1dmn: Difference between revisions

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<StructureSection load='1dmn' size='340' side='right'caption='[[1dmn]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
<StructureSection load='1dmn' size='340' side='right'caption='[[1dmn]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1dmn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DMN FirstGlance]. <br>
<table><tr><td colspan='2'>[[1dmn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DMN FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[8cho|8cho]], [[1qjg|1qjg]], [[1dmm|1dmm]], [[1dmq|1dmq]]</div></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]] 2.05&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] </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=1dmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmn OCA], [https://pdbe.org/1dmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dmn RCSB], [https://www.ebi.ac.uk/pdbsum/1dmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dmn ProSAT]</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=1dmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmn OCA], [https://pdbe.org/1dmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dmn RCSB], [https://www.ebi.ac.uk/pdbsum/1dmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dmn ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_PSEPU]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1dmn 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=1dmn ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Delta(5)-3-Ketosteroid isomerase from Pseudomonas putida biotype B is one of the most proficient enzymes catalyzing an allylic isomerization reaction at rates comparable to the diffusion limit. The hydrogen-bond network (Asp99... Wat504...Tyr14...Tyr55...Tyr30) which links the two catalytic residues, Tyr14 and Asp99, to Tyr30, Tyr55, and a water molecule in the highly apolar active site has been characterized in an effort to identify its roles in function and stability. The DeltaG(U)(H2O) determined from equilibrium unfolding experiments reveals that the elimination of the hydroxyl group of Tyr14 or Tyr55 or the replacement of Asp99 with leucine results in a loss of conformational stability of 3.5-4.4 kcal/mol, suggesting that the hydrogen bonds of Tyr14, Tyr55, and Asp99 contribute significantly to stability. While decreasing the stability by about 6.5-7.9 kcal/mol, the Y55F/D99L or Y30F/D99L double mutation also reduced activity significantly, exhibiting a synergistic effect on k(cat) relative to the respective single mutations. These results indicate that the hydrogen-bond network is important for both stability and function. Additionally, they suggest that Tyr14 cannot function efficiently alone without additional support from the hydrogen bonds of Tyr55 and Asp99. The crystal structure of Y55F as determined at 1.9 A resolution shows that Tyr14 OH undergoes an alteration in orientation to form a new hydrogen bond with Tyr30. This observation supports the role of Tyr55 OH in positioning Tyr14 properly to optimize the hydrogen bond between Tyr14 and C3-O of the steroid substrate. No significant structural changes were observed in the crystal structures of Y30F and Y30F/Y55F, which allowed us to estimate approximately the interaction energies mediated by the hydrogen bonds Tyr30...Tyr55 and Tyr14...Tyr55. Taken together, our results demonstrate that the hydrogen-bond network provides the structural support that is needed for the enzyme to maintain the active-site geometry optimized for both function and stability.
Contribution of the hydrogen-bond network involving a tyrosine triad in the active site to the structure and function of a highly proficient ketosteroid isomerase from Pseudomonas putida biotype B.,Kim DH, Jang DS, Nam GH, Choi G, Kim JS, Ha NC, Kim MS, Oh BH, Choi KY Biochemistry. 2000 Apr 25;39(16):4581-9. PMID:10769113<ref>PMID:10769113</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1dmn" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ketosteroid Isomerase|Ketosteroid Isomerase]]
*[[Ketosteroid Isomerase|Ketosteroid Isomerase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus fluorescens putidus flugge 1886]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Steroid Delta-isomerase]]
[[Category: Pseudomonas putida]]
[[Category: Choi, K Y]]
[[Category: Choi KY]]
[[Category: Jang, D S]]
[[Category: Jang DS]]
[[Category: Kim, D H]]
[[Category: Kim DH]]
[[Category: Nam, G H]]
[[Category: Nam GH]]
[[Category: Oh, B H]]
[[Category: Oh BH]]
[[Category: Closed barrel]]
[[Category: Coneshell]]
[[Category: Curved b-sheet]]
[[Category: Isomerase]]

Latest revision as of 09:56, 7 February 2024

CRYSTAL STRUCTURE OF MUTANT ENZYME Y32F/Y57F OF KETOSTEROID ISOMERASE FROM PSEUDOMONAS PUTIDA BIOTYPE BCRYSTAL STRUCTURE OF MUTANT ENZYME Y32F/Y57F OF KETOSTEROID ISOMERASE FROM PSEUDOMONAS PUTIDA BIOTYPE B

Structural highlights

1dmn is a 1 chain structure with sequence from Pseudomonas putida. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.05Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SDIS_PSEPU

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1dmn, resolution 2.05Å

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