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.

4omf

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:32, 25 January 2023

The F420-reducing [NiFe]-hydrogenase complex from Methanothermobacter marburgensis, the first X-ray structure of a group 3 family member

Structural highlights

4omf is a 3 chain structure with sequence from Methanothermobacter marburgensis str. Marburg. 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

D9PYF7_METTM

Publication Abstract from PubMed

The reversible redox reaction between coenzyme F420 and H2 to F420H2 is catalyzed by an F420-reducing [NiFe]-hydrogenase (FrhABG), which is an enzyme of the energy metabolism of methanogenic archaea. FrhABG is a group 3 [NiFe]-hydrogenase with a dodecameric quaternary structure of 1.25MDa as recently revealed by high-resolution cryo-electron microscopy. We report on the crystal structure of FrhABG from Methanothermobacter marburgensis at 1.7A resolution and compare it with the structures of group 1 [NiFe]-hydrogenases, the only group structurally characterized yet. FrhA is similar to the large subunit of group 1 [NiFe]-hydrogenases regarding its core structure and the embedded [NiFe]-center but is different because of the truncation of ca 160 residues that results in similar but modified H2 and proton transport pathways and in suitable interfaces for oligomerization. The small subunit FrhG is composed of an N-terminal domain related to group 1 enzymes and a new C-terminal ferredoxin-like domain carrying the distal and medial [4Fe-4S] clusters. FrhB adopts a novel fold, binds one [4Fe-4S] cluster as well as one FAD in a U-shaped conformation and provides the F420-binding site at the Si-face of the isoalloxazine ring. Similar electrochemical potentials of both catalytic reactions and the electron-transferring [4Fe-4S] clusters, determined to be E degrees ' approximately -400mV, are in full agreement with the equalized forward and backward rates of the FrhABG reaction. The protein might contribute to balanced redox potentials by the aspartate coordination of the proximal [4Fe-4S] cluster, the new ferredoxin module and a rather negatively charged FAD surrounding.

The F420-Reducing [NiFe]-Hydrogenase Complex from Methanothermobacter marburgensis, the First X-ray Structure of a Group 3 Family Member.,Vitt S, Ma K, Warkentin E, Moll J, Pierik AJ, Shima S, Ermler U J Mol Biol. 2014 Jul 29;426(15):2813-26. doi: 10.1016/j.jmb.2014.05.024. Epub, 2014 Jun 2. PMID:24887099^[1]

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

References

↑ Vitt S, Ma K, Warkentin E, Moll J, Pierik AJ, Shima S, Ermler U. The F420-Reducing [NiFe]-Hydrogenase Complex from Methanothermobacter marburgensis, the First X-ray Structure of a Group 3 Family Member. J Mol Biol. 2014 Jul 29;426(15):2813-26. doi: 10.1016/j.jmb.2014.05.024. Epub, 2014 Jun 2. PMID:24887099 doi:http://dx.doi.org/10.1016/j.jmb.2014.05.024

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/4omf"

@@ Line 3: / Line 3: @@
 <StructureSection load='4omf' size='340' side='right'caption='[[4omf]], [[Resolution|resolution]] 1.71&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4omf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_marburgensis Methanothermobacter marburgensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OMF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4omf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_marburgensis_str._Marburg Methanothermobacter marburgensis str. Marburg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OMF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DTZ:ZINC(II)HYDROGENSULFIDE'>DTZ</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=KEN:N,N-DIMETHYLMETHANAMINE'>KEN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DTZ:ZINC(II)HYDROGENSULFIDE'>DTZ</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=KEN:N,N-DIMETHYLMETHANAMINE'>KEN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coenzyme_F420_hydrogenase Coenzyme F420 hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.98.1 1.12.98.1] </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=4omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4omf OCA], [https://pdbe.org/4omf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4omf RCSB], [https://www.ebi.ac.uk/pdbsum/4omf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4omf ProSAT]</span></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=4omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4omf OCA], [http://pdbe.org/4omf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4omf RCSB], [http://www.ebi.ac.uk/pdbsum/4omf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4omf ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/D9PYF7_METTM D9PYF7_METTM]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Coenzyme F420 hydrogenase]]
 [[Category: Large Structures]]
-[[Category: Methanothermobacter marburgensis]]
+[[Category: Methanothermobacter marburgensis str. Marburg]]
-[[Category: Ermler, U]]
+[[Category: Ermler U]]
-[[Category: Ma, K]]
+[[Category: Ma K]]
-[[Category: Moll, J]]
+[[Category: Moll J]]
-[[Category: Pierik, A]]
+[[Category: Pierik A]]
-[[Category: Shima, S]]
+[[Category: Shima S]]
-[[Category: Vitt, S]]
+[[Category: Vitt S]]
-[[Category: Warkentin, E]]
+[[Category: Warkentin E]]
-[[Category: Anaerobic enzyme]]
-[[Category: Fad binding]]
-[[Category: Ferredoxin fold]]
-[[Category: Oxidoreductase]]
-[[Category: Potential f420 binding]]

4omf

From Proteopedia

Revision as of 07:32, 25 January 2023

The F420-reducing [NiFe]-hydrogenase complex from Methanothermobacter marburgensis, the first X-ray structure of a group 3 family member

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox