2q4x

From Proteopedia

(Difference between revisions)

Current revision

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g16990

Structural highlights

2q4x is a 2 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å, 8 models
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TENAE_ARATH Involved in thiamine salvage by hydrolyzing the thiamine breakdown product 4-amino-5-aminomethyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) (PubMed:25014715). Has a high formylamino-HMP amidohydrolase activity (PubMed:25014715). No activity with other thiamine degradation products such as thiamine mono- or diphosphate, oxothiamine, oxythiamine, thiamine disulfide, desthiothiamine or thiochrome as substrates (PubMed:25014715). Does not display thiaminase II activity, as it is unable to hydrolyze thiamine (PubMed:25014715). Is able to carry out two successive steps in the salvage of thiamine breakdown product, whereas two separate enzymes are required in Bacillus species (Probable). May also serve a damage pre-emption function by hydrolyzing products that would otherwise do harm (Probable).^[1] ^[2]

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

X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.

Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744^[3]

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

References

↑ Zallot R, Yazdani M, Goyer A, Ziemak MJ, Guan JC, McCarty DR, de Crécy-Lagard V, Gerdes S, Garrett TJ, Benach J, Hunt JF, Shintani DK, Hanson AD. Salvage of the thiamin pyrimidine moiety by plant TenA proteins lacking an active-site cysteine. Biochem J. 2014 Oct 1;463(1):145-55. PMID:25014715 doi:10.1042/BJ20140522
↑ Zallot R, Yazdani M, Goyer A, Ziemak MJ, Guan JC, McCarty DR, de Crécy-Lagard V, Gerdes S, Garrett TJ, Benach J, Hunt JF, Shintani DK, Hanson AD. Salvage of the thiamin pyrimidine moiety by plant TenA proteins lacking an active-site cysteine. Biochem J. 2014 Oct 1;463(1):145-55. PMID:25014715 doi:10.1042/BJ20140522
↑ Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040-52. PMID:17850744 doi:http://dx.doi.org/10.1016/j.str.2007.06.019

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/2q4x"

@@ Line 3: / Line 3: @@
 <StructureSection load='2q4x' size='340' side='right'caption='[[2q4x]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q4x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4X FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q4x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4X FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HMH:4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE'>HMH</scene>, <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]] 2.1&#8491;, 8 models</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=HMH:4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE'>HMH</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2f2g|2f2g]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At3g16990, K14A17_11, K14A17.22 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=2q4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4x OCA], [https://pdbe.org/2q4x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4x RCSB], [https://www.ebi.ac.uk/pdbsum/2q4x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4x ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/TENAE_ARATH TENAE_ARATH] Involved in thiamine salvage by hydrolyzing the thiamine breakdown product 4-amino-5-aminomethyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) (PubMed:25014715). Has a high formylamino-HMP amidohydrolase activity (PubMed:25014715). No activity with other thiamine degradation products such as thiamine mono- or diphosphate, oxothiamine, oxythiamine, thiamine disulfide, desthiothiamine or thiochrome as substrates (PubMed:25014715). Does not display thiaminase II activity, as it is unable to hydrolyze thiamine (PubMed:25014715). Is able to carry out two successive steps in the salvage of thiamine breakdown product, whereas two separate enzymes are required in Bacillus species (Probable). May also serve a damage pre-emption function by hydrolyzing products that would otherwise do harm (Probable).<ref>PMID:25014715</ref> <ref>PMID:25014715</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q4/2q4x_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>
   </jmolCheckbox>
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Structural genomic]]
+[[Category: Kondrashov DA]]
-[[Category: Kondrashov, D A]]
+[[Category: Levin EJ]]
-[[Category: Levin, E J]]
+[[Category: Phillips Jr GN]]
-[[Category: Phillips, G N]]
+[[Category: Wesenberg GE]]
-[[Category: Wesenberg, G E]]
-[[Category: At3g16990]]
-[[Category: Cesg]]
-[[Category: Ensemble refinement]]
-[[Category: Plant protein]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Refinement methodology development]]
-[[Category: Tena/thi-4/pqqc family]]
-[[Category: Tena_thi-4 domain]]

2q4x

From Proteopedia

Current revision

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g16990

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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