1cqs: Difference between revisions

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~~[[Image:1cqs.gif|left|200px]]~~

~~{{Structure~~

==CRYSTAL STRUCTURE OF D103E MUTANT WITH EQUILENINEOF KSI IN PSEUDOMONAS PUTIDA==

~~|PDB~~= 1cqs ~~|SIZE~~=~~350|CAPTION~~= ~~<scene name~~='~~initialview01'>~~1cqs~~</scene>~~, resolution 1.90Å

~~|SITE~~=

== Structural highlights ==

~~|LIGAND~~= ~~<scene name~~=~~'pdbligand~~=~~EQU:EQUILENIN'~~>~~EQU~~<~~/scene~~>

<table><tr><td colspan='2'>[[1cqs]] is a 2 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=1CQS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CQS FirstGlance]. <br>

~~|ACTIVITY=~~ <~~span class~~='~~plainlinks~~'>[~~http~~://en.wikipedia.org/wiki/~~Steroid_Delta-isomerase Steroid Delta-isomerase~~]~~, with EC number~~ [http://~~www~~.~~brenda-enzymes~~.~~info~~/~~php~~/~~result_flat.php4~~?~~ecno~~=5.3.3.~~1 5~~.~~3.3.1~~] </~~span~~>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr>

|~~GENE=~~

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EQU:EQUILENIN'>EQU</scene></td></tr>

~~|DOMAIN~~=

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cqs OCA], [https://pdbe.org/1cqs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cqs RCSB], [https://www.ebi.ac.uk/pdbsum/1cqs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cqs ProSAT]</span></td></tr>

~~|RELATEDENTRY~~=[[~~1opy~~|~~1OPY~~]]

</table>

~~|RESOURCES~~=<span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1cqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cqs OCA], [~~http~~://www.ebi.ac.uk/pdbsum/1cqs PDBsum], [~~http~~://www.~~rcsb~~.org/~~pdb~~/~~explore~~.do?~~structureId~~=1cqs ~~RCSB~~]</~~span~~>

== Function ==

}}

[https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_PSEPU]

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Check<jmol>

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cq/1cqs_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=1cqs ConSurf].

~~'''CRYSTAL STRUCTURE OF D103E MUTANT WITH EQUILENINEOF KSI IN PSEUDOMONAS PUTIDA'''~~

==See Also==

*[[Ketosteroid Isomerase|Ketosteroid Isomerase]]

__TOC__

==~~Overview~~==

</StructureSection>

Delta 5-3-ketosteroid isomerase (KSI) catalyzes the allylic isomerization of Delta 5-3-ketosteroids at a rate approaching the diffusion limit by an intramolecular transfer of a proton. Despite the extensive studies on the catalytic mechanism, it still remains controversial whether the catalytic residue Asp-99 donates a hydrogen bond to the steroid or to Tyr-14. To clarify the role of Asp-99 in the catalysis, two single mutants of D99E and D99L and three double mutants of Y14F/D99E, Y14F/D99N, and Y14F/D99L have been prepared by site-directed mutagenesis. The D99E mutant whose side chain at position 99 is longer by an additional methylene group exhibits nearly the same kcat as the wild-type while the D99L mutant exhibits ca. 125-fold lower kcat than that of the wild-type. The mutations made at positions 14 and 99 exert synergistic or partially additive effect on kcat in the double mutants, which is inconsistent with the mechanism based on the hydrogen-bonded catalytic dyad, Asp-99 COOH...Tyr-14 OH...C3-O of the steroid. The crystal structure of D99E/D38N complexed with equilenin, an intermediate analogue, at 1.9 A resolution reveals that the distance between Tyr-14 O eta and Glu-99 O epsilon is ca. 4.2 A, which is beyond the range for a hydrogen bond, and that the distance between Glu-99 O epsilon and C3-O of the steroid is maintained to be ca. 2.4 A, short enough for a hydrogen bond to be formed. Taken together, these results strongly support the idea that Asp-99 contributes to the catalysis by donating a hydrogen bond directly to the intermediate.

[[Category: Large Structures]]

~~==About this Structure==~~

~~1CQS is a~~ [[~~Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida~~]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CQS OCA~~].

~~==Reference==~~

Asp-99 donates a hydrogen bond not to Tyr-14 but to the steroid directly in the catalytic mechanism of Delta 5-3-ketosteroid isomerase from Pseudomonas putida biotype B., Choi G, Ha NC, Kim SW, Kim DH, Park S, Oh BH, Choi KY, Biochemistry. 2000 Feb 8;39(5):903-9. PMID:[~~http~~:~~//www.ncbi.nlm.nih.gov/pubmed/10653633 10653633~~]

[[Category: Pseudomonas putida]]

~~[[Category: Single protein]]~~

[[Category: Choi G]]

~~[[Category: Steroid Delta-isomerase]]~~

[[Category: Choi KY]]

[[Category: Choi, G.]]

[[Category: Ha NC]]

[[Category: Choi~~, K Y.~~]]

[[Category: Kim DH]]

[[Category: Ha~~, N C.~~]]

[[Category: Kim SW]]

[[Category: Kim~~, D H.~~]]

[[Category: Oh BH]]

[[Category: Kim~~, S W.~~]]

[[Category: Park S]]

[[Category: Oh~~, B H.~~]]

[[Category: Park, S.]]

~~[[Category: equilenin]]~~

~~[[Category: ksi]]~~

~~[[Category: putida lbhb]]~~

~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:26:43 2008''~~

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@@ Line 1: / Line 1: @@
-[[Image:1cqs.gif|left|200px]]
- {{Structure
+==CRYSTAL STRUCTURE OF D103E MUTANT WITH EQUILENINEOF KSI IN PSEUDOMONAS PUTIDA==
-|PDB= 1cqs |SIZE=350|CAPTION= <scene name='initialview01'>1cqs</scene>, resolution 1.90&Aring;
+<StructureSection load='1cqs' size='340' side='right'caption='[[1cqs]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=EQU:EQUILENIN'>EQU</scene>
+<table><tr><td colspan='2'>[[1cqs]] is a 2 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=1CQS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CQS FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EQU:EQUILENIN'>EQU</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cqs OCA], [https://pdbe.org/1cqs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cqs RCSB], [https://www.ebi.ac.uk/pdbsum/1cqs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cqs ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1opy|1OPY]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1cqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cqs OCA], [http://www.ebi.ac.uk/pdbsum/1cqs PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1cqs RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_PSEPU]
+== 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/cq/1cqs_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=1cqs ConSurf].
+<div style="clear:both"></div>
-'''CRYSTAL STRUCTURE OF D103E MUTANT WITH EQUILENINEOF KSI IN PSEUDOMONAS PUTIDA'''
+==See Also==
+*[[Ketosteroid Isomerase|Ketosteroid Isomerase]]
+__TOC__
-==Overview==
+</StructureSection>
-Delta 5-3-ketosteroid isomerase (KSI) catalyzes the allylic isomerization of Delta 5-3-ketosteroids at a rate approaching the diffusion limit by an intramolecular transfer of a proton. Despite the extensive studies on the catalytic mechanism, it still remains controversial whether the catalytic residue Asp-99 donates a hydrogen bond to the steroid or to Tyr-14. To clarify the role of Asp-99 in the catalysis, two single mutants of D99E and D99L and three double mutants of Y14F/D99E, Y14F/D99N, and Y14F/D99L have been prepared by site-directed mutagenesis. The D99E mutant whose side chain at position 99 is longer by an additional methylene group exhibits nearly the same kcat as the wild-type while the D99L mutant exhibits ca. 125-fold lower kcat than that of the wild-type. The mutations made at positions 14 and 99 exert synergistic or partially additive effect on kcat in the double mutants, which is inconsistent with the mechanism based on the hydrogen-bonded catalytic dyad, Asp-99 COOH...Tyr-14 OH...C3-O of the steroid. The crystal structure of D99E/D38N complexed with equilenin, an intermediate analogue, at 1.9 A resolution reveals that the distance between Tyr-14 O eta and Glu-99 O epsilon is ca. 4.2 A, which is beyond the range for a hydrogen bond, and that the distance between Glu-99 O epsilon and C3-O of the steroid is maintained to be ca. 2.4 A, short enough for a hydrogen bond to be formed. Taken together, these results strongly support the idea that Asp-99 contributes to the catalysis by donating a hydrogen bond directly to the intermediate.
+[[Category: Large Structures]]
-==About this Structure==
-CQS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CQS OCA].
-==Reference==
-Asp-99 donates a hydrogen bond not to Tyr-14 but to the steroid directly in the catalytic mechanism of Delta 5-3-ketosteroid isomerase from Pseudomonas putida biotype B., Choi G, Ha NC, Kim SW, Kim DH, Park S, Oh BH, Choi KY, Biochemistry. 2000 Feb 8;39(5):903-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10653633 10653633]
 [[Category: Pseudomonas putida]]
-[[Category: Single protein]]
+[[Category: Choi G]]
-[[Category: Steroid Delta-isomerase]]
+[[Category: Choi KY]]
-[[Category: Choi, G.]]
+[[Category: Ha NC]]
-[[Category: Choi, K Y.]]
+[[Category: Kim DH]]
-[[Category: Ha, N C.]]
+[[Category: Kim SW]]
-[[Category: Kim, D H.]]
+[[Category: Oh BH]]
-[[Category: Kim, S W.]]
+[[Category: Park S]]
-[[Category: Oh, B H.]]
-[[Category: Park, S.]]
-[[Category: equilenin]]
-[[Category: ksi]]
-[[Category: putida lbhb]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:26:43 2008''