1te7

From Proteopedia

(Difference between revisions)

Current revision

Solution NMR Structure of Protein yqfB from Escherichia coli. Northeast Structural Genomics Consortium Target ET99

Structural highlights

1te7 is a 1 chain structure with sequence from Escherichia coli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

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.^[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

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^[2]

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

References

↑ Stanislauskienė R, Laurynėnas A, Rutkienė R, Aučynaitė A, Tauraitė D, Meškienė R, Urbelienė N, Kaupinis A, Valius M, Kaliniene L, Meškys R. YqfB protein from Escherichia coli: an atypical amidohydrolase active towards N(4)-acylcytosine derivatives. Sci Rep. 2020 Jan 21;10(1):788. PMID:31964920 doi:10.1038/s41598-020-57664-w
↑ Shen Y, Atreya HS, Liu G, Szyperski T. G-matrix Fourier transform NOESY-based protocol for high-quality protein structure determination. J Am Chem Soc. 2005 Jun 29;127(25):9085-99. PMID:15969587 doi:http://dx.doi.org/10.1021/ja0501870

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1te7"

@@ Line 1: / Line 1: @@
 ==Solution NMR Structure of Protein yqfB from Escherichia coli. Northeast Structural Genomics Consortium Target ET99==
-<StructureSection load='1te7' size='340' side='right' caption='[[1te7]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='1te7' size='340' side='right'caption='[[1te7]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1te7]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TE7 FirstGlance]. <br>
+<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><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YQFB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1te7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1te7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1te7 RCSB], [http://www.ebi.ac.uk/pdbsum/1te7 PDBsum], [http://www.topsan.org/Proteins/NESGC/1te7 TOPSAN]</span></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>
+</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>
+    <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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;">
@@ Line 24: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1te7" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 29: / Line 33: @@
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Arrowsmith, C.]]
+[[Category: Large Structures]]
-[[Category: Atreya, H S.]]
+[[Category: Arrowsmith C]]
-[[Category: NESG, Northeast Structural Genomics Consortium.]]
+[[Category: Atreya HS]]
-[[Category: Shen, Y.]]
+[[Category: Shen Y]]
-[[Category: Szyperski, T.]]
+[[Category: Szyperski T]]
-[[Category: Yee, A.]]
+[[Category: Yee A]]
-[[Category: Alpha + beta]]
-[[Category: Nesg]]
-[[Category: Northeast structural genomics consortium]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Structural genomic]]
-[[Category: Unknown function]]

1te7

From Proteopedia

Current revision

Solution NMR Structure of Protein yqfB from Escherichia coli. Northeast Structural Genomics Consortium Target ET99

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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