4x2r: Difference between revisions
m Protected "4x2r" [edit=sysop:move=sysop] |
No edit summary |
||
| (5 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
The | ==Crystal structure of PriA from Actinomyces urogenitalis== | ||
<StructureSection load='4x2r' size='340' side='right'caption='[[4x2r]], [[Resolution|resolution]] 1.05Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4x2r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinomyces_urogenitalis_DSM_15434 Actinomyces urogenitalis DSM 15434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X2R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X2R FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.05Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CXS:3-CYCLOHEXYL-1-PROPYLSULFONIC+ACID'>CXS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=4x2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x2r OCA], [https://pdbe.org/4x2r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x2r RCSB], [https://www.ebi.ac.uk/pdbsum/4x2r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x2r ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/C0W7K4_9ACTO C0W7K4_9ACTO] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes. | |||
Evolution of substrate specificity in a retained enzyme driven by gene loss.,Juarez-Vazquez AL, Edirisinghe JN, Verduzco-Castro EA, Michalska K, Wu C, Noda-Garcia L, Babnigg G, Endres M, Medina-Ruiz S, Santoyo-Flores J, Carrillo-Tripp M, Ton-That H, Joachimiak A, Henry CS, Barona-Gomez F Elife. 2017 Mar 31;6. pii: e22679. doi: 10.7554/eLife.22679. PMID:28362260<ref>PMID:28362260</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4x2r" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Actinomyces urogenitalis DSM 15434]] | |||
[[Category: Large Structures]] | |||
[[Category: BARONA-GOMEZ F]] | |||
[[Category: ENDRES M]] | |||
[[Category: JOACHIMIAK A]] | |||
[[Category: MICHALSKA K]] | |||
[[Category: VERDUZCO-CASTRO EA]] | |||
Latest revision as of 10:40, 27 September 2023
Crystal structure of PriA from Actinomyces urogenitalisCrystal structure of PriA from Actinomyces urogenitalis
Structural highlights
FunctionPublication Abstract from PubMedThe connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes. Evolution of substrate specificity in a retained enzyme driven by gene loss.,Juarez-Vazquez AL, Edirisinghe JN, Verduzco-Castro EA, Michalska K, Wu C, Noda-Garcia L, Babnigg G, Endres M, Medina-Ruiz S, Santoyo-Flores J, Carrillo-Tripp M, Ton-That H, Joachimiak A, Henry CS, Barona-Gomez F Elife. 2017 Mar 31;6. pii: e22679. doi: 10.7554/eLife.22679. PMID:28362260[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
|
| ||||||||||||||||||