6s6y
From Proteopedia
(Difference between revisions)
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<StructureSection load='6s6y' size='340' side='right'caption='[[6s6y]], [[Resolution|resolution]] 3.10Å' scene=''> | <StructureSection load='6s6y' size='340' side='right'caption='[[6s6y]], [[Resolution|resolution]] 3.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6s6y]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[6s6y]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Metep Metep]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6S6Y FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IAS:BETA-L-ASPARTIC+ACID'>IAS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=L6K:(2~{S})-3-[4-[[5-(aminomethyl)furan-3-yl]methoxy]phenyl]-2-(methylamino)propanoic+acid'>L6K</scene>, <scene name='pdbligand=MFN:N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE'>MFN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IAS:BETA-L-ASPARTIC+ACID'>IAS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=L6K:(2~{S})-3-[4-[[5-(aminomethyl)furan-3-yl]methoxy]phenyl]-2-(methylamino)propanoic+acid'>L6K</scene>, <scene name='pdbligand=MFN:N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE'>MFN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Mext_1824 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419610 METEP])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethanofuran--tetrahydromethanopterin_N-formyltransferase Formylmethanofuran--tetrahydromethanopterin N-formyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.101 2.3.1.101] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethanofuran--tetrahydromethanopterin_N-formyltransferase Formylmethanofuran--tetrahydromethanopterin N-formyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.101 2.3.1.101] </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=6s6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s6y OCA], [http://pdbe.org/6s6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s6y RCSB], [http://www.ebi.ac.uk/pdbsum/6s6y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s6y 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=6s6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s6y OCA], [http://pdbe.org/6s6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s6y RCSB], [http://www.ebi.ac.uk/pdbsum/6s6y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s6y ProSAT]</span></td></tr> | ||
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== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/A9W3R8_METEP A9W3R8_METEP]] Catalyzes the transfer of a formyl group from 5-formyl tetrahydromethanopterin (5-formyl-H(4)MPT) to methanofuran (MFR) so as to produce formylmethanofuran (formyl-MFR) and tetrahydromethanopterin (H(4)MPT).[HAMAP-Rule:MF_00579] | [[http://www.uniprot.org/uniprot/A9W3R8_METEP A9W3R8_METEP]] Catalyzes the transfer of a formyl group from 5-formyl tetrahydromethanopterin (5-formyl-H(4)MPT) to methanofuran (MFR) so as to produce formylmethanofuran (formyl-MFR) and tetrahydromethanopterin (H(4)MPT).[HAMAP-Rule:MF_00579] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Methylotrophy, the ability of microorganisms to grow on reduced one-carbon substrates such as methane or methanol, is a feature of various bacterial species. The prevailing oxidation pathway depends on tetrahydromethanopterin (H4MPT) and methylofuran (MYFR), an analog of methanofuran from methanogenic archaea. Formyltransferase/hydrolase complex (Fhc) generates formate from formyl-H4MPT in two consecutive reactions where MYFR acts as a carrier of one-carbon units. Recently, we chemically characterized MYFR from the model methylotroph Methylorubrum extorquens and identified an unusually long polyglutamate side chain of up to 24 glutamates. Here, we report on the crystal structure of Fhc to investigate the function of the polyglutamate side chain in MYFR and the relatedness of the enzyme complex with the orthologous enzymes in archaea. We identified MYFR as a prosthetic group that is tightly, but noncovalently, bound to Fhc. Surprisingly, the structure of Fhc together with MYFR revealed that the polyglutamate side chain of MYFR is branched and contains glutamates with amide bonds at both their alpha- and gamma-carboxyl groups. This negatively charged and branched polyglutamate side chain interacts with a cluster of conserved positively charged residues of Fhc, allowing for strong interactions. The MYFR binding site is located equidistantly from the active site of the formyltransferase (FhcD) and metallo-hydrolase (FhcA). The polyglutamate serves therefore an additional function as a swinging linker to shuttle the one-carbon carrying amine between the two active sites, thereby likely increasing overall catalysis while decreasing the need for high intracellular MYFR concentrations. | ||
| + | |||
| + | Methylofuran is a prosthetic group of the formyltransferase/hydrolase complex and shuttles one-carbon units between two active sites.,Hemmann JL, Wagner T, Shima S, Vorholt JA Proc Natl Acad Sci U S A. 2019 Nov 27. pii: 1911595116. doi:, 10.1073/pnas.1911595116. PMID:31776258<ref>PMID:31776258</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6s6y" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Formylmethanofuran--tetrahydromethanopterin N-formyltransferase]] | [[Category: Formylmethanofuran--tetrahydromethanopterin N-formyltransferase]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Metep]] | ||
[[Category: Hemmann, J L]] | [[Category: Hemmann, J L]] | ||
[[Category: Shima, S]] | [[Category: Shima, S]] | ||
Revision as of 18:47, 11 December 2019
X-ray crystal structure of the formyltransferase/hydrolase complex (FhcABCD) from Methylorubrum extorquens in complex with methylofuran
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Categories: Formylmethanofuran--tetrahydromethanopterin N-formyltransferase | Large Structures | Metep | Hemmann, J L | Shima, S | Vorholt, J | Wagner, T | Channeling | Formate dehydrogenase | Formyl-transferase | Hydrolase | Metallo-hydrolase | Methylofuran | Methylotrophy | Polyglutamate | Prosthetic group
