3qyh: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older editNewer edit →
No edit summary
No edit summary
Line 3: Line 3:
<StructureSection load='3qyh' size='340' side='right'caption='[[3qyh]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3qyh' size='340' side='right'caption='[[3qyh]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3qyh]] is a 8 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=3QYH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QYH FirstGlance]. <br>
<table><tr><td colspan='2'>[[3qyh]] is a 8 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=3QYH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QYH FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3CO:COBALT+(III)+ION'>3CO</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&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3CO:COBALT+(III)+ION'>3CO</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</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;'>[[3qxe|3qxe]], [[3qyg|3qyg]], [[3qz9|3qz9]], [[3qz5|3qz5]]</div></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=3qyh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyh OCA], [https://pdbe.org/3qyh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qyh RCSB], [https://www.ebi.ac.uk/pdbsum/3qyh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyh 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=3qyh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyh OCA], [https://pdbe.org/3qyh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qyh RCSB], [https://www.ebi.ac.uk/pdbsum/3qyh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyh ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell and these in turn interact with residues in a third shell. These residues in the second and third layers may have distinct roles in maintaining the essential chemical properties of the first-shell catalytic residues, particularly their spatial arrangement relative to the substrate binding pocket, and their electrostatic and dynamic properties. The extent to which these remote residues participate in catalysis and precisely how they affect first-shell residues remains unexplored. To improve our understanding of the roles of second- and third-shell residues in catalysis, we used THEMATICS to identify residues in the second and third shells of the Co-type nitrile hydratase from Pseudomonas putida (ppNHase) that may be important for catalysis. Five of these predicted residues, and three additional, conserved residues that were not predicted, have been conservatively mutated, and their effects have been studied both kinetically and structurally. The eight residues have no direct contact with the active site metal ion or bound substrate. These results demonstrate that three of the predicted second-shell residues (alpha-Asp164, beta-Glu56, and beta-His147) and one predicted third-shell residue (beta-His71) have significant effects on the catalytic efficiency of the enzyme. One of the predicted residues (alpha-Glu168) and the three residues not predicted (alpha-Arg170, alpha-Tyr171, and beta-Tyr215) do not have any significant effects on the catalytic efficiency of the enzyme.
Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida.,Brodkin HR, Novak WR, Milne AC, D'Aquino JA, Karabacak NM, Goldberg IG, Agar JN, Payne MS, Petsko GA, Ondrechen MJ, Ringe D Biochemistry. 2011 Jun 7;50(22):4923-35. Epub 2011 May 12. PMID:21473592<ref>PMID:21473592</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3qyh" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Nitrile hydratase|Nitrile hydratase]]
*[[Nitrile hydratase|Nitrile hydratase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus fluorescens putidus flugge 1886]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Brodkin, H R]]
[[Category: Pseudomonas putida]]
[[Category: Novak, W R.P]]
[[Category: Brodkin HR]]
[[Category: Petsko, G A]]
[[Category: Novak WRP]]
[[Category: Ringe, D]]
[[Category: Petsko GA]]
[[Category: Co]]
[[Category: Ringe D]]
[[Category: Cobalt]]
[[Category: Cysteine sulfinic acid]]
[[Category: Lyase]]
[[Category: Nitrile hydratase]]

Revision as of 15:03, 14 March 2024

Crystal Structure of Co-type Nitrile Hydratase beta-H71L from Pseudomonas putida.Crystal Structure of Co-type Nitrile Hydratase beta-H71L from Pseudomonas putida.

Structural highlights

3qyh is a 8 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 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

3qyh, resolution 2.00Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=3qyh&oldid=4096190"