2wp9

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhB His207Thr mutant

Structural highlights

2wp9 is a 12 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:	, , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SDHA_ECOLI Two distinct, membrane-bound, FAD-containing enzymes are responsible for the catalysis of fumarate and succinate interconversion; the fumarate reductase is used in anaerobic growth, and the succinate dehydrogenase is used in aerobic growth.^[1] ^[2] ^[3] ^[4]

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

Succinate-ubiquinone oxidoreductase (SQR) and menaquinol-fumarate oxidoreductase (QFR) from Escherichia coli are members of the complex II family of enzymes. SQR and QFR catalyze similar reactions with quinones, however, SQR preferentially reacts with higher potential ubiquinones and QFR with lower potential napthoquinones. Both enzymes have a single functional quinone-binding site proximal to a [3Fe-4S] iron-sulfur cluster. A difference between SQR and QFR is that the redox potential of the [3Fe-4S] cluster in SQR is 140 mV higher than that found in QFR. This may reflect the character of the different quinones with which the two enzymes preferentially react. To investigate how the environment around the [3Fe-4S] cluster affects its redox properties and catalysis with quinones a conserved amino acid proximal to the cluster was mutated in both enzymes. It was found that substitution of SdhB His207 by threonine (like found in QFR) resulted in a 70 mV lowering of the redox potential of the cluster as measured by EPR. The converse mutation in QFR raised the redox potential of the cluster. X-ray structural analysis suggests that placing a charged residue near the [3Fe-4S] cluster is a primary reason for the alteration in redox potential with the hydrogen-bonding environment having a lesser effect. Steady state enzyme kinetic characterization of the mutant enzymes shows that the redox properties of the [3Fe-4S] cluster has only minor effect on catalysis.

Perturbation of the quinone binding site of complex II alters the electronic properties of the proximal [3Fe-4S] iron-sulfur cluster.,Ruprecht J, Iwata S, Rothery RA, Weiner JH, Maklashina E, Cecchini G J Biol Chem. 2011 Feb 10. PMID:21310949^[5]

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

References

↑ McNeil MB, Hampton HG, Hards KJ, Watson BN, Cook GM, Fineran PC. The succinate dehydrogenase assembly factor, SdhE, is required for the flavinylation and activation of fumarate reductase in bacteria. FEBS Lett. 2014 Jan 31;588(3):414-21. doi: 10.1016/j.febslet.2013.12.019. Epub, 2013 Dec 25. PMID:24374335 doi:http://dx.doi.org/10.1016/j.febslet.2013.12.019
↑ Yankovskaya V, Horsefield R, Tornroth S, Luna-Chavez C, Miyoshi H, Leger C, Byrne B, Cecchini G, Iwata S. Architecture of succinate dehydrogenase and reactive oxygen species generation. Science. 2003 Jan 31;299(5607):700-4. PMID:12560550 doi:10.1126/science.1079605
↑ Horsefield R, Yankovskaya V, Sexton G, Whittingham W, Shiomi K, Omura S, Byrne B, Cecchini G, Iwata S. Structural and computational analysis of the quinone-binding site of complex II (succinate-ubiquinone oxidoreductase): a mechanism of electron transfer and proton conduction during ubiquinone reduction. J Biol Chem. 2006 Mar 17;281(11):7309-16. Epub 2005 Dec 27. PMID:16407191 doi:http://dx.doi.org/10.1074/jbc.M508173200
↑ Ruprecht J, Yankovskaya V, Maklashina E, Iwata S, Cecchini G. Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site. J Biol Chem. 2009 Oct 23;284(43):29836-46. Epub 2009 Aug 25. PMID:19710024 doi:10.1074/jbc.M109.010058
↑ Ruprecht J, Iwata S, Rothery RA, Weiner JH, Maklashina E, Cecchini G. Perturbation of the quinone binding site of complex II alters the electronic properties of the proximal [3Fe-4S] iron-sulfur cluster. J Biol Chem. 2011 Feb 10. PMID:21310949 doi:10.1074/jbc.M110.209874

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/2wp9"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 2wp9 is ON HOLD  until Paper Publication
+==Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhB His207Thr mutant==
+<StructureSection load='2wp9' size='340' side='right'caption='[[2wp9]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2wp9]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WP9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WP9 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBE:2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE'>CBE</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TEO:MALATE+LIKE+INTERMEDIATE'>TEO</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=2wp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wp9 OCA], [https://pdbe.org/2wp9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wp9 RCSB], [https://www.ebi.ac.uk/pdbsum/2wp9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wp9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SDHA_ECOLI SDHA_ECOLI] Two distinct, membrane-bound, FAD-containing enzymes are responsible for the catalysis of fumarate and succinate interconversion; the fumarate reductase is used in anaerobic growth, and the succinate dehydrogenase is used in aerobic growth.<ref>PMID:24374335</ref> <ref>PMID:12560550</ref> <ref>PMID:16407191</ref> <ref>PMID:19710024</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/wp/2wp9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2wp9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Succinate-ubiquinone oxidoreductase (SQR) and menaquinol-fumarate oxidoreductase (QFR) from Escherichia coli are members of the complex II family of enzymes. SQR and QFR catalyze similar reactions with quinones, however, SQR preferentially reacts with higher potential ubiquinones and QFR with lower potential napthoquinones. Both enzymes have a single functional quinone-binding site proximal to a [3Fe-4S] iron-sulfur cluster. A difference between SQR and QFR is that the redox potential of the [3Fe-4S] cluster in SQR is 140 mV higher than that found in QFR. This may reflect the character of the different quinones with which the two enzymes preferentially react. To investigate how the environment around the [3Fe-4S] cluster affects its redox properties and catalysis with quinones a conserved amino acid proximal to the cluster was mutated in both enzymes. It was found that substitution of SdhB His207 by threonine (like found in QFR) resulted in a 70 mV lowering of the redox potential of the cluster as measured by EPR. The converse mutation in QFR raised the redox potential of the cluster. X-ray structural analysis suggests that placing a charged residue near the [3Fe-4S] cluster is a primary reason for the alteration in redox potential with the hydrogen-bonding environment having a lesser effect. Steady state enzyme kinetic characterization of the mutant enzymes shows that the redox properties of the [3Fe-4S] cluster has only minor effect on catalysis.
-Authors: Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.
+Perturbation of the quinone binding site of complex II alters the electronic properties of the proximal [3Fe-4S] iron-sulfur cluster.,Ruprecht J, Iwata S, Rothery RA, Weiner JH, Maklashina E, Cecchini G J Biol Chem. 2011 Feb 10. PMID:21310949<ref>PMID:21310949</ref>
-Description: Crystal structure of the E. coli succinate:quinone oxidoreductase ( SQR) SdhB His207Thr mutant
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2wp9" style="background-color:#fffaf0;"></div>
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 12 12:19:59 2009''
+==See Also==
+*[[Succinate dehydrogenase 3D structures|Succinate dehydrogenase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Cecchini G]]
+[[Category: Iwata S]]
+[[Category: Maklashina E]]
+[[Category: Ruprecht J]]
+[[Category: Yankovskaya V]]

2wp9

From Proteopedia

Current revision

Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhB His207Thr mutant

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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