3bjp: Difference between revisions

Latest revision as of 14:47, 1 November 2023

Urate oxidase cyanide uric acid ternary complex

Structural highlights

3bjp is a 1 chain structure with sequence from Aspergillus flavus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	ACE, CYN, NA, URC
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

URIC_ASPFL Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.

Evolutionary Conservation

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

Publication Abstract from PubMed

BACKGROUND: Urate oxidase (EC 1.7.3.3 or UOX) catalyzes the conversion of uric acid and gaseous molecular oxygen to 5-hydroxyisourate and hydrogen peroxide, in the absence of cofactor or particular metal cation. The functional enzyme is a homo-tetramer with four active sites located at dimeric interfaces. RESULTS: The catalytic mechanism was investigated through a ternary complex formed between the enzyme, uric acid, and cyanide that stabilizes an intermediate state of the reaction. When uric acid is replaced by a competitive inhibitor, no complex with cyanide is formed. CONCLUSION: The X-ray structure of this compulsory ternary complex led to a number of mechanistic evidences that support a sequential mechanism in which the two reagents, dioxygen and a water molecule, process through a common site located 3.3 A above the mean plane of the ligand. This site is built by the side chains of Asn 254, and Thr 57, two conserved residues belonging to two different subunits of the homo-tetramer. The absence of a ternary complex between the enzyme, a competitive inhibitor, and cyanide suggests that cyanide inhibits the hydroxylation step of the reaction, after the initial formation of a hydroperoxyde type intermediate.

Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: mechanistic implications.,Gabison L, Prange T, Colloc'h N, El Hajji M, Castro B, Chiadmi M BMC Struct Biol. 2008 Jul 20;8:32. PMID:18638417^[1]

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

References

↑ Gabison L, Prange T, Colloc'h N, El Hajji M, Castro B, Chiadmi M. Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: mechanistic implications. BMC Struct Biol. 2008 Jul 20;8:32. PMID:18638417 doi:10.1186/1472-6807-8-32

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OCA

[1] Gabison L, Prange T, Colloc'h N, El Hajji M, Castro B, Chiadmi M. Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: mechanistic implications. BMC Struct Biol. 2008 Jul 20;8:32. PMID:18638417 doi:10.1186/1472-6807-8-32

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='3bjp' size='340' side='right'caption='[[3bjp]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bjp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspfl Aspfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BJP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3BJP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bjp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BJP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BJP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=URC:URIC+ACID'>URC</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]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1r4s|1r4s]], [[1r4u|1r4u]], [[1r51|1r51]], [[1r56|1r56]], [[1wrr|1wrr]], [[1ws2|1ws2]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=URC:URIC+ACID'>URC</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </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=3bjp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bjp OCA], [https://pdbe.org/3bjp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bjp RCSB], [https://www.ebi.ac.uk/pdbsum/3bjp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bjp ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3bjp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bjp OCA], [http://pdbe.org/3bjp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bjp RCSB], [http://www.ebi.ac.uk/pdbsum/3bjp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bjp ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/URIC_ASPFL URIC_ASPFL]] Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.
+[https://www.uniprot.org/uniprot/URIC_ASPFL URIC_ASPFL] Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 31: @@
 ==See Also==
-*[[Urate Oxidase|Urate Oxidase]]
+*[[Urate oxidase 3D structures|Urate oxidase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Aspfl]]
+[[Category: Aspergillus flavus]]
-[[Category: Factor independent urate hydroxylase]]
 [[Category: Large Structures]]
-[[Category: Castro, B]]
+[[Category: Castro B]]
-[[Category: Chiadmi, M]]
+[[Category: Chiadmi M]]
-[[Category: Gabison, L]]
+[[Category: Colloc'h N]]
-[[Category: Hajji, M El]]
+[[Category: El Hajji M]]
-[[Category: Prange, T]]
+[[Category: Gabison L]]
-[[Category: H, N Colloc]]
+[[Category: Prange T]]
-[[Category: Acetylation]]
-[[Category: Cyanide]]
-[[Category: Degradation mechanism]]
-[[Category: Inhibition]]
-[[Category: Oxidoreductase]]
-[[Category: Peroxisome]]
-[[Category: Purine metabolism]]
-[[Category: Uric acid]]

3bjp: Difference between revisions

Latest revision as of 14:47, 1 November 2023

Urate oxidase cyanide uric acid ternary complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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