E.]]
  <jmolCheckbox>
[[Category: Obmolova, G.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nm/1nmp_consurf.spt"</scriptWhenChecked>
[[Category: S2F, Structure 2.Function Project.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: Teplyakov, A.]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: MG]]
  </jmolCheckbox>
[[Category: hypothetical protein]]
</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=1nmp ConSurf].
[[Category: s2f]]
<div style="clear:both"></div>
[[Category: structural genomics]]
== References ==
[[Category: structure 2 function project]]
<references/>
[[Category: toroidal structure]]
__TOC__
[[Category: ybgi]]
</StructureSection>
 
[[Category: Escherichia coli]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:07:49 2008''
[[Category: Escherichia coli O157:H7]]
[[Category: Large Structures]]
[[Category: Camerini-Otero RD]]
[[Category: Gilliland GL]]
[[Category: Khil PP]]
[[Category: Ladner JE]]
[[Category: Obmolova G]]
[[Category: Teplyakov A]]
Retrieved from "https://proteopedia.org/1nmp"