3unc: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older editNewer edit →
No edit summary
No edit summary
Line 1: Line 1:
[[Image:3unc.jpg|left|200px]]
==Crystal Structure of Bovine Milk Xanthine Dehydrogenase to 1.65A Resolution==
<StructureSection load='3unc' size='340' side='right' caption='[[3unc]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3unc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UNC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UNC FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MOS:DIOXOTHIOMOLYBDENUM(VI)+ION'>MOS</scene>, <scene name='pdbligand=MTE:PHOSPHONIC+ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER'>MTE</scene>, <scene name='pdbligand=SAL:2-HYDROXYBENZOIC+ACID'>SAL</scene><br>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fo4|1fo4]], [[3una|3una]], [[3uni|3uni]]</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3unc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3unc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3unc RCSB], [http://www.ebi.ac.uk/pdbsum/3unc PDBsum]</span></td></tr>
<table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In mammals, xanthine oxidoreductase can exist as xanthine dehydrogenase (XDH) and xanthine oxidase (XO). The two enzymes possess common redox active cofactors, which form an electron transfer (ET) pathway terminated by a flavin cofactor. In spite of identical protein primary structures, the redox potential difference between XDH and XO for the flavin semiquinone/hydroquinone pair (E(sq/hq)) is ~170 mV, a striking difference. The former greatly prefers NAD(+) as ultimate substrate for ET from the iron-sulfur cluster FeS-II via flavin while the latter only accepts dioxygen. In XDH (without NAD(+)), however, the redox potential of the electron donor FeS-II is 180 mV higher than that for the acceptor flavin, yielding an energetically uphill ET. On the basis of new 1.65, 2.3, 1.9, and 2.2 A resolution crystal structures for XDH, XO, the NAD(+)- and NADH-complexed XDH, E(sq/hq) were calculated to better understand how the enzyme activates an ET from FeS-II to flavin. The majority of the E(sq/hq) difference between XDH and XO originates from a conformational change in the loop at positions 423-433 near the flavin binding site, causing the differences in stability of the semiquinone state. There was no large conformational change observed in response to NAD(+) binding at XDH. Instead, the positive charge of the NAD(+) ring, deprotonation of Asp429, and capping of the bulk surface of the flavin by the NAD(+) molecule all contribute to altering E(sq/hq) upon NAD(+) binding to XDH.


<!--
Protein conformational gating of enzymatic activity in xanthine oxidoreductase.,Ishikita H, Eger BT, Okamoto K, Nishino T, Pai EF J Am Chem Soc. 2012 Jan 18;134(2):999-1009. Epub 2011 Dec 29. PMID:22145797<ref>PMID:22145797</ref>
The line below this paragraph, containing "STRUCTURE_3unc", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_3unc|  PDB=3unc  |  SCENE=  }}


===Crystal Structure of Bovine Milk Xanthine Dehydrogenase to 1.65A Resolution===
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>


 
==See Also==
<!--
*[[Xanthine dehydrogenase|Xanthine dehydrogenase]]
The line below this paragraph, {{ABSTRACT_PUBMED_22145797}}, adds the Publication Abstract to the page
== References ==
(as it appears on PubMed at http://www.pubmed.gov), where 22145797 is the PubMed ID number.
<references/>
-->
__TOC__
{{ABSTRACT_PUBMED_22145797}}
</StructureSection>
 
==About this Structure==
[[3unc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UNC OCA].
 
==Reference==
<ref group="xtra">PMID:022145797</ref><references group="xtra"/>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Eger, B T.]]
[[Category: Eger, B T.]]

Revision as of 08:47, 5 June 2014

Crystal Structure of Bovine Milk Xanthine Dehydrogenase to 1.65A ResolutionCrystal Structure of Bovine Milk Xanthine Dehydrogenase to 1.65A Resolution

Structural highlights

3unc is a 2 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , , , , , ,
Related:1fo4, 3una, 3uni
Resources:FirstGlance, OCA, RCSB, PDBsum

Publication Abstract from PubMed

In mammals, xanthine oxidoreductase can exist as xanthine dehydrogenase (XDH) and xanthine oxidase (XO). The two enzymes possess common redox active cofactors, which form an electron transfer (ET) pathway terminated by a flavin cofactor. In spite of identical protein primary structures, the redox potential difference between XDH and XO for the flavin semiquinone/hydroquinone pair (E(sq/hq)) is ~170 mV, a striking difference. The former greatly prefers NAD(+) as ultimate substrate for ET from the iron-sulfur cluster FeS-II via flavin while the latter only accepts dioxygen. In XDH (without NAD(+)), however, the redox potential of the electron donor FeS-II is 180 mV higher than that for the acceptor flavin, yielding an energetically uphill ET. On the basis of new 1.65, 2.3, 1.9, and 2.2 A resolution crystal structures for XDH, XO, the NAD(+)- and NADH-complexed XDH, E(sq/hq) were calculated to better understand how the enzyme activates an ET from FeS-II to flavin. The majority of the E(sq/hq) difference between XDH and XO originates from a conformational change in the loop at positions 423-433 near the flavin binding site, causing the differences in stability of the semiquinone state. There was no large conformational change observed in response to NAD(+) binding at XDH. Instead, the positive charge of the NAD(+) ring, deprotonation of Asp429, and capping of the bulk surface of the flavin by the NAD(+) molecule all contribute to altering E(sq/hq) upon NAD(+) binding to XDH.

Protein conformational gating of enzymatic activity in xanthine oxidoreductase.,Ishikita H, Eger BT, Okamoto K, Nishino T, Pai EF J Am Chem Soc. 2012 Jan 18;134(2):999-1009. Epub 2011 Dec 29. PMID:22145797[1]

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

See Also

References

  1. ↑ Ishikita H, Eger BT, Okamoto K, Nishino T, Pai EF. Protein conformational gating of enzymatic activity in xanthine oxidoreductase. J Am Chem Soc. 2012 Jan 18;134(2):999-1009. Epub 2011 Dec 29. PMID:22145797 doi:http://dx.doi.org/10.1021/ja207173p

3unc, resolution 1.65Å

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=3unc&oldid=1941370"