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.

4wcx

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of HydG: A maturase of the [FeFe]-hydrogenase

Structural highlights

4wcx is a 2 chain structure with sequence from Thermoanaerobacter italicus Ab9. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.59Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

D3T7F1_THEIA

Publication Abstract from PubMed

Hydrogenases use complex metal cofactors to catalyze the reversible formation of hydrogen. In [FeFe]-hydrogenases, the H-cluster cofactor includes a diiron subcluster containing azadithiolate, three CO, and two CN(-) ligands. During the assembly of the H cluster, the radical S-adenosyl methionine (SAM) enzyme HydG lyses the substrate tyrosine to yield the diatomic ligands. These diatomic products form an enzyme-bound Fe(CO)x(CN)y synthon that serves as a precursor for eventual H-cluster assembly. To further elucidate the mechanism of this complex reaction, we report the crystal structure and EPR analysis of HydG. At one end of the HydG (betaalpha)8 triosephosphate isomerase (TIM) barrel, a canonical [4Fe-4S] cluster binds SAM in close proximity to the proposed tyrosine binding site. At the opposite end of the active-site cavity, the structure reveals the auxiliary Fe-S cluster in two states: one monomer contains a [4Fe-5S] cluster, and the other monomer contains a [5Fe-5S] cluster consisting of a [4Fe-4S] cubane bridged by a mu2-sulfide ion to a mononuclear Fe(2+) center. This fifth iron is held in place by a single highly conserved protein-derived ligand: histidine 265. EPR analysis confirms the presence of the [5Fe-5S] cluster, which on incubation with cyanide, undergoes loss of the labile iron to yield a [4Fe-4S] cluster. We hypothesize that the labile iron of the [5Fe-5S] cluster is the site of Fe(CO)x(CN)y synthon formation and that the limited bonding between this iron and HydG may facilitate transfer of the intact synthon to its cognate acceptor for subsequent H-cluster assembly.

X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase H-cluster assembly.,Dinis P, Suess DL, Fox SJ, Harmer JE, Driesener RC, De La Paz L, Swartz JR, Essex JW, Britt RD, Roach PL Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):1362-7. doi: 10.1073/pnas.1417252112., Epub 2015 Jan 20. PMID:25605932^[1]

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

References

↑ Dinis P, Suess DL, Fox SJ, Harmer JE, Driesener RC, De La Paz L, Swartz JR, Essex JW, Britt RD, Roach PL. X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase H-cluster assembly. Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):1362-7. doi: 10.1073/pnas.1417252112., Epub 2015 Jan 20. PMID:25605932 doi:http://dx.doi.org/10.1073/pnas.1417252112

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/4wcx"

@@ Line 1: / Line 1: @@
 ==Crystal structure of HydG: A maturase of the [FeFe]-hydrogenase==
-<StructureSection load='4wcx' size='340' side='right' caption='[[4wcx]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
+<StructureSection load='4wcx' size='340' side='right'caption='[[4wcx]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4wcx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WCX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WCX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4wcx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacter_italicus_Ab9 Thermoanaerobacter italicus Ab9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WCX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WCX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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]] 1.59&#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=4wcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wcx OCA], [http://pdbe.org/4wcx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wcx RCSB], [http://www.ebi.ac.uk/pdbsum/4wcx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wcx ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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'>[https://proteopedia.org/fgij/fg.htm?mol=4wcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wcx OCA], [https://pdbe.org/4wcx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wcx RCSB], [https://www.ebi.ac.uk/pdbsum/4wcx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wcx ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/D3T7F1_THEIA D3T7F1_THEIA]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Dinis, P C]]
+[[Category: Large Structures]]
-[[Category: Driesener, R C]]
+[[Category: Thermoanaerobacter italicus Ab9]]
-[[Category: Harmer, J E]]
+[[Category: Dinis PC]]
-[[Category: Roach, P L]]
+[[Category: Driesener RC]]
-[[Category: Lyase]]
+[[Category: Harmer JE]]
-[[Category: Maturase]]
+[[Category: Roach PL]]

4wcx

From Proteopedia

Current revision

Crystal structure of HydG: A maturase of the [FeFe]-hydrogenase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox