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1wyg

From Proteopedia

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Crystal Structure of a Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)

Structural highlights

1wyg is a 1 chain structure with sequence from Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XDH_RAT Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species.^[1]

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

Mammalian xanthine dehydrogenase can be converted to xanthine oxidase by modification of cysteine residues or by proteolysis of the enzyme polypeptide chain. Here we present evidence that the Cys(535) and Cys(992) residues of rat liver enzyme are indeed involved in the rapid conversion from the dehydrogenase to the oxidase. The purified mutants C535A and/or C992R were significantly resistant to conversion by incubation with 4,4'-dithiodipyridine, whereas the recombinant wild-type enzyme converted readily to the oxidase type, indicating that these residues are responsible for the rapid conversion. The C535A/C992R mutant, however, converted very slowly during prolonged incubation with 4,4'-dithiodipyridine, and this slow conversion was blocked by the addition of NADH, suggesting that another cysteine couple located near the NAD(+) binding site is responsible for the slower conversion. On the other hand, the C535A/C992R/C1316S and C535A/C992R/C1324S mutants were completely resistant to conversion, even on prolonged incubation with 4,4'-dithiodipyridine, indicating that Cys(1316) and Cys(1324) are responsible for the slow conversion. The crystal structure of the C535A/C992R/C1324S mutant was determined in its demolybdo form, confirming its dehydrogenase conformation.

Mechanism of the conversion of xanthine dehydrogenase to xanthine oxidase: identification of the two cysteine disulfide bonds and crystal structure of a non-convertible rat liver xanthine dehydrogenase mutant.,Nishino T, Okamoto K, Kawaguchi Y, Hori H, Matsumura T, Eger BT, Pai EF, Nishino T J Biol Chem. 2005 Jul 1;280(26):24888-94. Epub 2005 May 4. PMID:15878860^[2]

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

References

↑ Asai R, Nishino T, Matsumura T, Okamoto K, Igarashi K, Pai EF, Nishino T. Two mutations convert mammalian xanthine oxidoreductase to highly superoxide-productive xanthine oxidase. J Biochem. 2007 Apr;141(4):525-34. Epub 2007 Feb 14. PMID:17301076 doi:10.1093/jb/mvm054
↑ Nishino T, Okamoto K, Kawaguchi Y, Hori H, Matsumura T, Eger BT, Pai EF, Nishino T. Mechanism of the conversion of xanthine dehydrogenase to xanthine oxidase: identification of the two cysteine disulfide bonds and crystal structure of a non-convertible rat liver xanthine dehydrogenase mutant. J Biol Chem. 2005 Jul 1;280(26):24888-94. Epub 2005 May 4. PMID:15878860 doi:10.1074/jbc.M501830200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1wyg"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of a Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)==
-<StructureSection load='1wyg' size='340' side='right' caption='[[1wyg]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='1wyg' size='340' side='right'caption='[[1wyg]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1wyg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WYG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1wyg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WYG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAL:2-HYDROXYBENZOIC+ACID'>SAL</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]] 2.6&#8491;</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=1wyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyg OCA], [http://pdbe.org/1wyg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wyg RCSB], [http://www.ebi.ac.uk/pdbsum/1wyg PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAL:2-HYDROXYBENZOIC+ACID'>SAL</scene></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=1wyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyg OCA], [https://pdbe.org/1wyg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wyg RCSB], [https://www.ebi.ac.uk/pdbsum/1wyg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wyg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/XDH_RAT XDH_RAT]] Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species.<ref>PMID:17301076</ref>
+[https://www.uniprot.org/uniprot/XDH_RAT XDH_RAT] Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species.<ref>PMID:17301076</ref>
 == 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/wy/1wyg_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/1wyg_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 31: @@
 ==See Also==
-*[[Xanthine dehydrogenase|Xanthine dehydrogenase]]
+*[[Xanthine dehydrogenase 3D structures|Xanthine dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Buffalo rat]]
+[[Category: Large Structures]]
-[[Category: Eger, B T]]
+[[Category: Rattus norvegicus]]
-[[Category: Hori, H]]
+[[Category: Eger BT]]
-[[Category: Kawaguchi, Y]]
+[[Category: Hori H]]
-[[Category: Matsumura, T]]
+[[Category: Kawaguchi Y]]
-[[Category: Nishino, T]]
+[[Category: Matsumura T]]
-[[Category: Okamoto, K]]
+[[Category: Nishino T]]
-[[Category: Pai, E F]]
+[[Category: Okamoto K]]
-[[Category: Dehydrogenase to oxidase conversion]]
+[[Category: Pai EF]]
-[[Category: Oxidoreductase]]

1wyg

From Proteopedia

Current revision

Crystal Structure of a Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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