4cfs

From Proteopedia

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Current revision

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) CATALYTICALLY INACTIVE H251A VARIANT COMPLEXED WITH ITS NATURAL SUBSTRATE 1-H-3-HYDROXY-4- OXOQUINALDINE

Structural highlights

4cfs is a 4 chain structure with sequence from Paenarthrobacter nitroguajacolicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.94Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HOD_PAENT Ring-cleaving dioxygenase involved in quinaldine degradation and utilization.^[1]

Publication Abstract from PubMed

Dioxygenases catalyze a diverse range of chemical reactions that involve the incorporation of oxygen into a substrate and typically use a transition metal or organic cofactor for reaction. Bacterial 1-H-3- hydroxy-4-oxoquinaldine-2,4-dioxygenase (HOD) belongs to a class of oxygenases able to catalyze this energetically unfavourable reaction without any cofactor. In the quinaldine metabolic pathway HOD breaks down its natural N-heteroaromatic substrate using a mechanism that is still incompletely understood. Experimental and computational approaches were combined to study the initial step of the catalytic cycle. We have investigated the role of the active site His251/Asp126 dyad, proposed to be involved in substrate hydroxyl group deprotonation, a critical requirement for subsequent oxygen reaction. The pH profiles obtained under steady-state conditions for the H251A and D126A variants show a strong pH effect on their kcat and kcat/Km constants, with a decrease in kcat/Km of 5500-fold and 9-fold at pH 10.5, respectively. Substrate deprotonation studies under transient-state conditions show that this step is not rate limiting and yield a pKa value of ~7.2 for wt HOD. A large solvent isotope effect was found and the pKa value was shifted to ~8.3 in D2O. Crystallographic and computational studies reveal that the mutations have minor effect on substrate positioning. Computational work shows that both His251 and Asp126 are essential for the proton transfer driving force of the initial reaction. This multi-disciplinary study offers unambiguous support to the view that substrate deprotonation, driven by the His/Asp dyad, is an essential requirement for its activation.

Origin of the proton-transfer step in the cofactor-free 1-H-3-hydroxy-4-oxoquinaldine 2,4- dioxygenase: Effect of the basicity of an active site His residue.,Hernandez-Ortega A, Quesne MG, Bui S, Heuts DP, Steiner RA, Heyes DJ, de Visser SP, Scrutton NS J Biol Chem. 2014 Jan 30. PMID:24482238^[2]

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

References

↑ Betz A, Facey SJ, Hauer B, Tshisuaka B, Lingens F. Molecular cloning, sequencing, expression, and site-directed mutagenesis of the 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase gene from Arthrobacter spec. Ru61a. J Basic Microbiol. 2000;40(1):7-23. PMID:10746195
↑ Hernandez-Ortega A, Quesne MG, Bui S, Heuts DP, Steiner RA, Heyes DJ, de Visser SP, Scrutton NS. Origin of the proton-transfer step in the cofactor-free 1-H-3-hydroxy-4-oxoquinaldine 2,4- dioxygenase: Effect of the basicity of an active site His residue. J Biol Chem. 2014 Jan 30. PMID:24482238 doi:http://dx.doi.org/10.1074/jbc.M113.543033

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4cfs"

Categories: Large Structures | Paenarthrobacter nitroguajacolicus | Bui S | Steiner RA

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) CATALYTICALLY INACTIVE H251A VARIANT COMPLEXED WITH ITS NATURAL SUBSTRATE 1-H-3-HYDROXY-4- OXOQUINALDINE==
-<StructureSection load='4cfs' size='340' side='right' caption='[[4cfs]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
+<StructureSection load='4cfs' size='340' side='right'caption='[[4cfs]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4cfs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Artnt Artnt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CFS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CFS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4cfs]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenarthrobacter_nitroguajacolicus Paenarthrobacter nitroguajacolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CFS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HQD:3-HYDROXY-2-METHYLQUINOLIN-4(1H)-ONE'>HQD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</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]] 1.94&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxy-2-methylquinolin-4-one_2,4-dioxygenase 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.48 1.13.11.48] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HQD:3-HYDROXY-2-METHYLQUINOLIN-4(1H)-ONE'>HQD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4cfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cfs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cfs RCSB], [http://www.ebi.ac.uk/pdbsum/4cfs PDBsum]</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=4cfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cfs OCA], [https://pdbe.org/4cfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cfs RCSB], [https://www.ebi.ac.uk/pdbsum/4cfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cfs ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HOD_ARTNT HOD_ARTNT]] Ring-cleaving dioxygenase involved in quinaldine degradation and utilization.<ref>PMID:10746195</ref>
+[https://www.uniprot.org/uniprot/HOD_PAENT HOD_PAENT] Ring-cleaving dioxygenase involved in quinaldine degradation and utilization.<ref>PMID:10746195</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4cfs" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase]]
+[[Category: Large Structures]]
-[[Category: Artnt]]
+[[Category: Paenarthrobacter nitroguajacolicus]]
-[[Category: Bui, S]]
+[[Category: Bui S]]
-[[Category: Steiner, R A]]
+[[Category: Steiner RA]]
-[[Category: Alpha-beta hydrolase complex]]
-[[Category: Cofactor-devoid]]
-[[Category: Dioxygenase]]
-[[Category: Oxidoreductase]]

4cfs

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) CATALYTICALLY INACTIVE H251A VARIANT COMPLEXED WITH ITS NATURAL SUBSTRATE 1-H-3-HYDROXY-4- OXOQUINALDINE

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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