This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4u0p

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine

Structural highlights

4u0p is a 1 chain structure with sequence from Thermosynechococcus vestitus BP-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.623Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LIPA2_THEVB Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives.[HAMAP-Rule:MF_00206]

Publication Abstract from PubMed

Lipoyl cofactors are essential for living organisms and are produced by the insertion of two sulfur atoms into the relatively unreactive C-H bonds of an octanoyl substrate. This reaction requires lipoyl synthase, a member of the radical SAM enzyme superfamily. Herein we present crystal structures of lipoyl synthase with two [4Fe-4S] clusters bound at opposite ends of the TIM barrel, the usual fold of the radical SAM superfamily. The cluster required for reductive SAM cleavage conserves the features of the radical SAM superfamily, but the auxiliary cluster is bound by a CX4CX5C motif unique to lipoyl synthase. The fourth ligand to the auxiliary cluster is an extremely unusual serine residue. Site directed mutants show this conserved serine ligand is essential for the sulfur insertion steps. One crystallized LipA complex contains MTA, a breakdown product of SAM, bound in the likely SAM binding site. Modelling has identified an 18 A deep channel, well-proportioned to accommodate an octanoyl substrate. These results suggest the auxiliary cluster is the likely sulfur donor, but access to a sulfide ion for the second sulfur insertion reaction requires the loss of an iron atom from the auxiliary cluster, which the serine ligand may enabled.

Structures of lipoyl synthase reveal a compact active site for controlling sequential sulfur insertion reactions.,Harmer JE, Hiscox MJ, Dinis PC, Fox SJ, Iliopoulos A, Hussey JE, Sandy J, Van Beek FT, Essex JW, Roach PL Biochem J. 2014 Aug 6. PMID:25100160^[1]

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

References

↑ Harmer JE, Hiscox MJ, Dinis PC, Fox SJ, Iliopoulos A, Hussey JE, Sandy J, Van Beek FT, Essex JW, Roach PL. Structures of lipoyl synthase reveal a compact active site for controlling sequential sulfur insertion reactions. Biochem J. 2014 Aug 6. PMID:25100160 doi:http://dx.doi.org/10.1042/BJ20140895

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/4u0p"

@@ Line 1: / Line 1: @@
 ==The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine==
-<StructureSection load='4u0p' size='340' side='right' caption='[[4u0p]], [[Resolution|resolution]] 1.62&Aring;' scene=''>
+<StructureSection load='4u0p' size='340' side='right'caption='[[4u0p]], [[Resolution|resolution]] 1.62&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4u0p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U0P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4u0p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4U0P FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.623&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lipoyl_synthase Lipoyl synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.8.1.8 2.8.1.8] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=4u0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4u0p RCSB], [http://www.ebi.ac.uk/pdbsum/4u0p 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=4u0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0p OCA], [https://pdbe.org/4u0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4u0p RCSB], [https://www.ebi.ac.uk/pdbsum/4u0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4u0p ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LIPA2_THEVB LIPA2_THEVB] Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives.[HAMAP-Rule:MF_00206]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 15: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4u0p" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Lipoyl synthase]]
+[[Category: Large Structures]]
-[[Category: Dinis, P C.]]
+[[Category: Thermosynechococcus vestitus BP-1]]
-[[Category: Harmer, J E.]]
+[[Category: Dinis PC]]
-[[Category: Hiscox, M J.]]
+[[Category: Harmer JE]]
-[[Category: Roach, P L.]]
+[[Category: Hiscox MJ]]
-[[Category: Sandy, J.]]
+[[Category: Roach PL]]
-[[Category: Fes cluster]]
+[[Category: Sandy J]]
-[[Category: Radical sam]]
-[[Category: Thiotransferase]]
-[[Category: Tim barrel]]
-[[Category: Transferase]]

4u0p

From Proteopedia

Current revision

The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox