3iix

From Proteopedia

(Difference between revisions)

Revision as of 20:36, 12 April 2023

X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with methionine and 5'deoxyadenosine

Structural highlights

3iix is a 1 chain structure with sequence from Thermotoga maritima MSB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HYDE_THEMA Required for the maturation of the [FeFe]-hydrogenase HydA (By similarity). Catalyzes the reductive cleavage of S-adenosyl-L-methionine (in vitro), suggesting it may contribute to the biosynthesis of an essential sulfur-containing ligand that binds to the hydrogenase active site [2Fe-2S] cluster (PubMed:16137685).[UniProtKB:Q97IK9]^[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

Radical S-adenosine-L-methionine (SAM or AdoMet) proteins are involved in chemically difficult reactions including the synthesis of cofactors, the generation of protein radicals, and the maturation of complex organometallic catalytic sites. In the first and common step of the reaction, a conserved [Fe(4)S(4)] cluster donates an electron to perform the reductive cleavage of AdoMet into methionine and a reactive radical 5'-dA. species. The latter extracts a hydrogen atom from substrate eliciting one of the about 40 reactions so far characterized for this family of proteins. It has been suggested that the radical-generating mechanism differs depending on whether AdoMet is a cofactor or a substrate. It has also been speculated that electron transfer from the [Fe(4)S(4)] cluster to AdoMet is sulfur-based. Here we have used protein crystallography and theoretical calculations to show that regardless whether AdoMet serves as a cofactor or a substrate, the 5'-dA. generating mechanism should be common to the radical SAM proteins studied so far, and that electron transfer is mediated by a unique Fe from the conserved [Fe(4)S(4)] cluster. This unusual electron transfer is determined by the sulfonium ion in AdoMet.

Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins.,Nicolet Y, Amara P, Mouesca JM, Fontecilla-Camps JC Proc Natl Acad Sci U S A. 2009 Aug 17. PMID:19706452^[2]

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

References

↑ Rubach JK, Brazzolotto X, Gaillard J, Fontecave M. Biochemical characterization of the HydE and HydG iron-only hydrogenase maturation enzymes from Thermatoga maritima. FEBS Lett. 2005 Sep 12;579(22):5055-60. PMID:16137685 doi:http://dx.doi.org/10.1016/j.febslet.2005.07.092
↑ Nicolet Y, Amara P, Mouesca JM, Fontecilla-Camps JC. Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins. Proc Natl Acad Sci U S A. 2009 Aug 17. PMID:19706452

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3iix"

@@ Line 3: / Line 3: @@
 <StructureSection load='3iix' size='340' side='right'caption='[[3iix]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3iix]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IIX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3iix]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IIX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=OTY:2-HYDROXY-L-TYROSINE'>OTY</scene>, <scene name='pdbligand=S3H:TRISULFANE'>S3H</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=OTY:2-HYDROXY-L-TYROSINE'>OTY</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ciw|3ciw]], [[3cix|3cix]], [[3iiz|3iiz]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TM_1269 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</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=3iix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iix OCA], [https://pdbe.org/3iix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iix RCSB], [https://www.ebi.ac.uk/pdbsum/3iix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iix ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/HYDE_THEMA HYDE_THEMA] Required for the maturation of the [FeFe]-hydrogenase HydA (By similarity). Catalyzes the reductive cleavage of S-adenosyl-L-methionine (in vitro), suggesting it may contribute to the biosynthesis of an essential sulfur-containing ligand that binds to the hydrogenase active site [2Fe-2S] cluster (PubMed:16137685).[UniProtKB:Q97IK9]<ref>PMID:16137685</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 43589]]
 [[Category: Large Structures]]
-[[Category: Amara, P]]
+[[Category: Thermotoga maritima MSB8]]
-[[Category: Fontecilla-Camps, J C]]
+[[Category: Amara P]]
-[[Category: Mouesca, J M]]
+[[Category: Fontecilla-Camps JC]]
-[[Category: Nicolet, Y]]
+[[Category: Mouesca JM]]
-[[Category: Adomet binding protein]]
+[[Category: Nicolet Y]]
-[[Category: Adomet cleavage]]
-[[Category: Adomet radical]]
-[[Category: Beta barrel]]
-[[Category: Deoxyadenosine]]
-[[Category: Fe4s4 cluster]]
-[[Category: Hyde]]
-[[Category: Hydrogenase]]
-[[Category: Maturation]]
-[[Category: Sam radical]]

3iix

From Proteopedia

Revision as of 20:36, 12 April 2023

X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with methionine and 5'deoxyadenosine

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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