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| | <StructureSection load='6q2e' size='340' side='right'caption='[[6q2e]], [[Resolution|resolution]] 1.77Å' scene=''> | | <StructureSection load='6q2e' size='340' side='right'caption='[[6q2e]], [[Resolution|resolution]] 1.77Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6q2e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35061 Atcc 35061]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q2E FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6q2e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanobrevibacter_smithii Methanobrevibacter smithii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q2E 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=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</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]] 1.768Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Msm_1358 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2173 ATCC 35061])</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=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-(3-amino-3-carboxypropyl)histidine_synthase 2-(3-amino-3-carboxypropyl)histidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.108 2.5.1.108] </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=6q2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q2e OCA], [https://pdbe.org/6q2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q2e RCSB], [https://www.ebi.ac.uk/pdbsum/6q2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q2e 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=6q2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q2e OCA], [http://pdbe.org/6q2e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q2e RCSB], [http://www.ebi.ac.uk/pdbsum/6q2e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q2e ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A5UMY5_METS3 A5UMY5_METS3]] Catalyzes the first step of diphthamide biosynthesis, i.e. the transfer of the 3-amino-3-carboxypropyl group from S-adenosyl-L-methionine (SAM) to the C2 position of the imidazole ring of the target histidine residue in translation elongation factor 2 (EF-2).[PIRNR:PIRNR004967] | + | [https://www.uniprot.org/uniprot/A5UMY5_METS3 A5UMY5_METS3] Catalyzes the first step of diphthamide biosynthesis, i.e. the transfer of the 3-amino-3-carboxypropyl group from S-adenosyl-L-methionine (SAM) to the C2 position of the imidazole ring of the target histidine residue in translation elongation factor 2 (EF-2).[PIRNR:PIRNR004967] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 35061]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Dong, M]] | + | [[Category: Methanobrevibacter smithii]] |
| - | [[Category: Ealick, S E]] | + | [[Category: Dong M]] |
| - | [[Category: Fenwick, M K]]
| + | [[Category: Ealick SE]] |
| - | [[Category: Lin, H]] | + | [[Category: Fenwick MK]] |
| - | [[Category: Enzyme]] | + | [[Category: Lin H]] |
| - | [[Category: Iron sulfur cluster]] | + | |
| - | [[Category: Radical]]
| + | |
| - | [[Category: S-adenosylmethionine]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
A5UMY5_METS3 Catalyzes the first step of diphthamide biosynthesis, i.e. the transfer of the 3-amino-3-carboxypropyl group from S-adenosyl-L-methionine (SAM) to the C2 position of the imidazole ring of the target histidine residue in translation elongation factor 2 (EF-2).[PIRNR:PIRNR004967]
Publication Abstract from PubMed
Elongation factor 2 (EF-2), a five-domain, GTP-dependent ribosomal translocase of archaebacteria and eukaryotes, undergoes post-translational modification to form diphthamide on a specific histidine residue in domain IV prior to binding the ribosome. The first step of diphthamide biosynthesis in archaebacteria is catalyzed by Dph2, a homodimeric radical S-adenosylmethionine (SAM) enzyme having a noncanonical architecture. Here, we describe a 3.5 A resolution crystal structure of the Methanobrevibacter smithii (Ms) Dph2 homodimer bound to two molecules of MsEF-2, one of which is ordered and the other largely disordered. MsEF-2 is bound to both protomers of MsDph2, with domain IV bound to the active site of one protomer and domain III bound to a surface alpha-helix of an adjacent protomer. The histidine substrate of domain IV is inserted into the active site, which reveals for the first time the architecture of the Dph2 active site in complex with its target substrate. We also determined a high-resolution crystal structure of isolated MsDph2 bound to 5'-methylthioadenosine that shows a conserved arginine residue preoriented by conserved phenylalanine and aspartate residues for binding the carboxylate group of SAM. Mutagenesis experiments suggest that the arginine plays an important role in the first step of diphthamide biosynthesis.
The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis.,Fenwick MK, Dong M, Lin H, Ealick SE Biochemistry. 2019 Oct 14. doi: 10.1021/acs.biochem.9b00718. PMID:31566354[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Fenwick MK, Dong M, Lin H, Ealick SE. The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis. Biochemistry. 2019 Oct 14. doi: 10.1021/acs.biochem.9b00718. PMID:31566354 doi:http://dx.doi.org/10.1021/acs.biochem.9b00718
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