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| | <StructureSection load='1nrk' size='340' side='right'caption='[[1nrk]], [[Resolution|resolution]] 2.80Å' scene=''> | | <StructureSection load='1nrk' size='340' side='right'caption='[[1nrk]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1nrk]] is a 1 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=1NRK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NRK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1nrk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NRK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.8Å</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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YGFZ OR B2898 ([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=1nrk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrk OCA], [https://pdbe.org/1nrk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nrk RCSB], [https://www.ebi.ac.uk/pdbsum/1nrk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nrk ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nrk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrk OCA], [http://pdbe.org/1nrk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nrk RCSB], [http://www.ebi.ac.uk/pdbsum/1nrk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nrk ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/YGFZ_ECOLI YGFZ_ECOLI] Folate-binding protein involved in regulating the level of ATP-DnaA and in the modification of some tRNAs. It is probably a key factor in regulatory networks that act via tRNA modification, such as initiation of chromosomal replication.<ref>PMID:16359333</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nr/1nrk_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nr/1nrk_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: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Gilliland, G L]] | + | [[Category: Gilliland GL]] |
| - | [[Category: Obmolova, G]] | + | [[Category: Obmolova G]] |
| - | [[Category: S2F, Structure 2.Function Project]]
| + | [[Category: Teplyakov A]] |
| - | [[Category: Teplyakov, A]] | + | |
| - | [[Category: S2f]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Structure 2 function project]]
| + | |
| - | [[Category: Unknown function]]
| + | |
| - | [[Category: Ygfz]]
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| Structural highlights
Function
YGFZ_ECOLI Folate-binding protein involved in regulating the level of ATP-DnaA and in the modification of some tRNAs. It is probably a key factor in regulatory networks that act via tRNA modification, such as initiation of chromosomal replication.[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
The ygfZ gene product of Escherichia coli represents a large protein family conserved in bacteria to eukaryotes. The members of this family are uncharacterized proteins with marginal sequence similarity to the T-protein (aminomethyltransferase) of the glycine cleavage system. To assist with the functional assignment of the YgfZ family, the crystal structure of the E. coli protein was determined by multiwavelength anomalous diffraction. The protein molecule has a three-domain architecture with a central hydrophobic channel. The structure is very similar to that of bacterial dimethylglycine oxidase, an enzyme of the glycine betaine pathway and a homolog of the T-protein. Based on structural superposition, a folate-binding site was identified in the central channel of YgfZ, and the ability of YgfZ to bind folate derivatives was confirmed experimentally. However, in contrast to dimethylglycine oxidase and T-protein, the YgfZ family lacks amino acid conservation at the folate site, which implies that YgfZ is not an aminomethyltransferase but is likely a folate-dependent regulatory protein involved in one-carbon metabolism.
Crystal structure of the YgfZ protein from Escherichia coli suggests a folate-dependent regulatory role in one-carbon metabolism.,Teplyakov A, Obmolova G, Sarikaya E, Pullalarevu S, Krajewski W, Galkin A, Howard AJ, Herzberg O, Gilliland GL J Bacteriol. 2004 Nov;186(21):7134-40. PMID:15489424[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ote T, Hashimoto M, Ikeuchi Y, Su'etsugu M, Suzuki T, Katayama T, Kato J. Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation. Mol Microbiol. 2006 Jan;59(1):265-75. PMID:16359333 doi:http://dx.doi.org/MMI4932
- ↑ Teplyakov A, Obmolova G, Sarikaya E, Pullalarevu S, Krajewski W, Galkin A, Howard AJ, Herzberg O, Gilliland GL. Crystal structure of the YgfZ protein from Escherichia coli suggests a folate-dependent regulatory role in one-carbon metabolism. J Bacteriol. 2004 Nov;186(21):7134-40. PMID:15489424 doi:186/21/7134
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