1te7: Difference between revisions
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< | ==Solution NMR Structure of Protein yqfB from Escherichia coli. Northeast Structural Genomics Consortium Target ET99== | ||
<StructureSection load='1te7' size='340' side='right'caption='[[1te7]]' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1te7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TE7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TE7 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1te7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1te7 OCA], [https://pdbe.org/1te7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1te7 RCSB], [https://www.ebi.ac.uk/pdbsum/1te7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1te7 ProSAT], [https://www.topsan.org/Proteins/NESGC/1te7 TOPSAN]</span></td></tr> | ||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/AC4CH_ECOLI AC4CH_ECOLI] Catalyzes the hydrolysis of N(4)-acetylcytidine (ac4C). Can also hydrolyze N(4)-acetyl-2'-deoxycytidine and N(4)-acetylcytosine with lower efficiency. Has weaker activity towards a wide range of structurally different N(4)-acylated cytosines and cytidines.<ref>PMID:31964920</ref> | |||
== 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/te/1te7_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=1te7 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A protocol for high-quality structure determination based on G-matrix Fourier transform (GFT) NMR is presented. Five through-bond chemical shift correlation experiments providing 4D and 5D spectral information at high digital resolution are performed for resonance assignment. These are combined with a newly implemented (4,3)D GFT NOESY experiment which encodes information of 4D 15N/15N-, 13C(alipahtic)/15N-, and 13C(aliphatic)/13C(aliphatic)-resolved [1H,1H]-NOESY in two subspectra, each containing one component of chemical shift doublets arising from 4D --> 3D projection at omega1:Omega(1H) +/- Omega(X) [X = 15N,13C(aliphatic)]. The peaks located at the centers of the doublets are obtained from simultaneous 3D 15N/13C(aliphatic)/13C(aromatic)-resolved [1H,1H]-NOESY, wherein NOEs detected on aromatic protons are also obtained. The protocol was applied for determining a high-quality structure of the 14 kDa Northeast Structural Genomics consortium target protein, YqfB (PDB ID ). Through-bond correlation and NOESY spectra were acquired, respectively, in 16.9 and 39 h (30 h for shift doublets, 9 h for central peaks) on a 600 MHz spectrometer equipped with a cryogenic probe. The rapidly collected highly resolved 4D NOESY information allows one to assign the majority of NOEs directly from chemical shifts, which yields accurate initial structures "within" approximately 2 angstroms of the final structure. Information theoretical "QUEEN" analysis of initial distance limit constraint networks revealed that, in contrast to structure-based protocols, such NOE assignment is not biased toward identifying additional constraints that tend to be redundant with respect to the available constraint network. The protocol enables rapid NMR data collection for robust high-quality structure determination of proteins up to approximately 20-25 kDa in high-throughput. | |||
G-matrix Fourier transform NOESY-based protocol for high-quality protein structure determination.,Shen Y, Atreya HS, Liu G, Szyperski T J Am Chem Soc. 2005 Jun 29;127(25):9085-99. PMID:15969587<ref>PMID:15969587</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1te7" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Arrowsmith C]] | ||
[[Category: | [[Category: Atreya HS]] | ||
[[Category: Shen | [[Category: Shen Y]] | ||
[[Category: Szyperski | [[Category: Szyperski T]] | ||
[[Category: Yee | [[Category: Yee A]] | ||
Latest revision as of 12:12, 22 May 2024
Solution NMR Structure of Protein yqfB from Escherichia coli. Northeast Structural Genomics Consortium Target ET99Solution NMR Structure of Protein yqfB from Escherichia coli. Northeast Structural Genomics Consortium Target ET99
Structural highlights
FunctionAC4CH_ECOLI Catalyzes the hydrolysis of N(4)-acetylcytidine (ac4C). Can also hydrolyze N(4)-acetyl-2'-deoxycytidine and N(4)-acetylcytosine with lower efficiency. Has weaker activity towards a wide range of structurally different N(4)-acylated cytosines and cytidines.[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 PubMedA protocol for high-quality structure determination based on G-matrix Fourier transform (GFT) NMR is presented. Five through-bond chemical shift correlation experiments providing 4D and 5D spectral information at high digital resolution are performed for resonance assignment. These are combined with a newly implemented (4,3)D GFT NOESY experiment which encodes information of 4D 15N/15N-, 13C(alipahtic)/15N-, and 13C(aliphatic)/13C(aliphatic)-resolved [1H,1H]-NOESY in two subspectra, each containing one component of chemical shift doublets arising from 4D --> 3D projection at omega1:Omega(1H) +/- Omega(X) [X = 15N,13C(aliphatic)]. The peaks located at the centers of the doublets are obtained from simultaneous 3D 15N/13C(aliphatic)/13C(aromatic)-resolved [1H,1H]-NOESY, wherein NOEs detected on aromatic protons are also obtained. The protocol was applied for determining a high-quality structure of the 14 kDa Northeast Structural Genomics consortium target protein, YqfB (PDB ID ). Through-bond correlation and NOESY spectra were acquired, respectively, in 16.9 and 39 h (30 h for shift doublets, 9 h for central peaks) on a 600 MHz spectrometer equipped with a cryogenic probe. The rapidly collected highly resolved 4D NOESY information allows one to assign the majority of NOEs directly from chemical shifts, which yields accurate initial structures "within" approximately 2 angstroms of the final structure. Information theoretical "QUEEN" analysis of initial distance limit constraint networks revealed that, in contrast to structure-based protocols, such NOE assignment is not biased toward identifying additional constraints that tend to be redundant with respect to the available constraint network. The protocol enables rapid NMR data collection for robust high-quality structure determination of proteins up to approximately 20-25 kDa in high-throughput. G-matrix Fourier transform NOESY-based protocol for high-quality protein structure determination.,Shen Y, Atreya HS, Liu G, Szyperski T J Am Chem Soc. 2005 Jun 29;127(25):9085-99. PMID:15969587[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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