4pde

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of FdhD in complex with GDP

Structural highlights

4pde is a 1 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 2.8Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FDHD_ECOLI Required for formate dehydrogenase (FDH) activity (PubMed:3077634, PubMed:8522521, PubMed:22194618, PubMed:25649206). Acts as a sulfur carrier protein that transfers sulfur from IscS to the molybdenum cofactor prior to its insertion into FDH. Specifically interacts with IscS and stimulates its cysteine desulfurase activity. Also binds the molybdenum cofactor (PubMed:22194618, PubMed:25649206). Required for activity of formate dehydrogenase N (FDH-N), formate dehydrogenase O (FDH-O) and formate dehydrogenase H (FDH-H) (PubMed:3077634, PubMed:8522521, PubMed:22194618).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Formate dehydrogenases (FDHs) are of interest as they are natural catalysts that sequester atmospheric CO2, generating reduced carbon compounds with possible uses as fuel. FDHs activity in Escherichia coli strictly requires the sulphurtransferase EcFdhD, which likely transfers sulphur from IscS to the molybdenum cofactor (Mo-bisPGD) of FDHs. Here we show that EcFdhD binds Mo-bisPGD in vivo and has submicromolar affinity for GDP-used as a surrogate of the molybdenum cofactor's nucleotide moieties. The crystal structure of EcFdhD in complex with GDP shows two symmetrical binding sites located on the same face of the dimer. These binding sites are connected via a tunnel-like cavity to the opposite face of the dimer where two dynamic loops, each harbouring two functionally important cysteine residues, are present. On the basis of structure-guided mutagenesis, we propose a model for the sulphuration mechanism of Mo-bisPGD where the sulphur atom shuttles across the chaperone dimer.

Sulphur shuttling across a chaperone during molybdenum cofactor maturation.,Arnoux P, Ruppelt C, Oudouhou F, Lavergne J, Siponen MI, Toci R, Mendel RR, Bittner F, Pignol D, Magalon A, Walburger A Nat Commun. 2015 Feb 4;6:6148. doi: 10.1038/ncomms7148. PMID:25649206^[5]

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

References

↑ Thome R, Gust A, Toci R, Mendel R, Bittner F, Magalon A, Walburger A. A sulfurtransferase is essential for activity of formate dehydrogenases in Escherichia coli. J Biol Chem. 2012 Feb 10;287(7):4671-8. doi: 10.1074/jbc.M111.327122. Epub 2011 , Dec 22. PMID:22194618 doi:http://dx.doi.org/10.1074/jbc.M111.327122
↑ Arnoux P, Ruppelt C, Oudouhou F, Lavergne J, Siponen MI, Toci R, Mendel RR, Bittner F, Pignol D, Magalon A, Walburger A. Sulphur shuttling across a chaperone during molybdenum cofactor maturation. Nat Commun. 2015 Feb 4;6:6148. doi: 10.1038/ncomms7148. PMID:25649206 doi:http://dx.doi.org/10.1038/ncomms7148
↑ Mandrand-Berthelot MA, Couchoux-Luthaud G, Santini CL, Giordano G. Mutants of Escherichia coli specifically deficient in respiratory formate dehydrogenase activity. J Gen Microbiol. 1988 Dec;134(12):3129-39. doi: 10.1099/00221287-134-12-3129. PMID:3077634 doi:http://dx.doi.org/10.1099/00221287-134-12-3129
↑ Abaibou H, Pommier J, Benoit S, Giordano G, Mandrand-Berthelot MA. Expression and characterization of the Escherichia coli fdo locus and a possible physiological role for aerobic formate dehydrogenase. J Bacteriol. 1995 Dec;177(24):7141-9. PMID:8522521
↑ Arnoux P, Ruppelt C, Oudouhou F, Lavergne J, Siponen MI, Toci R, Mendel RR, Bittner F, Pignol D, Magalon A, Walburger A. Sulphur shuttling across a chaperone during molybdenum cofactor maturation. Nat Commun. 2015 Feb 4;6:6148. doi: 10.1038/ncomms7148. PMID:25649206 doi:http://dx.doi.org/10.1038/ncomms7148

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/4pde"

@@ Line 1: / Line 1: @@
 ==Crystal structure of FdhD in complex with GDP==
-<StructureSection load='4pde' size='340' side='right' caption='[[4pde]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='4pde' size='340' side='right'caption='[[4pde]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4pde]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PDE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4pde]] is a 1 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=4PDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PDE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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]] 2.8&#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=4pde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pde OCA], [http://pdbe.org/4pde PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pde RCSB], [http://www.ebi.ac.uk/pdbsum/4pde PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pde ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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=4pde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pde OCA], [https://pdbe.org/4pde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pde RCSB], [https://www.ebi.ac.uk/pdbsum/4pde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pde ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/J7QY30_ECOLX J7QY30_ECOLX]] Necessary for formate dehydrogenase activity.[HAMAP-Rule:MF_00187][SAAS:SAAS00093836]
+[https://www.uniprot.org/uniprot/FDHD_ECOLI FDHD_ECOLI] Required for formate dehydrogenase (FDH) activity (PubMed:3077634, PubMed:8522521, PubMed:22194618, PubMed:25649206). Acts as a sulfur carrier protein that transfers sulfur from IscS to the molybdenum cofactor prior to its insertion into FDH. Specifically interacts with IscS and stimulates its cysteine desulfurase activity. Also binds the molybdenum cofactor (PubMed:22194618, PubMed:25649206). Required for activity of formate dehydrogenase N (FDH-N), formate dehydrogenase O (FDH-O) and formate dehydrogenase H (FDH-H) (PubMed:3077634, PubMed:8522521, PubMed:22194618).<ref>PMID:22194618</ref> <ref>PMID:25649206</ref> <ref>PMID:3077634</ref> <ref>PMID:8522521</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Arnoux, P]]
+[[Category: Escherichia coli]]
-[[Category: Magalon, A]]
+[[Category: Large Structures]]
-[[Category: Pignol, D]]
+[[Category: Arnoux P]]
-[[Category: Walburger, A]]
+[[Category: Magalon A]]
-[[Category: Gdp]]
+[[Category: Pignol D]]
-[[Category: Hydrolase]]
+[[Category: Walburger A]]
-[[Category: Mo-bispgd sulfuration]]

4pde

From Proteopedia

Current revision

Crystal structure of FdhD in complex with GDP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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