1nmo: Difference between revisions

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==Structural genomics, protein ybgI, unknown function==
==Structural genomics, protein ybgI, unknown function==
<StructureSection load='1nmo' size='340' side='right' caption='[[1nmo]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='1nmo' size='340' side='right'caption='[[1nmo]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1nmo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NMO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NMO FirstGlance]. <br>
<table><tr><td colspan='2'>[[1nmo]] 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=1NMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NMO FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YBGI OR B0710 OR Z0861 OR ECS0735 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1nmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmo OCA], [https://pdbe.org/1nmo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nmo RCSB], [https://www.ebi.ac.uk/pdbsum/1nmo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nmo ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nmo OCA], [http://pdbe.org/1nmo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nmo RCSB], [http://www.ebi.ac.uk/pdbsum/1nmo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nmo ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/GTPC1_ECOLI GTPC1_ECOLI]] Converts GTP to dihydroneopterin triphosphate.  
[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>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nm/1nmo_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nm/1nmo_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Camerini-Otero, R D]]
[[Category: Escherichia coli O157:H7]]
[[Category: Gilliland, G L]]
[[Category: Large Structures]]
[[Category: Khil, P P]]
[[Category: Camerini-Otero RD]]
[[Category: Ladner, J E]]
[[Category: Gilliland GL]]
[[Category: Obmolova, G]]
[[Category: Khil PP]]
[[Category: S2F, Structure 2.Function Project]]
[[Category: Ladner JE]]
[[Category: Teplyakov, A]]
[[Category: Obmolova G]]
[[Category: Hypothetical protein]]
[[Category: Teplyakov A]]
[[Category: S2f]]
[[Category: Structural genomic]]
[[Category: Structure 2 function project]]
[[Category: Toroidal structure]]
[[Category: Unknown function]]
[[Category: Ybgi]]

Latest revision as of 07:45, 17 October 2024

Structural genomics, protein ybgI, unknown functionStructural genomics, protein ybgI, unknown function

Structural highlights

1nmo is a 6 chain structure with sequence from Escherichia coli and Escherichia coli O157:H7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GCH1L_ECOLI Provides significant protection from radiation damage and may be involved in the degradation of radiation-damaged nucleotides.[1]

Evolutionary Conservation

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

Publication Abstract from PubMed

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.

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:14519207[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Byrne RT, Chen SH, Wood EA, Cabot EL, Cox MM. Escherichia coli genes and pathways involved in surviving extreme exposure to ionizing radiation. J Bacteriol. 2014 Oct;196(20):3534-45. PMID:25049088 doi:10.1128/JB.01589-14
  2. ↑ Ladner JE, Obmolova G, Teplyakov A, Howard AJ, Khil PP, Camerini-Otero RD, Gilliland GL. Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site. BMC Struct Biol. 2003 Sep 30;3:7. PMID:14519207 doi:10.1186/1472-6807-3-7

1nmo, resolution 2.20Å

Drag the structure with the mouse to rotate

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